An automated workflow for parallel processing of large multiview SPIM recordings

PubMed Central

Schmied, Christopher; Steinbach, Peter; Pietzsch, Tobias; Preibisch, Stephan; Tomancak, Pavel

2016-01-01

Summary: Selective Plane Illumination Microscopy (SPIM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via dedicated graphical user interface (GUI) applications. The consecutive processing steps can be easily automated and the individual time points can be processed independently, which lends itself to trivial parallelization on a high performance computing (HPC) cluster. Here, we introduce an automated workflow for processing large multiview, multichannel, multiillumination time-lapse SPIM data on a single workstation or in parallel on a HPC cluster. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing SPIM data in a fraction of the time required to collect it. Availability and implementation: The code is distributed free and open source under the MIT license http://opensource.org/licenses/MIT. The source code can be downloaded from github: https://github.com/mpicbg-scicomp/snakemake-workflows. Documentation can be found here: http://fiji.sc/Automated_workflow_for_parallel_Multiview_Reconstruction. Contact: schmied@mpi-cbg.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26628585

An automated workflow for parallel processing of large multiview SPIM recordings.

PubMed

Schmied, Christopher; Steinbach, Peter; Pietzsch, Tobias; Preibisch, Stephan; Tomancak, Pavel

2016-04-01

Selective Plane Illumination Microscopy (SPIM) allows to image developing organisms in 3D at unprecedented temporal resolution over long periods of time. The resulting massive amounts of raw image data requires extensive processing interactively via dedicated graphical user interface (GUI) applications. The consecutive processing steps can be easily automated and the individual time points can be processed independently, which lends itself to trivial parallelization on a high performance computing (HPC) cluster. Here, we introduce an automated workflow for processing large multiview, multichannel, multiillumination time-lapse SPIM data on a single workstation or in parallel on a HPC cluster. The pipeline relies on snakemake to resolve dependencies among consecutive processing steps and can be easily adapted to any cluster environment for processing SPIM data in a fraction of the time required to collect it. The code is distributed free and open source under the MIT license http://opensource.org/licenses/MIT The source code can be downloaded from github: https://github.com/mpicbg-scicomp/snakemake-workflows Documentation can be found here: http://fiji.sc/Automated_workflow_for_parallel_Multiview_Reconstruction : schmied@mpi-cbg.de Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

Application of Six Sigma methodology to a diagnostic imaging process.

PubMed

Taner, Mehmet Tolga; Sezen, Bulent; Atwat, Kamal M

2012-01-01

This paper aims to apply the Six Sigma methodology to improve workflow by eliminating the causes of failure in the medical imaging department of a private Turkish hospital. Implementation of the design, measure, analyse, improve and control (DMAIC) improvement cycle, workflow chart, fishbone diagrams and Pareto charts were employed, together with rigorous data collection in the department. The identification of root causes of repeat sessions and delays was followed by failure, mode and effect analysis, hazard analysis and decision tree analysis. The most frequent causes of failure were malfunction of the RIS/PACS system and improper positioning of patients. Subsequent to extensive training of professionals, the sigma level was increased from 3.5 to 4.2. The data were collected over only four months. Six Sigma's data measurement and process improvement methodology is the impetus for health care organisations to rethink their workflow and reduce malpractice. It involves measuring, recording and reporting data on a regular basis. This enables the administration to monitor workflow continuously. The improvements in the workflow under study, made by determining the failures and potential risks associated with radiologic care, will have a positive impact on society in terms of patient safety. Having eliminated repeat examinations, the risk of being exposed to more radiation was also minimised. This paper supports the need to apply Six Sigma and present an evaluation of the process in an imaging department.

[Change in process management by implementing RIS, PACS and flat-panel detectors].

PubMed

Imhof, H; Dirisamer, A; Fischer, H; Grampp, S; Heiner, L; Kaderk, M; Krestan, C; Kainberger, F

2002-05-01

Implementation of radiological information systems (RIS) and picture archiving and communicating systems (PACS) results in significant changes of workflow in a radiological department. Additional connection with flat-panel detectors leads to a shortening of the work process. RIS and PACS implementation alone reduces the complete workflow by 21-80%. With flatpanel technology the image production process is further shortened by 25-30%. The workflow-steps are changed from original 17-12 with the implementation of RIS and PACS and to 5 with the integrated use of flatpanels. This clearly recognizable advantages in the workflow need an according financial investment. Several studies could show that the capitalisation-factor calculated over eight years is positive, with a gain range between 5-25%. Whether the additional implementation of flatpanel detectors results also in a positive capitalisation over the years, cannot be estimated exactly, at the moment, because the experiences are too short. Particularly critical are the interfaces, which needs a constant quality control. Our flatpanel detector-system is fixed, special images--as we have them in about 3-5% of all cases--need still conventional filmscreen or phosphorplate-systems. Full-spine and long-leg examinations cannot be performed with sufficient exactness. Without any questions implementation of integrated RIS, PACS and flatpanel detector-system needs excellent training of the employees, because of the changes in workflow etc. The main profits of such an integrated implementation are an increase in quality in image and report datas, easier handling--there are almost no more cassettes necessary--and excessive shortening of workflow.

Efficient Workflows for Curation of Heterogeneous Data Supporting Modeling of U-Nb Alloy Aging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ward, Logan Timothy; Hackenberg, Robert Errol

These are slides from a presentation summarizing a graduate research associate's summer project. The following topics are covered in these slides: data challenges in materials, aging in U-Nb Alloys, Building an Aging Model, Different Phase Trans. in U-Nb, the Challenge, Storing Materials Data, Example Data Source, Organizing Data: What is a Schema?, What does a "XML Schema" look like?, Our Data Schema: Nice and Simple, Storing Data: Materials Data Curation System (MDCS), Problem with MDCS: Slow Data Entry, Getting Literature into MDCS, Staging Data in Excel Document, Final Result: MDCS Records, Analyzing Image Data, Process for Making TTT Diagram, Bottleneckmore » Number 1: Image Analysis, Fitting a TTP Boundary, Fitting a TTP Curve: Comparable Results, How Does it Compare to Our Data?, Image Analysis Workflow, Curating Hardness Records, Hardness Data: Two Key Decisions, Before Peak Age? - Automation, Interactive Viz, Which Transformation?, Microstructure-Informed Model, Tracking the Entire Process, General Problem with Property Models, Pinyon: Toolkit for Managing Model Creation, Tracking Individual Decisions, Jupyter: Docs and Code in One File, Hardness Analysis Workflow, Workflow for Aging Models, and conclusions.« less

Image processing and classification procedures for analysis of sub-decimeter imagery acquired with an unmanned aircraft over arid rangelands

USDA-ARS?s Scientific Manuscript database

Using five centimeter resolution images acquired with an unmanned aircraft system (UAS), we developed and evaluated an image processing workflow that included the integration of resolution-appropriate field sampling, feature selection, object-based image analysis, and processing approaches for UAS i...

Progress in digital color workflow understanding in the International Color Consortium (ICC) Workflow WG

NASA Astrophysics Data System (ADS)

McCarthy, Ann

2006-01-01

The ICC Workflow WG serves as the bridge between ICC color management technologies and use of those technologies in real world color production applications. ICC color management is applicable to and is used in a wide range of color systems, from highly specialized digital cinema color special effects to high volume publications printing to home photography. The ICC Workflow WG works to align ICC technologies so that the color management needs of these diverse use case systems are addressed in an open, platform independent manner. This report provides a high level summary of the ICC Workflow WG objectives and work to date, focusing on the ways in which workflow can impact image quality and color systems performance. The 'ICC Workflow Primitives' and 'ICC Workflow Patterns and Dimensions' workflow models are covered in some detail. Consider the questions, "How much of dissatisfaction with color management today is the result of 'the wrong color transformation at the wrong time' and 'I can't get to the right conversion at the right point in my work process'?" Put another way, consider how image quality through a workflow can be negatively affected when the coordination and control level of the color management system is not sufficient.

Workflow-enabled distributed component-based information architecture for digital medical imaging enterprises.

PubMed

Wong, Stephen T C; Tjandra, Donny; Wang, Huili; Shen, Weimin

2003-09-01

Few information systems today offer a flexible means to define and manage the automated part of radiology processes, which provide clinical imaging services for the entire healthcare organization. Even fewer of them provide a coherent architecture that can easily cope with heterogeneity and inevitable local adaptation of applications and can integrate clinical and administrative information to aid better clinical, operational, and business decisions. We describe an innovative enterprise architecture of image information management systems to fill the needs. Such a system is based on the interplay of production workflow management, distributed object computing, Java and Web techniques, and in-depth domain knowledge in radiology operations. Our design adapts the approach of "4+1" architectural view. In this new architecture, PACS and RIS become one while the user interaction can be automated by customized workflow process. Clinical service applications are implemented as active components. They can be reasonably substituted by applications of local adaptations and can be multiplied for fault tolerance and load balancing. Furthermore, the workflow-enabled digital radiology system would provide powerful query and statistical functions for managing resources and improving productivity. This paper will potentially lead to a new direction of image information management. We illustrate the innovative design with examples taken from an implemented system.

A Web application for the management of clinical workflow in image-guided and adaptive proton therapy for prostate cancer treatments.

PubMed

Yeung, Daniel; Boes, Peter; Ho, Meng Wei; Li, Zuofeng

2015-05-08

Image-guided radiotherapy (IGRT), based on radiopaque markers placed in the prostate gland, was used for proton therapy of prostate patients. Orthogonal X-rays and the IBA Digital Image Positioning System (DIPS) were used for setup correction prior to treatment and were repeated after treatment delivery. Following a rationale for margin estimates similar to that of van Herk,(1) the daily post-treatment DIPS data were analyzed to determine if an adaptive radiotherapy plan was necessary. A Web application using ASP.NET MVC5, Entity Framework, and an SQL database was designed to automate this process. The designed features included state-of-the-art Web technologies, a domain model closely matching the workflow, a database-supporting concurrency and data mining, access to the DIPS database, secured user access and roles management, and graphing and analysis tools. The Model-View-Controller (MVC) paradigm allowed clean domain logic, unit testing, and extensibility. Client-side technologies, such as jQuery, jQuery Plug-ins, and Ajax, were adopted to achieve a rich user environment and fast response. Data models included patients, staff, treatment fields and records, correction vectors, DIPS images, and association logics. Data entry, analysis, workflow logics, and notifications were implemented. The system effectively modeled the clinical workflow and IGRT process.

Imaging workflow and calibration for CT-guided time-domain fluorescence tomography

PubMed Central

Tichauer, Kenneth M.; Holt, Robert W.; El-Ghussein, Fadi; Zhu, Qun; Dehghani, Hamid; Leblond, Frederic; Pogue, Brian W.

2011-01-01

In this study, several key optimization steps are outlined for a non-contact, time-correlated single photon counting small animal optical tomography system, using simultaneous collection of both fluorescence and transmittance data. The system is presented for time-domain image reconstruction in vivo, illustrating the sensitivity from single photon counting and the calibration steps needed to accurately process the data. In particular, laser time- and amplitude-referencing, detector and filter calibrations, and collection of a suitable instrument response function are all presented in the context of time-domain fluorescence tomography and a fully automated workflow is described. Preliminary phantom time-domain reconstructed images demonstrate the fidelity of the workflow for fluorescence tomography based on signal from multiple time gates. PMID:22076264

Worklist handling in workflow-enabled radiological application systems

NASA Astrophysics Data System (ADS)

Wendler, Thomas; Meetz, Kirsten; Schmidt, Joachim; von Berg, Jens

2000-05-01

For the next generation integrated information systems for health care applications, more emphasis has to be put on systems which, by design, support the reduction of cost, the increase inefficiency and the improvement of the quality of services. A substantial contribution to this will be the modeling. optimization, automation and enactment of processes in health care institutions. One of the perceived key success factors for the system integration of processes will be the application of workflow management, with workflow management systems as key technology components. In this paper we address workflow management in radiology. We focus on an important aspect of workflow management, the generation and handling of worklists, which provide workflow participants automatically with work items that reflect tasks to be performed. The display of worklists and the functions associated with work items are the visible part for the end-users of an information system using a workflow management approach. Appropriate worklist design and implementation will influence user friendliness of a system and will largely influence work efficiency. Technically, in current imaging department information system environments (modality-PACS-RIS installations), a data-driven approach has been taken: Worklist -- if present at all -- are generated from filtered views on application data bases. In a future workflow-based approach, worklists will be generated by autonomous workflow services based on explicit process models and organizational models. This process-oriented approach will provide us with an integral view of entire health care processes or sub- processes. The paper describes the basic mechanisms of this approach and summarizes its benefits.

Geometric processing workflow for vertical and oblique hyperspectral frame images collected using UAV

NASA Astrophysics Data System (ADS)

Markelin, L.; Honkavaara, E.; Näsi, R.; Nurminen, K.; Hakala, T.

2014-08-01

Remote sensing based on unmanned airborne vehicles (UAVs) is a rapidly developing field of technology. UAVs enable accurate, flexible, low-cost and multiangular measurements of 3D geometric, radiometric, and temporal properties of land and vegetation using various sensors. In this paper we present a geometric processing chain for multiangular measurement system that is designed for measuring object directional reflectance characteristics in a wavelength range of 400-900 nm. The technique is based on a novel, lightweight spectral camera designed for UAV use. The multiangular measurement is conducted by collecting vertical and oblique area-format spectral images. End products of the geometric processing are image exterior orientations, 3D point clouds and digital surface models (DSM). This data is needed for the radiometric processing chain that produces reflectance image mosaics and multiangular bidirectional reflectance factor (BRF) observations. The geometric processing workflow consists of the following three steps: (1) determining approximate image orientations using Visual Structure from Motion (VisualSFM) software, (2) calculating improved orientations and sensor calibration using a method based on self-calibrating bundle block adjustment (standard photogrammetric software) (this step is optional), and finally (3) creating dense 3D point clouds and DSMs using Photogrammetric Surface Reconstruction from Imagery (SURE) software that is based on semi-global-matching algorithm and it is capable of providing a point density corresponding to the pixel size of the image. We have tested the geometric processing workflow over various targets, including test fields, agricultural fields, lakes and complex 3D structures like forests.

Anima: Modular Workflow System for Comprehensive Image Data Analysis

PubMed Central

Rantanen, Ville; Valori, Miko; Hautaniemi, Sampsa

2014-01-01

Modern microscopes produce vast amounts of image data, and computational methods are needed to analyze and interpret these data. Furthermore, a single image analysis project may require tens or hundreds of analysis steps starting from data import and pre-processing to segmentation and statistical analysis; and ending with visualization and reporting. To manage such large-scale image data analysis projects, we present here a modular workflow system called Anima. Anima is designed for comprehensive and efficient image data analysis development, and it contains several features that are crucial in high-throughput image data analysis: programing language independence, batch processing, easily customized data processing, interoperability with other software via application programing interfaces, and advanced multivariate statistical analysis. The utility of Anima is shown with two case studies focusing on testing different algorithms developed in different imaging platforms and an automated prediction of alive/dead C. elegans worms by integrating several analysis environments. Anima is a fully open source and available with documentation at www.anduril.org/anima. PMID:25126541

SYRMEP Tomo Project: a graphical user interface for customizing CT reconstruction workflows.

PubMed

Brun, Francesco; Massimi, Lorenzo; Fratini, Michela; Dreossi, Diego; Billé, Fulvio; Accardo, Agostino; Pugliese, Roberto; Cedola, Alessia

2017-01-01

When considering the acquisition of experimental synchrotron radiation (SR) X-ray CT data, the reconstruction workflow cannot be limited to the essential computational steps of flat fielding and filtered back projection (FBP). More refined image processing is often required, usually to compensate artifacts and enhance the quality of the reconstructed images. In principle, it would be desirable to optimize the reconstruction workflow at the facility during the experiment (beamtime). However, several practical factors affect the image reconstruction part of the experiment and users are likely to conclude the beamtime with sub-optimal reconstructed images. Through an example of application, this article presents SYRMEP Tomo Project (STP), an open-source software tool conceived to let users design custom CT reconstruction workflows. STP has been designed for post-beamtime (off-line use) and for a new reconstruction of past archived data at user's home institution where simple computing resources are available. Releases of the software can be downloaded at the Elettra Scientific Computing group GitHub repository https://github.com/ElettraSciComp/STP-Gui.

To Image...or Not to Image?

ERIC Educational Resources Information Center

Bruley, Karina

1996-01-01

Provides a checklist of considerations for installing document image processing with an electronic document management system. Other topics include scanning; indexing; the image file life cycle; benefits of imaging; document-driven workflow; and planning for workplace changes like postsorting, creating a scanning room, redeveloping job tasks and…

Electronic workflow for imaging in clinical research.

PubMed

Hedges, Rebecca A; Goodman, Danielle; Sachs, Peter B

2014-08-01

In the transition from paper to electronic workflow, the University of Colorado Health System's implementation of a new electronic health record system (EHR) forced all clinical groups to reevaluate their practices including the infrastructure surrounding clinical trials. Radiological imaging is an important piece of many clinical trials and requires a high level of consistency and standardization. With EHR implementation, paper orders were manually transcribed into the EHR, digitizing an inefficient work flow. A team of schedulers, radiologists, technologists, research personnel, and EHR analysts worked together to optimize the EHR to accommodate the needs of research imaging protocols. The transition to electronic workflow posed several problems: (1) there needed to be effective communication throughout the imaging process from scheduling to radiologist interpretation. (2) The exam ordering process needed to be automated to allow scheduling of specific research studies on specific equipment. (3) The billing process needed to be controlled to accommodate radiologists already supported by grants. (4) There needed to be functionality allowing exams to finalize automatically skipping the PACS and interpretation process. (5) There needed to be a way to alert radiologists that a specialized research interpretation was needed on a given exam. These issues were resolved through the optimization of the "visit type," allowing a high-level control of an exam at the time of scheduling. Additionally, we added columns and fields to work queues displaying grant identification numbers. The build solutions we implemented reduced the mistakes made and increased imaging quality and compliance.

Ultramap: the all in One Photogrammetric Solution

NASA Astrophysics Data System (ADS)

Wiechert, A.; Gruber, M.; Karner, K.

2012-07-01

This paper describes in detail the dense matcher developed since years by Vexcel Imaging in Graz for Microsoft's Bing Maps project. This dense matcher was exclusively developed for and used by Microsoft for the production of the 3D city models of Virtual Earth. It will now be made available to the public with the UltraMap software release mid-2012. That represents a revolutionary step in digital photogrammetry. The dense matcher generates digital surface models (DSM) and digital terrain models (DTM) automatically out of a set of overlapping UltraCam images. The models have an outstanding point density of several hundred points per square meter and sub-pixel accuracy and are generated automatically. The dense matcher consists of two steps. The first step rectifies overlapping image areas to speed up the dense image matching process. This rectification step ensures a very efficient processing and detects occluded areas by applying a back-matching step. In this dense image matching process a cost function consisting of a matching score as well as a smoothness term is minimized. In the second step the resulting range image patches are fused into a DSM by optimizing a global cost function. The whole process is optimized for multi-core CPUs and optionally uses GPUs if available. UltraMap 3.0 features also an additional step which is presented in this paper, a complete automated true-ortho and ortho workflow. For this, the UltraCam images are combined with the DSM or DTM in an automated rectification step and that results in high quality true-ortho or ortho images as a result of a highly automated workflow. The paper presents the new workflow and first results.

MO-B-BRB-01: Optimize Treatment Planning Process in Clinical Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Feng, W.

The radiotherapy treatment planning process has evolved over the years with innovations in treatment planning, treatment delivery and imaging systems. Treatment modality and simulation technologies are also rapidly improving and affecting the planning process. For example, Image-guided-radiation-therapy has been widely adopted for patient setup, leading to margin reduction and isocenter repositioning after simulation. Stereotactic Body radiation therapy (SBRT) and Radiosurgery (SRS) have gradually become the standard of care for many treatment sites, which demand a higher throughput for the treatment plans even if the number of treatments per day remains the same. Finally, simulation, planning and treatment are traditionally sequentialmore » events. However, with emerging adaptive radiotherapy, they are becoming more tightly intertwined, leading to iterative processes. Enhanced efficiency of planning is therefore becoming more critical and poses serious challenge to the treatment planning process; Lean Six Sigma approaches are being utilized increasingly to balance the competing needs for speed and quality. In this symposium we will discuss the treatment planning process and illustrate effective techniques for managing workflow. Topics will include: Planning techniques: (a) beam placement, (b) dose optimization, (c) plan evaluation (d) export to RVS. Planning workflow: (a) import images, (b) Image fusion, (c) contouring, (d) plan approval (e) plan check (f) chart check, (g) sequential and iterative process Influence of upstream and downstream operations: (a) simulation, (b) immobilization, (c) motion management, (d) QA, (e) IGRT, (f) Treatment delivery, (g) SBRT/SRS (h) adaptive planning Reduction of delay between planning steps with Lean systems due to (a) communication, (b) limited resource, (b) contour, (c) plan approval, (d) treatment. Optimizing planning processes: (a) contour validation (b) consistent planning protocol, (c) protocol/template sharing, (d) semi-automatic plan evaluation, (e) quality checklist for error prevention, (f) iterative process, (g) balance of speed and quality Learning Objectives: Gain familiarity with the workflow of modern treatment planning process. Understand the scope and challenges of managing modern treatment planning processes. Gain familiarity with Lean Six Sigma approaches and their implementation in the treatment planning workflow.« less

MO-B-BRB-00: Optimizing the Treatment Planning Process

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

The radiotherapy treatment planning process has evolved over the years with innovations in treatment planning, treatment delivery and imaging systems. Treatment modality and simulation technologies are also rapidly improving and affecting the planning process. For example, Image-guided-radiation-therapy has been widely adopted for patient setup, leading to margin reduction and isocenter repositioning after simulation. Stereotactic Body radiation therapy (SBRT) and Radiosurgery (SRS) have gradually become the standard of care for many treatment sites, which demand a higher throughput for the treatment plans even if the number of treatments per day remains the same. Finally, simulation, planning and treatment are traditionally sequentialmore » events. However, with emerging adaptive radiotherapy, they are becoming more tightly intertwined, leading to iterative processes. Enhanced efficiency of planning is therefore becoming more critical and poses serious challenge to the treatment planning process; Lean Six Sigma approaches are being utilized increasingly to balance the competing needs for speed and quality. In this symposium we will discuss the treatment planning process and illustrate effective techniques for managing workflow. Topics will include: Planning techniques: (a) beam placement, (b) dose optimization, (c) plan evaluation (d) export to RVS. Planning workflow: (a) import images, (b) Image fusion, (c) contouring, (d) plan approval (e) plan check (f) chart check, (g) sequential and iterative process Influence of upstream and downstream operations: (a) simulation, (b) immobilization, (c) motion management, (d) QA, (e) IGRT, (f) Treatment delivery, (g) SBRT/SRS (h) adaptive planning Reduction of delay between planning steps with Lean systems due to (a) communication, (b) limited resource, (b) contour, (c) plan approval, (d) treatment. Optimizing planning processes: (a) contour validation (b) consistent planning protocol, (c) protocol/template sharing, (d) semi-automatic plan evaluation, (e) quality checklist for error prevention, (f) iterative process, (g) balance of speed and quality Learning Objectives: Gain familiarity with the workflow of modern treatment planning process. Understand the scope and challenges of managing modern treatment planning processes. Gain familiarity with Lean Six Sigma approaches and their implementation in the treatment planning workflow.« less

MO-B-BRB-03: Systems Engineering Tools for Treatment Planning Process Optimization in Radiation Medicine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kapur, A.

The radiotherapy treatment planning process has evolved over the years with innovations in treatment planning, treatment delivery and imaging systems. Treatment modality and simulation technologies are also rapidly improving and affecting the planning process. For example, Image-guided-radiation-therapy has been widely adopted for patient setup, leading to margin reduction and isocenter repositioning after simulation. Stereotactic Body radiation therapy (SBRT) and Radiosurgery (SRS) have gradually become the standard of care for many treatment sites, which demand a higher throughput for the treatment plans even if the number of treatments per day remains the same. Finally, simulation, planning and treatment are traditionally sequentialmore » events. However, with emerging adaptive radiotherapy, they are becoming more tightly intertwined, leading to iterative processes. Enhanced efficiency of planning is therefore becoming more critical and poses serious challenge to the treatment planning process; Lean Six Sigma approaches are being utilized increasingly to balance the competing needs for speed and quality. In this symposium we will discuss the treatment planning process and illustrate effective techniques for managing workflow. Topics will include: Planning techniques: (a) beam placement, (b) dose optimization, (c) plan evaluation (d) export to RVS. Planning workflow: (a) import images, (b) Image fusion, (c) contouring, (d) plan approval (e) plan check (f) chart check, (g) sequential and iterative process Influence of upstream and downstream operations: (a) simulation, (b) immobilization, (c) motion management, (d) QA, (e) IGRT, (f) Treatment delivery, (g) SBRT/SRS (h) adaptive planning Reduction of delay between planning steps with Lean systems due to (a) communication, (b) limited resource, (b) contour, (c) plan approval, (d) treatment. Optimizing planning processes: (a) contour validation (b) consistent planning protocol, (c) protocol/template sharing, (d) semi-automatic plan evaluation, (e) quality checklist for error prevention, (f) iterative process, (g) balance of speed and quality Learning Objectives: Gain familiarity with the workflow of modern treatment planning process. Understand the scope and challenges of managing modern treatment planning processes. Gain familiarity with Lean Six Sigma approaches and their implementation in the treatment planning workflow.« less

MO-B-BRB-02: Maintain the Quality of Treatment Planning for Time-Constraint Cases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, J.

The radiotherapy treatment planning process has evolved over the years with innovations in treatment planning, treatment delivery and imaging systems. Treatment modality and simulation technologies are also rapidly improving and affecting the planning process. For example, Image-guided-radiation-therapy has been widely adopted for patient setup, leading to margin reduction and isocenter repositioning after simulation. Stereotactic Body radiation therapy (SBRT) and Radiosurgery (SRS) have gradually become the standard of care for many treatment sites, which demand a higher throughput for the treatment plans even if the number of treatments per day remains the same. Finally, simulation, planning and treatment are traditionally sequentialmore » events. However, with emerging adaptive radiotherapy, they are becoming more tightly intertwined, leading to iterative processes. Enhanced efficiency of planning is therefore becoming more critical and poses serious challenge to the treatment planning process; Lean Six Sigma approaches are being utilized increasingly to balance the competing needs for speed and quality. In this symposium we will discuss the treatment planning process and illustrate effective techniques for managing workflow. Topics will include: Planning techniques: (a) beam placement, (b) dose optimization, (c) plan evaluation (d) export to RVS. Planning workflow: (a) import images, (b) Image fusion, (c) contouring, (d) plan approval (e) plan check (f) chart check, (g) sequential and iterative process Influence of upstream and downstream operations: (a) simulation, (b) immobilization, (c) motion management, (d) QA, (e) IGRT, (f) Treatment delivery, (g) SBRT/SRS (h) adaptive planning Reduction of delay between planning steps with Lean systems due to (a) communication, (b) limited resource, (b) contour, (c) plan approval, (d) treatment. Optimizing planning processes: (a) contour validation (b) consistent planning protocol, (c) protocol/template sharing, (d) semi-automatic plan evaluation, (e) quality checklist for error prevention, (f) iterative process, (g) balance of speed and quality Learning Objectives: Gain familiarity with the workflow of modern treatment planning process. Understand the scope and challenges of managing modern treatment planning processes. Gain familiarity with Lean Six Sigma approaches and their implementation in the treatment planning workflow.« less

Producing an Infrared Multiwavelength Galactic Plane Atlas Using Montage, Pegasus, and Amazon Web Services

NASA Astrophysics Data System (ADS)

Rynge, M.; Juve, G.; Kinney, J.; Good, J.; Berriman, B.; Merrihew, A.; Deelman, E.

2014-05-01

In this paper, we describe how to leverage cloud resources to generate large-scale mosaics of the galactic plane in multiple wavelengths. Our goal is to generate a 16-wavelength infrared Atlas of the Galactic Plane at a common spatial sampling of 1 arcsec, processed so that they appear to have been measured with a single instrument. This will be achieved by using the Montage image mosaic engine process observations from the 2MASS, GLIMPSE, MIPSGAL, MSX and WISE datasets, over a wavelength range of 1 μm to 24 μm, and by using the Pegasus Workflow Management System for managing the workload. When complete, the Atlas will be made available to the community as a data product. We are generating images that cover ±180° in Galactic longitude and ±20° in Galactic latitude, to the extent permitted by the spatial coverage of each dataset. Each image will be 5°x5° in size (including an overlap of 1° with neighboring tiles), resulting in an atlas of 1,001 images. The final size will be about 50 TBs. This paper will focus on the computational challenges, solutions, and lessons learned in producing the Atlas. To manage the computation we are using the Pegasus Workflow Management System, a mature, highly fault-tolerant system now in release 4.2.2 that has found wide applicability across many science disciplines. A scientific workflow describes the dependencies between the tasks and in most cases the workflow is described as a directed acyclic graph, where the nodes are tasks and the edges denote the task dependencies. A defining property for a scientific workflow is that it manages data flow between tasks. Applied to the galactic plane project, each 5 by 5 mosaic is a Pegasus workflow. Pegasus is used to fetch the source images, execute the image mosaicking steps of Montage, and store the final outputs in a storage system. As these workflows are very I/O intensive, care has to be taken when choosing what infrastructure to execute the workflow on. In our setup, we choose to use dynamically provisioned compute clusters running on the Amazon Elastic Compute Cloud (EC2). All our instances are using the same base image, which is configured to come up as a master node by default. The master node is a central instance from where the workflow can be managed. Additional worker instances are provisioned and configured to accept work assignments from the master node. The system allows for adding/removing workers in an ad hoc fashion, and could be run in large configurations. To-date we have performed 245,000 CPU hours of computing and generated 7,029 images and totaling 30 TB. With the current set up our runtime would be 340,000 CPU hours for the whole project. Using spot m2.4xlarge instances, the cost would be approximately $5,950. Using faster AWS instances, such as cc2.8xlarge could potentially decrease the total CPU hours and further reduce the compute costs. The paper will explore these tradeoffs.

TH-AB-BRA-04: Dosimetric Evaluation of MR-Guided HDR Brachytherapy Planning for Cervical Cancer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamio, Y; Barkati, M; Beliveau-Nadeau, D

2016-06-15

Purpose: To perform a retrospective study on 16 patients that had both CT and T2-weighted MR scans done at first fraction using the Utrecht CT/MR applicator (Elekta Brachytherapy) in order to evaluate uncertainties associated with an MR-only planning workflow. Methods: MR-workflow uncertainties were classified in three categories: reconstruction, registration and contouring. A systematic comparison of the CT and MR contouring, manual reconstruction and optimization process was performed to evaluate the impact of these uncertainties on the recommended GEC ESTRO DVH parameters: D90% and V100% for HR-CTV as well as D2cc for bladder, rectum, sigmoid colon and small bowel. This comparisonmore » was done using the following four steps: 1. Catheter reconstruction done on MR images with original CT-plan contours and dwell times. 2. OAR contours adjusted on MR images with original CT-plan reconstruction and dwell times. 3. Both reconstruction and contours done on MR images with original CT-plan dwell times. 4. Entire MR-based workflow optimized dwell times reimported to the original CT-plan. Results: The MR-based reconstruction process showed average D2cc deviations of 4.5 ± 3.0%, 1.5 ± 2.0%, 2.5 ± 2.0% and 2.0 ± 1.0% for the bladder, rectum, sigmoid colon and small bowels respectively with a maximum of 10%, 6%, 6% and 4%. The HR-CTV’s D90% and V100% average deviations was found to be 4.0 ± 3.0%, and 2.0 ± 2.0% respectively with a maximum of 10% and 6%. Adjusting contours on MR-images was found to have a similar impact. Finally, the optimized MR-based workflow dwell times were found to still give acceptable plans when re-imported to the original CT-plan which validated the entire workflow. Conclusion: This work illustrates a systematic validation method for centers wanting to move towards an MR-only workflow. This work will be expanded to model based reconstruction, PD-weighted images and other types of applicators.« less

Integration of CBIR in radiological routine in accordance with IHE

NASA Astrophysics Data System (ADS)

Welter, Petra; Deserno, Thomas M.; Fischer, Benedikt; Wein, Berthold B.; Ott, Bastian; Günther, Rolf W.

2009-02-01

Increasing use of digital imaging processing leads to an enormous amount of imaging data. The access to picture archiving and communication systems (PACS), however, is solely textually, leading to sparse retrieval results because of ambiguous or missing image descriptions. Content-based image retrieval (CBIR) systems can improve the clinical diagnostic outcome significantly. However, current CBIR systems are not able to integrate their results with clinical workflow and PACS. Existing communication standards like DICOM and HL7 leave many options for implementation and do not ensure full interoperability. We present a concept of the standardized integration of a CBIR system for the radiology workflow in accordance with the Integrating the Healthcare Enterprise (IHE) framework. This is based on the IHE integration profile 'Post-Processing Workflow' (PPW) defining responsibilities as well as standardized communication and utilizing the DICOM Structured Report (DICOM SR). Because nowadays most of PACS and RIS systems are not yet fully IHE compliant to PPW, we also suggest an intermediate approach with the concepts of the CAD-PACS Toolkit. The integration is independent of the particular PACS and RIS system. Therefore, it supports the widespread application of CBIR in radiological routine. As a result, the approach is exemplarily applied to the Image Retrieval in Medical Applications (IRMA) framework.

A Scientific Workflow Platform for Generic and Scalable Object Recognition on Medical Images

NASA Astrophysics Data System (ADS)

Möller, Manuel; Tuot, Christopher; Sintek, Michael

In the research project THESEUS MEDICO we aim at a system combining medical image information with semantic background knowledge from ontologies to give clinicians fully cross-modal access to biomedical image repositories. Therefore joint efforts have to be made in more than one dimension: Object detection processes have to be specified in which an abstraction is performed starting from low-level image features across landmark detection utilizing abstract domain knowledge up to high-level object recognition. We propose a system based on a client-server extension of the scientific workflow platform Kepler that assists the collaboration of medical experts and computer scientists during development and parameter learning.

A multimodal imaging workflow to visualize metal mixtures in the human placenta and explore colocalization with biological response markers.

PubMed

Niedzwiecki, Megan M; Austin, Christine; Remark, Romain; Merad, Miriam; Gnjatic, Sacha; Estrada-Gutierrez, Guadalupe; Espejel-Nuñez, Aurora; Borboa-Olivares, Hector; Guzman-Huerta, Mario; Wright, Rosalind J; Wright, Robert O; Arora, Manish

2016-04-01

Fetal exposure to essential and toxic metals can influence life-long health trajectories. The placenta regulates chemical transmission from maternal circulation to the fetus and itself exhibits a complex response to environmental stressors. The placenta can thus be a useful matrix to monitor metal exposures and stress responses in utero, but strategies to explore the biologic effects of metal mixtures in this organ are not well-developed. In this proof-of-concept study, we used laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) to measure the distributions of multiple metals in placental tissue from a low-birth-weight pregnancy, and we developed an approach to identify the components of metal mixtures that colocalized with biological response markers. Our novel workflow, which includes custom-developed software tools and algorithms for spatial outlier identification and background subtraction in multidimensional elemental image stacks, enables rapid image processing and seamless integration of data from elemental imaging and immunohistochemistry. Using quantitative spatial statistics, we identified distinct patterns of metal accumulation at sites of inflammation. Broadly, our multiplexed approach can be used to explore the mechanisms mediating complex metal exposures and biologic responses within placentae and other tissue types. Our LA-ICP-MS image processing workflow can be accessed through our interactive R Shiny application 'shinyImaging', which is available at or through our laboratory's website, .

Thermal Remote Sensing with Uav-Based Workflows

NASA Astrophysics Data System (ADS)

Boesch, R.

2017-08-01

Climate change will have a significant influence on vegetation health and growth. Predictions of higher mean summer temperatures and prolonged summer draughts may pose a threat to agriculture areas and forest canopies. Rising canopy temperatures can be an indicator of plant stress because of the closure of stomata and a decrease in the transpiration rate. Thermal cameras are available for decades, but still often used for single image analysis, only in oblique view manner or with visual evaluations of video sequences. Therefore remote sensing using a thermal camera can be an important data source to understand transpiration processes. Photogrammetric workflows allow to process thermal images similar to RGB data. But low spatial resolution of thermal cameras, significant optical distortion and typically low contrast require an adapted workflow. Temperature distribution in forest canopies is typically completely unknown and less distinct than for urban or industrial areas, where metal constructions and surfaces yield high contrast and sharp edge information. The aim of this paper is to investigate the influence of interior camera orientation, tie point matching and ground control points on the resulting accuracy of bundle adjustment and dense cloud generation with a typically used photogrammetric workflow for UAVbased thermal imagery in natural environments.

Prototype of Kepler Processing Workflows For Microscopy And Neuroinformatics

PubMed Central

Astakhov, V.; Bandrowski, A.; Gupta, A.; Kulungowski, A.W.; Grethe, J.S.; Bouwer, J.; Molina, T.; Rowley, V.; Penticoff, S.; Terada, M.; Wong, W.; Hakozaki, H.; Kwon, O.; Martone, M.E.; Ellisman, M.

2016-01-01

We report on progress of employing the Kepler workflow engine to prototype “end-to-end” application integration workflows that concern data coming from microscopes deployed at the National Center for Microscopy Imaging Research (NCMIR). This system is built upon the mature code base of the Cell Centered Database (CCDB) and integrated rule-oriented data system (IRODS) for distributed storage. It provides integration with external projects such as the Whole Brain Catalog (WBC) and Neuroscience Information Framework (NIF), which benefit from NCMIR data. We also report on specific workflows which spawn from main workflows and perform data fusion and orchestration of Web services specific for the NIF project. This “Brain data flow” presents a user with categorized information about sources that have information on various brain regions. PMID:28479932

Impacting key performance indicators in an academic MR imaging department through process improvement.

PubMed

Recht, Michael; Macari, Michael; Lawson, Kirk; Mulholland, Tom; Chen, David; Kim, Danny; Babb, James

2013-03-01

The aim of this study was to evaluate all aspects of workflow in a large academic MRI department to determine whether process improvement (PI) efforts could improve key performance indicators (KPIs). KPI metrics in the investigators' MR imaging department include daily inpatient backlogs, on-time performance for outpatient examinations, examination volumes, appointment backlogs for pediatric anesthesia cases, and scan duration relative to time allotted for an examination. Over a 3-week period in April 2011, key members of the MR imaging department (including technologists, nurses, schedulers, physicians, and administrators) tracked all aspects of patient flow through the department, from scheduling to examination interpretation. Data were analyzed by the group to determine where PI could improve KPIs. Changes to MRI workflow were subsequently implemented, and KPIs were compared before (January 1, 2011, to April 30, 2011) and after (August 1, 2011, to December 31, 2011) using Mann-Whitney and Fisher's exact tests. The data analysis done during this PI led to multiple changes in the daily workflow of the MR department. In addition, a new sense of teamwork and empowerment was established within the MR staff. All of the measured KPIs showed statistically significant changes after the reengineering project. Intradepartmental PI efforts can significantly affect KPI metrics within an MR imaging department, making the process more patient centered. In addition, the process allowed significant growth without the need for additional equipment or personnel. Copyright © 2013 American College of Radiology. Published by Elsevier Inc. All rights reserved.

Biomedical image analysis and processing in clouds

NASA Astrophysics Data System (ADS)

Bednarz, Tomasz; Szul, Piotr; Arzhaeva, Yulia; Wang, Dadong; Burdett, Neil; Khassapov, Alex; Chen, Shiping; Vallotton, Pascal; Lagerstrom, Ryan; Gureyev, Tim; Taylor, John

2013-10-01

Cloud-based Image Analysis and Processing Toolbox project runs on the Australian National eResearch Collaboration Tools and Resources (NeCTAR) cloud infrastructure and allows access to biomedical image processing and analysis services to researchers via remotely accessible user interfaces. By providing user-friendly access to cloud computing resources and new workflow-based interfaces, our solution enables researchers to carry out various challenging image analysis and reconstruction tasks. Several case studies will be presented during the conference.

A midas plugin to enable construction of reproducible web-based image processing pipelines

PubMed Central

Grauer, Michael; Reynolds, Patrick; Hoogstoel, Marion; Budin, Francois; Styner, Martin A.; Oguz, Ipek

2013-01-01

Image processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that pipeline even by those biomedical researchers with limited image processing knowledge. These tools are implemented as a plugin for Midas, an open-source toolkit for creating web based scientific data storage and processing platforms. Using this plugin, an image processing expert can construct a pipeline, create a web-based User Interface, manage jobs, and visualize intermediate results. Pipelines are executed on a grid computing platform using BatchMake and HTCondor. This represents a new capability for biomedical researchers and offers an innovative platform for scientific collaboration. Current tools work well, but can be inaccessible for those lacking image processing expertise. Using this plugin, researchers in collaboration with image processing experts can create workflows with reasonable default settings and streamlined user interfaces, and data can be processed easily from a lab environment without the need for a powerful desktop computer. This platform allows simplified troubleshooting, centralized maintenance, and easy data sharing with collaborators. These capabilities enable reproducible science by sharing datasets and processing pipelines between collaborators. In this paper, we present a description of this innovative Midas plugin, along with results obtained from building and executing several ITK based image processing workflows for diffusion weighted MRI (DW MRI) of rodent brain images, as well as recommendations for building automated image processing pipelines. Although the particular image processing pipelines developed were focused on rodent brain MRI, the presented plugin can be used to support any executable or script-based pipeline. PMID:24416016

A midas plugin to enable construction of reproducible web-based image processing pipelines.

PubMed

Grauer, Michael; Reynolds, Patrick; Hoogstoel, Marion; Budin, Francois; Styner, Martin A; Oguz, Ipek

2013-01-01

Image processing is an important quantitative technique for neuroscience researchers, but difficult for those who lack experience in the field. In this paper we present a web-based platform that allows an expert to create a brain image processing pipeline, enabling execution of that pipeline even by those biomedical researchers with limited image processing knowledge. These tools are implemented as a plugin for Midas, an open-source toolkit for creating web based scientific data storage and processing platforms. Using this plugin, an image processing expert can construct a pipeline, create a web-based User Interface, manage jobs, and visualize intermediate results. Pipelines are executed on a grid computing platform using BatchMake and HTCondor. This represents a new capability for biomedical researchers and offers an innovative platform for scientific collaboration. Current tools work well, but can be inaccessible for those lacking image processing expertise. Using this plugin, researchers in collaboration with image processing experts can create workflows with reasonable default settings and streamlined user interfaces, and data can be processed easily from a lab environment without the need for a powerful desktop computer. This platform allows simplified troubleshooting, centralized maintenance, and easy data sharing with collaborators. These capabilities enable reproducible science by sharing datasets and processing pipelines between collaborators. In this paper, we present a description of this innovative Midas plugin, along with results obtained from building and executing several ITK based image processing workflows for diffusion weighted MRI (DW MRI) of rodent brain images, as well as recommendations for building automated image processing pipelines. Although the particular image processing pipelines developed were focused on rodent brain MRI, the presented plugin can be used to support any executable or script-based pipeline.

Embedded, real-time UAV control for improved, image-based 3D scene reconstruction

Treesearch

Jean Liénard; Andre Vogs; Demetrios Gatziolis; Nikolay Strigul

2016-01-01

Unmanned Aerial Vehicles (UAVs) are already broadly employed for 3D modeling of large objects such as trees and monuments via photogrammetry. The usual workflow includes two distinct steps: image acquisition with UAV and computationally demanding postflight image processing. Insufficient feature overlaps across images is a common shortcoming in post-flight image...

Development of a novel imaging informatics-based system with an intelligent workflow engine (IWEIS) to support imaging-based clinical trials

PubMed Central

Wang, Ximing; Liu, Brent J; Martinez, Clarisa; Zhang, Xuejun; Winstein, Carolee J

2015-01-01

Imaging based clinical trials can benefit from a solution to efficiently collect, analyze, and distribute multimedia data at various stages within the workflow. Currently, the data management needs of these trials are typically addressed with custom-built systems. However, software development of the custom- built systems for versatile workflows can be resource-consuming. To address these challenges, we present a system with a workflow engine for imaging based clinical trials. The system enables a project coordinator to build a data collection and management system specifically related to study protocol workflow without programming. Web Access to DICOM Objects (WADO) module with novel features is integrated to further facilitate imaging related study. The system was initially evaluated by an imaging based rehabilitation clinical trial. The evaluation shows that the cost of the development of system can be much reduced compared to the custom-built system. By providing a solution to customize a system and automate the workflow, the system will save on development time and reduce errors especially for imaging clinical trials. PMID:25870169

Automatic DNA Diagnosis for 1D Gel Electrophoresis Images using Bio-image Processing Technique.

PubMed

Intarapanich, Apichart; Kaewkamnerd, Saowaluck; Shaw, Philip J; Ukosakit, Kittipat; Tragoonrung, Somvong; Tongsima, Sissades

2015-01-01

DNA gel electrophoresis is a molecular biology technique for separating different sizes of DNA fragments. Applications of DNA gel electrophoresis include DNA fingerprinting (genetic diagnosis), size estimation of DNA, and DNA separation for Southern blotting. Accurate interpretation of DNA banding patterns from electrophoretic images can be laborious and error prone when a large number of bands are interrogated manually. Although many bio-imaging techniques have been proposed, none of them can fully automate the typing of DNA owing to the complexities of migration patterns typically obtained. We developed an image-processing tool that automatically calls genotypes from DNA gel electrophoresis images. The image processing workflow comprises three main steps: 1) lane segmentation, 2) extraction of DNA bands and 3) band genotyping classification. The tool was originally intended to facilitate large-scale genotyping analysis of sugarcane cultivars. We tested the proposed tool on 10 gel images (433 cultivars) obtained from polyacrylamide gel electrophoresis (PAGE) of PCR amplicons for detecting intron length polymorphisms (ILP) on one locus of the sugarcanes. These gel images demonstrated many challenges in automated lane/band segmentation in image processing including lane distortion, band deformity, high degree of noise in the background, and bands that are very close together (doublets). Using the proposed bio-imaging workflow, lanes and DNA bands contained within are properly segmented, even for adjacent bands with aberrant migration that cannot be separated by conventional techniques. The software, called GELect, automatically performs genotype calling on each lane by comparing with an all-banding reference, which was created by clustering the existing bands into the non-redundant set of reference bands. The automated genotype calling results were verified by independent manual typing by molecular biologists. This work presents an automated genotyping tool from DNA gel electrophoresis images, called GELect, which was written in Java and made available through the imageJ framework. With a novel automated image processing workflow, the tool can accurately segment lanes from a gel matrix, intelligently extract distorted and even doublet bands that are difficult to identify by existing image processing tools. Consequently, genotyping from DNA gel electrophoresis can be performed automatically allowing users to efficiently conduct large scale DNA fingerprinting via DNA gel electrophoresis. The software is freely available from http://www.biotec.or.th/gi/tools/gelect.

Workflow Dynamics and the Imaging Value Chain: Quantifying the Effect of Designating a Nonimage-Interpretive Task Workflow.

PubMed

Lee, Matthew H; Schemmel, Andrew J; Pooler, B Dustin; Hanley, Taylor; Kennedy, Tabassum A; Field, Aaron S; Wiegmann, Douglas; Yu, John-Paul J

To assess the impact of separate non-image interpretive task and image-interpretive task workflows in an academic neuroradiology practice. A prospective, randomized, observational investigation of a centralized academic neuroradiology reading room was performed. The primary reading room fellow was observed over a one-month period using a time-and-motion methodology, recording frequency and duration of tasks performed. Tasks were categorized into separate image interpretive and non-image interpretive workflows. Post-intervention observation of the primary fellow was repeated following the implementation of a consult assistant responsible for non-image interpretive tasks. Pre- and post-intervention data were compared. Following separation of image-interpretive and non-image interpretive workflows, time spent on image-interpretive tasks by the primary fellow increased from 53.8% to 73.2% while non-image interpretive tasks decreased from 20.4% to 4.4%. Mean time duration of image interpretation nearly doubled, from 05:44 to 11:01 (p = 0.002). Decreases in specific non-image interpretive tasks, including phone calls/paging (2.86/hr versus 0.80/hr), in-room consultations (1.36/hr versus 0.80/hr), and protocoling (0.99/hr versus 0.10/hr), were observed. The consult assistant experienced 29.4 task switching events per hour. Rates of specific non-image interpretive tasks for the CA were 6.41/hr for phone calls/paging, 3.60/hr for in-room consultations, and 3.83/hr for protocoling. Separating responsibilities into NIT and IIT workflows substantially increased image interpretation time and decreased TSEs for the primary fellow. Consolidation of NITs into a separate workflow may allow for more efficient task completion. Copyright © 2017 Elsevier Inc. All rights reserved.

An image analysis system for near-infrared (NIR) fluorescence lymph imaging

NASA Astrophysics Data System (ADS)

Zhang, Jingdan; Zhou, Shaohua Kevin; Xiang, Xiaoyan; Rasmussen, John C.; Sevick-Muraca, Eva M.

2011-03-01

Quantitative analysis of lymphatic function is crucial for understanding the lymphatic system and diagnosing the associated diseases. Recently, a near-infrared (NIR) fluorescence imaging system is developed for real-time imaging lymphatic propulsion by intradermal injection of microdose of a NIR fluorophore distal to the lymphatics of interest. However, the previous analysis software3, 4 is underdeveloped, requiring extensive time and effort to analyze a NIR image sequence. In this paper, we develop a number of image processing techniques to automate the data analysis workflow, including an object tracking algorithm to stabilize the subject and remove the motion artifacts, an image representation named flow map to characterize lymphatic flow more reliably, and an automatic algorithm to compute lymph velocity and frequency of propulsion. By integrating all these techniques to a system, the analysis workflow significantly reduces the amount of required user interaction and improves the reliability of the measurement.

Sci-Fri PM: Radiation Therapy, Planning, Imaging, and Special Techniques - 08: Retrospective Dose Accumulation Workflow in Head and Neck Cancer Patients Using RayStation 4.5.2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wong, Olive; Chan, Biu; Moseley, Joanne

Purpose: We have developed a semi-automated dose accumulation workflow for Head and Neck Cancer (HNC) patients to evaluate volumetric and dosimetric changes that take place during radiotherapy. This work will be used to assess how dosimetric changes affect both toxicity and disease control, hence inform the feasibility and design of a prospective HNC adaptive trial. Methods: RayStation 4.5.2 features deformable image registration (DIR), where structures already defined on the planning CT image set can be deformably mapped onto cone-beam computed tomography (CBCT) images, accounting for daily treatment set-up shifts and changes in patient anatomy. The daily delivered dose can bemore » calculated on each CBCT and mapped back to the planning CT to allow dose accumulation. The process is partially automated using Python scripts developed in collaboration with RaySearch. Results: To date we have performed dose accumulation on 18 HNC patients treated at our institution during 2013–2015 under REB approval. Our semi-automated process establishes clinical feasibility. Generally, dose accumulation for the entire treatment course of one case takes 60–120 minutes: importing all CBCTs requires 20–30 minutes as each patient has 30 to 40 treated fractions; image registration and dose accumulation require 60–90 minutes. This is in contrast to the process without automated scripts where dose accumulation alone would take 3–5 hours. Conclusions: We have developed a reliable workflow for retrospective dose tracking in HNC using RayStation. The process has been validated for HNC patients treated on both Elekta and Varian linacs with CBCTs acquired on XVI and OBI platforms respectively.« less

Development of a user customizable imaging informatics-based intelligent workflow engine system to enhance rehabilitation clinical trials

NASA Astrophysics Data System (ADS)

Wang, Ximing; Martinez, Clarisa; Wang, Jing; Liu, Ye; Liu, Brent

2014-03-01

Clinical trials usually have a demand to collect, track and analyze multimedia data according to the workflow. Currently, the clinical trial data management requirements are normally addressed with custom-built systems. Challenges occur in the workflow design within different trials. The traditional pre-defined custom-built system is usually limited to a specific clinical trial and normally requires time-consuming and resource-intensive software development. To provide a solution, we present a user customizable imaging informatics-based intelligent workflow engine system for managing stroke rehabilitation clinical trials with intelligent workflow. The intelligent workflow engine provides flexibility in building and tailoring the workflow in various stages of clinical trials. By providing a solution to tailor and automate the workflow, the system will save time and reduce errors for clinical trials. Although our system is designed for clinical trials for rehabilitation, it may be extended to other imaging based clinical trials as well.

An Automatic Image Processing Workflow for Daily Magnetic Resonance Imaging Quality Assurance.

PubMed

Peltonen, Juha I; Mäkelä, Teemu; Sofiev, Alexey; Salli, Eero

2017-04-01

The performance of magnetic resonance imaging (MRI) equipment is typically monitored with a quality assurance (QA) program. The QA program includes various tests performed at regular intervals. Users may execute specific tests, e.g., daily, weekly, or monthly. The exact interval of these measurements varies according to the department policies, machine setup and usage, manufacturer's recommendations, and available resources. In our experience, a single image acquired before the first patient of the day offers a low effort and effective system check. When this daily QA check is repeated with identical imaging parameters and phantom setup, the data can be used to derive various time series of the scanner performance. However, daily QA with manual processing can quickly become laborious in a multi-scanner environment. Fully automated image analysis and results output can positively impact the QA process by decreasing reaction time, improving repeatability, and by offering novel performance evaluation methods. In this study, we have developed a daily MRI QA workflow that can measure multiple scanner performance parameters with minimal manual labor required. The daily QA system is built around a phantom image taken by the radiographers at the beginning of day. The image is acquired with a consistent phantom setup and standardized imaging parameters. Recorded parameters are processed into graphs available to everyone involved in the MRI QA process via a web-based interface. The presented automatic MRI QA system provides an efficient tool for following the short- and long-term stability of MRI scanners.

The Image Gently pediatric digital radiography safety checklist: tools for improving pediatric radiography.

PubMed

John, Susan D; Moore, Quentin T; Herrmann, Tracy; Don, Steven; Powers, Kevin; Smith, Susan N; Morrison, Greg; Charkot, Ellen; Mills, Thalia T; Rutz, Lois; Goske, Marilyn J

2013-10-01

Transition from film-screen to digital radiography requires changes in radiographic technique and workflow processes to ensure that the minimum radiation exposure is used while maintaining diagnostic image quality. Checklists have been demonstrated to be useful tools for decreasing errors and improving safety in several areas, including commercial aviation and surgical procedures. The Image Gently campaign, through a competitive grant from the FDA, developed a checklist for technologists to use during the performance of digital radiography in pediatric patients. The checklist outlines the critical steps in digital radiography workflow, with an emphasis on steps that affect radiation exposure and image quality. The checklist and its accompanying implementation manual and practice quality improvement project are open source and downloadable at www.imagegently.org. The authors describe the process of developing and testing the checklist and offer suggestions for using the checklist to minimize radiation exposure to children during radiography. Copyright © 2013 American College of Radiology. All rights reserved.

BioImageXD: an open, general-purpose and high-throughput image-processing platform.

PubMed

Kankaanpää, Pasi; Paavolainen, Lassi; Tiitta, Silja; Karjalainen, Mikko; Päivärinne, Joacim; Nieminen, Jonna; Marjomäki, Varpu; Heino, Jyrki; White, Daniel J

2012-06-28

BioImageXD puts open-source computer science tools for three-dimensional visualization and analysis into the hands of all researchers, through a user-friendly graphical interface tuned to the needs of biologists. BioImageXD has no restrictive licenses or undisclosed algorithms and enables publication of precise, reproducible and modifiable workflows. It allows simple construction of processing pipelines and should enable biologists to perform challenging analyses of complex processes. We demonstrate its performance in a study of integrin clustering in response to selected inhibitors.

A Hybrid Task Graph Scheduler for High Performance Image Processing Workflows.

PubMed

Blattner, Timothy; Keyrouz, Walid; Bhattacharyya, Shuvra S; Halem, Milton; Brady, Mary

2017-12-01

Designing applications for scalability is key to improving their performance in hybrid and cluster computing. Scheduling code to utilize parallelism is difficult, particularly when dealing with data dependencies, memory management, data motion, and processor occupancy. The Hybrid Task Graph Scheduler (HTGS) improves programmer productivity when implementing hybrid workflows for multi-core and multi-GPU systems. The Hybrid Task Graph Scheduler (HTGS) is an abstract execution model, framework, and API that increases programmer productivity when implementing hybrid workflows for such systems. HTGS manages dependencies between tasks, represents CPU and GPU memories independently, overlaps computations with disk I/O and memory transfers, keeps multiple GPUs occupied, and uses all available compute resources. Through these abstractions, data motion and memory are explicit; this makes data locality decisions more accessible. To demonstrate the HTGS application program interface (API), we present implementations of two example algorithms: (1) a matrix multiplication that shows how easily task graphs can be used; and (2) a hybrid implementation of microscopy image stitching that reduces code size by ≈ 43% compared to a manually coded hybrid workflow implementation and showcases the minimal overhead of task graphs in HTGS. Both of the HTGS-based implementations show good performance. In image stitching the HTGS implementation achieves similar performance to the hybrid workflow implementation. Matrix multiplication with HTGS achieves 1.3× and 1.8× speedup over the multi-threaded OpenBLAS library for 16k × 16k and 32k × 32k size matrices, respectively.

Grid infrastructure for automatic processing of SAR data for flood applications

NASA Astrophysics Data System (ADS)

Kussul, Natalia; Skakun, Serhiy; Shelestov, Andrii

2010-05-01

More and more geosciences applications are being put on to the Grids. Due to the complexity of geosciences applications that is caused by complex workflow, the use of computationally intensive environmental models, the need of management and integration of heterogeneous data sets, Grid offers solutions to tackle these problems. Many geosciences applications, especially those related to the disaster management and mitigations require the geospatial services to be delivered in proper time. For example, information on flooded areas should be provided to corresponding organizations (local authorities, civil protection agencies, UN agencies etc.) no more than in 24 h to be able to effectively allocate resources required to mitigate the disaster. Therefore, providing infrastructure and services that will enable automatic generation of products based on the integration of heterogeneous data represents the tasks of great importance. In this paper we present Grid infrastructure for automatic processing of synthetic-aperture radar (SAR) satellite images to derive flood products. In particular, we use SAR data acquired by ESA's ENVSAT satellite, and neural networks to derive flood extent. The data are provided in operational mode from ESA rolling archive (within ESA Category-1 grant). We developed a portal that is based on OpenLayers frameworks and provides access point to the developed services. Through the portal the user can define geographical region and search for the required data. Upon selection of data sets a workflow is automatically generated and executed on the resources of Grid infrastructure. For workflow execution and management we use Karajan language. The workflow of SAR data processing consists of the following steps: image calibration, image orthorectification, image processing with neural networks, topographic effects removal, geocoding and transformation to lat/long projection, and visualisation. These steps are executed by different software, and can be executed by different resources of the Grid system. The resulting geospatial services are available in various OGC standards such as KML and WMS. Currently, the Grid infrastructure integrates the resources of several geographically distributed organizations, in particular: Space Research Institute NASU-NSAU (Ukraine) with deployed computational and storage nodes based on Globus Toolkit 4 (htpp://www.globus.org) and gLite 3 (http://glite.web.cern.ch) middleware, access to geospatial data and a Grid portal; Institute of Cybernetics of NASU (Ukraine) with deployed computational and storage nodes (SCIT-1/2/3 clusters) based on Globus Toolkit 4 middleware and access to computational resources (approximately 500 processors); Center of Earth Observation and Digital Earth Chinese Academy of Sciences (CEODE-CAS, China) with deployed computational nodes based on Globus Toolkit 4 middleware and access to geospatial data (approximately 16 processors). We are currently adding new geospatial services based on optical satellite data, namely MODIS. This work is carried out jointly with the CEODE-CAS. Using workflow patterns that were developed for SAR data processing we are building new workflows for optical data processing.

Uav Photgrammetric Workflows: a best Practice Guideline

NASA Astrophysics Data System (ADS)

Federman, A.; Santana Quintero, M.; Kretz, S.; Gregg, J.; Lengies, M.; Ouimet, C.; Laliberte, J.

2017-08-01

The increasing commercialization of unmanned aerial vehicles (UAVs) has opened the possibility of performing low-cost aerial image acquisition for the documentation of cultural heritage sites through UAV photogrammetry. The flying of UAVs in Canada is regulated through Transport Canada and requires a Special Flight Operations Certificate (SFOC) in order to fly. Various image acquisition techniques have been explored in this review, as well as well software used to register the data. A general workflow procedure has been formulated based off of the literature reviewed. A case study example of using UAV photogrammetry at Prince of Wales Fort is discussed, specifically in relation to the data acquisition and processing. Some gaps in the literature reviewed highlight the need for streamlining the SFOC application process, and incorporating UAVs into cultural heritage documentation courses.

RayPlus: a Web-Based Platform for Medical Image Processing.

PubMed

Yuan, Rong; Luo, Ming; Sun, Zhi; Shi, Shuyue; Xiao, Peng; Xie, Qingguo

2017-04-01

Medical image can provide valuable information for preclinical research, clinical diagnosis, and treatment. As the widespread use of digital medical imaging, many researchers are currently developing medical image processing algorithms and systems in order to accommodate a better result to clinical community, including accurate clinical parameters or processed images from the original images. In this paper, we propose a web-based platform to present and process medical images. By using Internet and novel database technologies, authorized users can easily access to medical images and facilitate their workflows of processing with server-side powerful computing performance without any installation. We implement a series of algorithms of image processing and visualization in the initial version of Rayplus. Integration of our system allows much flexibility and convenience for both research and clinical communities.

Towards Exascale Seismic Imaging and Inversion

NASA Astrophysics Data System (ADS)

Tromp, J.; Bozdag, E.; Lefebvre, M. P.; Smith, J. A.; Lei, W.; Ruan, Y.

2015-12-01

Post-petascale supercomputers are now available to solve complex scientific problems that were thought unreachable a few decades ago. They also bring a cohort of concerns tied to obtaining optimum performance. Several issues are currently being investigated by the HPC community. These include energy consumption, fault resilience, scalability of the current parallel paradigms, workflow management, I/O performance and feature extraction with large datasets. In this presentation, we focus on the last three issues. In the context of seismic imaging and inversion, in particular for simulations based on adjoint methods, workflows are well defined.They consist of a few collective steps (e.g., mesh generation or model updates) and of a large number of independent steps (e.g., forward and adjoint simulations of each seismic event, pre- and postprocessing of seismic traces). The greater goal is to reduce the time to solution, that is, obtaining a more precise representation of the subsurface as fast as possible. This brings us to consider both the workflow in its entirety and the parts comprising it. The usual approach is to speedup the purely computational parts based on code optimization in order to reach higher FLOPS and better memory management. This still remains an important concern, but larger scale experiments show that the imaging workflow suffers from severe I/O bottlenecks. Such limitations occur both for purely computational data and seismic time series. The latter are dealt with by the introduction of a new Adaptable Seismic Data Format (ASDF). Parallel I/O libraries, namely HDF5 and ADIOS, are used to drastically reduce the cost of disk access. Parallel visualization tools, such as VisIt, are able to take advantage of ADIOS metadata to extract features and display massive datasets. Because large parts of the workflow are embarrassingly parallel, we are investigating the possibility of automating the imaging process with the integration of scientific workflow management tools, specifically Pegasus.

Multispectral remote sensing from unmanned aircraft: image processing workflows and applications for rangeland environments

USDA-ARS?s Scientific Manuscript database

Using unmanned aircraft systems (UAS) as remote sensing platforms offers the unique ability for repeated deployment for acquisition of high temporal resolution data at very high spatial resolution. Most image acquisitions from UAS have been in the visible bands, while multispectral remote sensing ap...

Conventions and workflows for using Situs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wriggers, Willy, E-mail: wriggers@biomachina.org

2012-04-01

Recent developments of the Situs software suite for multi-scale modeling are reviewed. Typical workflows and conventions encountered during processing of biophysical data from electron microscopy, tomography or small-angle X-ray scattering are described. Situs is a modular program package for the multi-scale modeling of atomic resolution structures and low-resolution biophysical data from electron microscopy, tomography or small-angle X-ray scattering. This article provides an overview of recent developments in the Situs package, with an emphasis on workflows and conventions that are important for practical applications. The modular design of the programs facilitates scripting in the bash shell that allows specific programs tomore » be combined in creative ways that go beyond the original intent of the developers. Several scripting-enabled functionalities, such as flexible transformations of data type, the use of symmetry constraints or the creation of two-dimensional projection images, are described. The processing of low-resolution biophysical maps in such workflows follows not only first principles but often relies on implicit conventions. Situs conventions related to map formats, resolution, correlation functions and feature detection are reviewed and summarized. The compatibility of the Situs workflow with CCP4 conventions and programs is discussed.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zoberi, J.

Brachytherapy has proven to be an effective treatment option for prostate cancer. Initially, prostate brachytherapy was delivered through permanently implanted low dose rate (LDR) radioactive sources; however, high dose rate (HDR) temporary brachytherapy for prostate cancer is gaining popularity. Needle insertion during prostate brachytherapy is most commonly performed under ultrasound (U/S) guidance; however, treatment planning may be performed utilizing several imaging modalities either in an intra- or post-operative setting. During intra-operative prostate HDR, the needles are imaged during implantation, and planning may be performed in real time. At present, the most common imaging modality utilized for intra-operative prostate HDR ismore » U/S. Alternatively, in the post-operative setting, following needle implantation, patients may be simulated with computed tomography (CT) or magnetic resonance imaging (MRI). Each imaging modality and workflow provides its share of benefits and limitations. Prostate HDR has been adopted in a number of cancer centers across the nation. In this educational session, we will explore the role of U/S, CT, and MRI in HDR prostate brachytherapy. Example workflows and operational details will be shared, and we will discuss how to establish a prostate HDR program in a clinical setting. Learning Objectives: Review prostate HDR techniques based on the imaging modality Discuss the challenges and pitfalls introduced by the three imagebased options for prostate HDR brachytherapy Review the QA process and learn about the development of clinical workflows for these imaging options at different institutions.« less

An open data mining framework for the analysis of medical images: application on obstructive nephropathy microscopy images.

PubMed

Doukas, Charalampos; Goudas, Theodosis; Fischer, Simon; Mierswa, Ingo; Chatziioannou, Aristotle; Maglogiannis, Ilias

2010-01-01

This paper presents an open image-mining framework that provides access to tools and methods for the characterization of medical images. Several image processing and feature extraction operators have been implemented and exposed through Web Services. Rapid-Miner, an open source data mining system has been utilized for applying classification operators and creating the essential processing workflows. The proposed framework has been applied for the detection of salient objects in Obstructive Nephropathy microscopy images. Initial classification results are quite promising demonstrating the feasibility of automated characterization of kidney biopsy images.

A Web application for the management of clinical workflow in image‐guided and adaptive proton therapy for prostate cancer treatments

PubMed Central

Boes, Peter; Ho, Meng Wei; Li, Zuofeng

2015-01-01

Image‐guided radiotherapy (IGRT), based on radiopaque markers placed in the prostate gland, was used for proton therapy of prostate patients. Orthogonal X‐rays and the IBA Digital Image Positioning System (DIPS) were used for setup correction prior to treatment and were repeated after treatment delivery. Following a rationale for margin estimates similar to that of van Herk,(1) the daily post‐treatment DIPS data were analyzed to determine if an adaptive radiotherapy plan was necessary. A Web application using ASP.NET MVC5, Entity Framework, and an SQL database was designed to automate this process. The designed features included state‐of‐the‐art Web technologies, a domain model closely matching the workflow, a database‐supporting concurrency and data mining, access to the DIPS database, secured user access and roles management, and graphing and analysis tools. The Model‐View‐Controller (MVC) paradigm allowed clean domain logic, unit testing, and extensibility. Client‐side technologies, such as jQuery, jQuery Plug‐ins, and Ajax, were adopted to achieve a rich user environment and fast response. Data models included patients, staff, treatment fields and records, correction vectors, DIPS images, and association logics. Data entry, analysis, workflow logics, and notifications were implemented. The system effectively modeled the clinical workflow and IGRT process. PACS number: 87 PMID:26103504

Routine Digital Pathology Workflow: The Catania Experience

PubMed Central

Fraggetta, Filippo; Garozzo, Salvatore; Zannoni, Gian Franco; Pantanowitz, Liron; Rossi, Esther Diana

2017-01-01

Introduction: Successful implementation of whole slide imaging (WSI) for routine clinical practice has been accomplished in only a few pathology laboratories worldwide. We report the transition to an effective and complete digital surgical pathology workflow in the pathology laboratory at Cannizzaro Hospital in Catania, Italy. Methods: All (100%) permanent histopathology glass slides were digitized at ×20 using Aperio AT2 scanners. Compatible stain and scanning slide racks were employed to streamline operations. eSlide Manager software was bidirectionally interfaced with the anatomic pathology laboratory information system. Virtual slide trays connected to the two-dimensional (2D) barcode tracking system allowed pathologists to confirm that they were correctly assigned slides and that all tissues on these glass slides were scanned. Results: Over 115,000 glass slides were digitized with a scan fail rate of around 1%. Drying glass slides before scanning minimized them sticking to scanner racks. Implementation required introduction of a 2D barcode tracking system and modification of histology workflow processes. Conclusion: Our experience indicates that effective adoption of WSI for primary diagnostic use was more dependent on optimizing preimaging variables and integration with the laboratory information system than on information technology infrastructure and ensuring pathologist buy-in. Implementation of digital pathology for routine practice not only leveraged the benefits of digital imaging but also creates an opportunity for establishing standardization of workflow processes in the pathology laboratory. PMID:29416914

Routine Digital Pathology Workflow: The Catania Experience.

PubMed

Fraggetta, Filippo; Garozzo, Salvatore; Zannoni, Gian Franco; Pantanowitz, Liron; Rossi, Esther Diana

2017-01-01

Successful implementation of whole slide imaging (WSI) for routine clinical practice has been accomplished in only a few pathology laboratories worldwide. We report the transition to an effective and complete digital surgical pathology workflow in the pathology laboratory at Cannizzaro Hospital in Catania, Italy. All (100%) permanent histopathology glass slides were digitized at ×20 using Aperio AT2 scanners. Compatible stain and scanning slide racks were employed to streamline operations. eSlide Manager software was bidirectionally interfaced with the anatomic pathology laboratory information system. Virtual slide trays connected to the two-dimensional (2D) barcode tracking system allowed pathologists to confirm that they were correctly assigned slides and that all tissues on these glass slides were scanned. Over 115,000 glass slides were digitized with a scan fail rate of around 1%. Drying glass slides before scanning minimized them sticking to scanner racks. Implementation required introduction of a 2D barcode tracking system and modification of histology workflow processes. Our experience indicates that effective adoption of WSI for primary diagnostic use was more dependent on optimizing preimaging variables and integration with the laboratory information system than on information technology infrastructure and ensuring pathologist buy-in. Implementation of digital pathology for routine practice not only leveraged the benefits of digital imaging but also creates an opportunity for establishing standardization of workflow processes in the pathology laboratory.

Implementation and evaluation of a new workflow for registration and segmentation of pulmonary MRI data for regional lung perfusion assessment.

PubMed

Böttger, T; Grunewald, K; Schöbinger, M; Fink, C; Risse, F; Kauczor, H U; Meinzer, H P; Wolf, Ivo

2007-03-07

Recently it has been shown that regional lung perfusion can be assessed using time-resolved contrast-enhanced magnetic resonance (MR) imaging. Quantification of the perfusion images has been attempted, based on definition of small regions of interest (ROIs). Use of complete lung segmentations instead of ROIs could possibly increase quantification accuracy. Due to the low signal-to-noise ratio, automatic segmentation algorithms cannot be applied. On the other hand, manual segmentation of the lung tissue is very time consuming and can become inaccurate, as the borders of the lung to adjacent tissues are not always clearly visible. We propose a new workflow for semi-automatic segmentation of the lung from additionally acquired morphological HASTE MR images. First the lung is delineated semi-automatically in the HASTE image. Next the HASTE image is automatically registered with the perfusion images. Finally, the transformation resulting from the registration is used to align the lung segmentation from the morphological dataset with the perfusion images. We evaluated rigid, affine and locally elastic transformations, suitable optimizers and different implementations of mutual information (MI) metrics to determine the best possible registration algorithm. We located the shortcomings of the registration procedure and under which conditions automatic registration will succeed or fail. Segmentation results were evaluated using overlap and distance measures. Integration of the new workflow reduces the time needed for post-processing of the data, simplifies the perfusion quantification and reduces interobserver variability in the segmentation process. In addition, the matched morphological data set can be used to identify morphologic changes as the source for the perfusion abnormalities.

Comprehensive, powerful, efficient, intuitive: a new software framework for clinical imaging applications

NASA Astrophysics Data System (ADS)

Augustine, Kurt E.; Holmes, David R., III; Hanson, Dennis P.; Robb, Richard A.

2006-03-01

One of the greatest challenges for a software engineer is to create a complex application that is comprehensive enough to be useful to a diverse set of users, yet focused enough for individual tasks to be carried out efficiently with minimal training. This "powerful yet simple" paradox is particularly prevalent in advanced medical imaging applications. Recent research in the Biomedical Imaging Resource (BIR) at Mayo Clinic has been directed toward development of an imaging application framework that provides powerful image visualization/analysis tools in an intuitive, easy-to-use interface. It is based on two concepts very familiar to physicians - Cases and Workflows. Each case is associated with a unique patient and a specific set of routine clinical tasks, or a workflow. Each workflow is comprised of an ordered set of general-purpose modules which can be re-used for each unique workflow. Clinicians help describe and design the workflows, and then are provided with an intuitive interface to both patient data and analysis tools. Since most of the individual steps are common to many different workflows, the use of general-purpose modules reduces development time and results in applications that are consistent, stable, and robust. While the development of individual modules may reflect years of research by imaging scientists, new customized workflows based on the new modules can be developed extremely fast. If a powerful, comprehensive application is difficult to learn and complicated to use, it will be unacceptable to most clinicians. Clinical image analysis tools must be intuitive and effective or they simply will not be used.

Evaluation of an image-based tracking workflow using a passive marker and resonant micro-coil fiducials for automatic image plane alignment in interventional MRI.

PubMed

Neumann, M; Breton, E; Cuvillon, L; Pan, L; Lorenz, C H; de Mathelin, M

2012-01-01

In this paper, an original workflow is presented for MR image plane alignment based on tracking in real-time MR images. A test device consisting of two resonant micro-coils and a passive marker is proposed for detection using image-based algorithms. Micro-coils allow for automated initialization of the object detection in dedicated low flip angle projection images; then the passive marker is tracked in clinical real-time MR images, with alternation between two oblique orthogonal image planes along the test device axis; in case the passive marker is lost in real-time images, the workflow is reinitialized. The proposed workflow was designed to minimize dedicated acquisition time to a single dedicated acquisition in the ideal case (no reinitialization required). First experiments have shown promising results for test-device tracking precision, with a mean position error of 0.79 mm and a mean orientation error of 0.24°.

Evaluation of an image-based tracking workflow with Kalman filtering for automatic image plane alignment in interventional MRI.

PubMed

Neumann, M; Cuvillon, L; Breton, E; de Matheli, M

2013-01-01

Recently, a workflow for magnetic resonance (MR) image plane alignment based on tracking in real-time MR images was introduced. The workflow is based on a tracking device composed of 2 resonant micro-coils and a passive marker, and allows for tracking of the passive marker in clinical real-time images and automatic (re-)initialization using the microcoils. As the Kalman filter has proven its benefit as an estimator and predictor, it is well suited for use in tracking applications. In this paper, a Kalman filter is integrated in the previously developed workflow in order to predict position and orientation of the tracking device. Measurement noise covariances of the Kalman filter are dynamically changed in order to take into account that, according to the image plane orientation, only a subset of the 3D pose components is available. The improved tracking performance of the Kalman extended workflow could be quantified in simulation results. Also, a first experiment in the MRI scanner was performed but without quantitative results yet.

Algorithm sensitivity analysis and parameter tuning for tissue image segmentation pipelines

PubMed Central

Kurç, Tahsin M.; Taveira, Luís F. R.; Melo, Alba C. M. A.; Gao, Yi; Kong, Jun; Saltz, Joel H.

2017-01-01

Abstract Motivation: Sensitivity analysis and parameter tuning are important processes in large-scale image analysis. They are very costly because the image analysis workflows are required to be executed several times to systematically correlate output variations with parameter changes or to tune parameters. An integrated solution with minimum user interaction that uses effective methodologies and high performance computing is required to scale these studies to large imaging datasets and expensive analysis workflows. Results: The experiments with two segmentation workflows show that the proposed approach can (i) quickly identify and prune parameters that are non-influential; (ii) search a small fraction (about 100 points) of the parameter search space with billions to trillions of points and improve the quality of segmentation results (Dice and Jaccard metrics) by as much as 1.42× compared to the results from the default parameters; (iii) attain good scalability on a high performance cluster with several effective optimizations. Conclusions: Our work demonstrates the feasibility of performing sensitivity analyses, parameter studies and auto-tuning with large datasets. The proposed framework can enable the quantification of error estimations and output variations in image segmentation pipelines. Availability and Implementation: Source code: https://github.com/SBU-BMI/region-templates/. Contact: teodoro@unb.br Supplementary information: Supplementary data are available at Bioinformatics online. PMID:28062445

Algorithm sensitivity analysis and parameter tuning for tissue image segmentation pipelines.

PubMed

Teodoro, George; Kurç, Tahsin M; Taveira, Luís F R; Melo, Alba C M A; Gao, Yi; Kong, Jun; Saltz, Joel H

2017-04-01

Sensitivity analysis and parameter tuning are important processes in large-scale image analysis. They are very costly because the image analysis workflows are required to be executed several times to systematically correlate output variations with parameter changes or to tune parameters. An integrated solution with minimum user interaction that uses effective methodologies and high performance computing is required to scale these studies to large imaging datasets and expensive analysis workflows. The experiments with two segmentation workflows show that the proposed approach can (i) quickly identify and prune parameters that are non-influential; (ii) search a small fraction (about 100 points) of the parameter search space with billions to trillions of points and improve the quality of segmentation results (Dice and Jaccard metrics) by as much as 1.42× compared to the results from the default parameters; (iii) attain good scalability on a high performance cluster with several effective optimizations. Our work demonstrates the feasibility of performing sensitivity analyses, parameter studies and auto-tuning with large datasets. The proposed framework can enable the quantification of error estimations and output variations in image segmentation pipelines. Source code: https://github.com/SBU-BMI/region-templates/ . teodoro@unb.br. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Advanced medical imaging protocol workflow-a flexible electronic solution to optimize process efficiency, care quality and patient safety in the National VA Enterprise.

PubMed

Medverd, Jonathan R; Cross, Nathan M; Font, Frank; Casertano, Andrew

2013-08-01

Radiologists routinely make decisions with only limited information when assigning protocol instructions for the performance of advanced medical imaging examinations. Opportunity exists to simultaneously improve the safety, quality and efficiency of this workflow through the application of an electronic solution leveraging health system resources to provide concise, tailored information and decision support in real-time. Such a system has been developed using an open source, open standards design for use within the Veterans Health Administration. The Radiology Protocol Tool Recorder (RAPTOR) project identified key process attributes as well as inherent weaknesses of paper processes and electronic emulators of paper processes to guide the development of its optimized electronic solution. The design provides a kernel that can be expanded to create an integrated radiology environment. RAPTOR has implications relevant to the greater health care community, and serves as a case model for modernization of legacy government health information systems.

Grid-based platform for training in Earth Observation

NASA Astrophysics Data System (ADS)

Petcu, Dana; Zaharie, Daniela; Panica, Silviu; Frincu, Marc; Neagul, Marian; Gorgan, Dorian; Stefanut, Teodor

2010-05-01

GiSHEO platform [1] providing on-demand services for training and high education in Earth Observation is developed, in the frame of an ESA funded project through its PECS programme, to respond to the needs of powerful education resources in remote sensing field. It intends to be a Grid-based platform of which potential for experimentation and extensibility are the key benefits compared with a desktop software solution. Near-real time applications requiring simultaneous multiple short-time-response data-intensive tasks, as in the case of a short time training event, are the ones that are proved to be ideal for this platform. The platform is based on Globus Toolkit 4 facilities for security and process management, and on the clusters of four academic institutions involved in the project. The authorization uses a VOMS service. The main public services are the followings: the EO processing services (represented through special WSRF-type services); the workflow service exposing a particular workflow engine; the data indexing and discovery service for accessing the data management mechanisms; the processing services, a collection allowing easy access to the processing platform. The WSRF-type services for basic satellite image processing are reusing free image processing tools, OpenCV and GDAL. New algorithms and workflows were develop to tackle with challenging problems like detecting the underground remains of old fortifications, walls or houses. More details can be found in [2]. Composed services can be specified through workflows and are easy to be deployed. The workflow engine, OSyRIS (Orchestration System using a Rule based Inference Solution), is based on DROOLS, and a new rule-based workflow language, SILK (SImple Language for worKflow), has been built. Workflow creation in SILK can be done with or without a visual designing tools. The basics of SILK are the tasks and relations (rules) between them. It is similar with the SCUFL language, but not relying on XML in order to allow the introduction of more workflow specific issues. Moreover, an event-condition-action (ECA) approach allows a greater flexibility when expressing data and task dependencies, as well as the creation of adaptive workflows which can react to changes in the configuration of the Grid or in the workflow itself. Changes inside the grid are handled by creating specific rules which allow resource selection based on various task scheduling criteria. Modifications of the workflow are usually accomplished either by inserting or retracting at runtime rules belonging to it or by modifying the executor of the task in case a better one is found. The former implies changes in its structure while the latter does not necessarily mean changes of the resource but more precisely changes of the algorithm used for solving the task. More details can be found in [3]. Another important platform component is the data indexing and storage service, GDIS, providing features for data storage, indexing data using a specialized RDBMS, finding data by various conditions, querying external services and keeping track of temporary data generated by other components. The data storage component part of GDIS is responsible for storing the data by using available storage backends such as local disk file systems (ext3), local cluster storage (GFS) or distributed file systems (HDFS). A front-end GridFTP service is capable of interacting with the storage domains on behalf of the clients and in a uniform way and also enforces the security restrictions provided by other specialized services and related with data access. The data indexing is performed by PostGIS. An advanced and flexible interface for searching the project's geographical repository is built around a custom query language (LLQL - Lisp Like Query Language) designed to provide fine grained access to the data in the repository and to query external services (e.g. for exploiting the connection with GENESI-DR catalog). More details can be found in [4]. The Workload Management System (WMS) provides two types of resource managers. The first one will be based on Condor HTC and use Condor as a job manager for task dispatching and working nodes (for development purposes) while the second one will use GT4 GRAM (for production purposes). The WMS main component, the Grid Task Dispatcher (GTD), is responsible for the interaction with other internal services as the composition engine in order to facilitate access to the processing platform. Its main responsibilities are to receive tasks from the workflow engine or directly from user interface, to use a task description language (the ClassAd meta language in case of Condor HTC) for job units, to submit and check the status of jobs inside the workload management system and to retrieve job logs for debugging purposes. More details can be found in [4]. A particular component of the platform is eGLE, the eLearning environment. It provides the functionalities necessary to create the visual appearance of the lessons through the usage of visual containers like tools, patterns and templates. The teacher uses the platform for testing the already created lessons, as well as for developing new lesson resources, such as new images and workflows describing graph-based processing. The students execute the lessons or describe and experiment with new workflows or different data. The eGLE database includes several workflow-based lesson descriptions, teaching materials and lesson resources, selected satellite and spatial data. More details can be found in [5]. A first training event of using the platform was organized in September 2009 during 11th SYNASC symposium (links to the demos, testing interface, and exercises are available on project site [1]). The eGLE component was presented at 4th GPC conference in May 2009. Moreover, the functionality of the platform will be presented as demo in April 2010 at 5th EGEE User forum. References: [1] GiSHEO consortium, Project site, http://gisheo.info.uvt.ro [2] D. Petcu, D. Zaharie, M. Neagul, S. Panica, M. Frincu, D. Gorgan, T. Stefanut, V. Bacu, Remote Sensed Image Processing on Grids for Training in Earth Observation. In Image Processing, V. Kordic (ed.), In-Tech, January 2010. [3] M. Neagul, S. Panica, D. Petcu, D. Zaharie, D. Gorgan, Web and Grid Services for Training in Earth Observation, IDAACS 2009, IEEE Computer Press, 241-246 [4] M. Frincu, S. Panica, M. Neagul, D. Petcu, Gisheo: On Demand Grid Service Based Platform for EO Data Processing. HiperGrid 2009, Politehnica Press, 415-422. [5] D. Gorgan, T. Stefanut, V. Bacu, Grid Based Training Environment for Earth Observation, GPC 2009, LNCS 5529, 98-109

MO-B-BRC-00: Prostate HDR Treatment Planning - Considering Different Imaging Modalities

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

2016-06-15

Brachytherapy has proven to be an effective treatment option for prostate cancer. Initially, prostate brachytherapy was delivered through permanently implanted low dose rate (LDR) radioactive sources; however, high dose rate (HDR) temporary brachytherapy for prostate cancer is gaining popularity. Needle insertion during prostate brachytherapy is most commonly performed under ultrasound (U/S) guidance; however, treatment planning may be performed utilizing several imaging modalities either in an intra- or post-operative setting. During intra-operative prostate HDR, the needles are imaged during implantation, and planning may be performed in real time. At present, the most common imaging modality utilized for intra-operative prostate HDR ismore » U/S. Alternatively, in the post-operative setting, following needle implantation, patients may be simulated with computed tomography (CT) or magnetic resonance imaging (MRI). Each imaging modality and workflow provides its share of benefits and limitations. Prostate HDR has been adopted in a number of cancer centers across the nation. In this educational session, we will explore the role of U/S, CT, and MRI in HDR prostate brachytherapy. Example workflows and operational details will be shared, and we will discuss how to establish a prostate HDR program in a clinical setting. Learning Objectives: Review prostate HDR techniques based on the imaging modality Discuss the challenges and pitfalls introduced by the three imagebased options for prostate HDR brachytherapy Review the QA process and learn about the development of clinical workflows for these imaging options at different institutions.« less

Targeting safety improvements through identification of incident origination and detection in a near-miss incident learning system.

PubMed

Novak, Avrey; Nyflot, Matthew J; Ermoian, Ralph P; Jordan, Loucille E; Sponseller, Patricia A; Kane, Gabrielle M; Ford, Eric C; Zeng, Jing

2016-05-01

Radiation treatment planning involves a complex workflow that has multiple potential points of vulnerability. This study utilizes an incident reporting system to identify the origination and detection points of near-miss errors, in order to guide their departmental safety improvement efforts. Previous studies have examined where errors arise, but not where they are detected or applied a near-miss risk index (NMRI) to gauge severity. From 3/2012 to 3/2014, 1897 incidents were analyzed from a departmental incident learning system. All incidents were prospectively reviewed weekly by a multidisciplinary team and assigned a NMRI score ranging from 0 to 4 reflecting potential harm to the patient (no potential harm to potential critical harm). Incidents were classified by point of incident origination and detection based on a 103-step workflow. The individual steps were divided among nine broad workflow categories (patient assessment, imaging for radiation therapy (RT) planning, treatment planning, pretreatment plan review, treatment delivery, on-treatment quality management, post-treatment completion, equipment/software quality management, and other). The average NMRI scores of incidents originating or detected within each broad workflow area were calculated. Additionally, out of 103 individual process steps, 35 were classified as safety barriers, the process steps whose primary function is to catch errors. The safety barriers which most frequently detected incidents were identified and analyzed. Finally, the distance between event origination and detection was explored by grouping events by the number of broad workflow area events passed through before detection, and average NMRI scores were compared. Near-miss incidents most commonly originated within treatment planning (33%). However, the incidents with the highest average NMRI scores originated during imaging for RT planning (NMRI = 2.0, average NMRI of all events = 1.5), specifically during the documentation of patient positioning and localization of the patient. Incidents were most frequently detected during treatment delivery (30%), and incidents identified at this point also had higher severity scores than other workflow areas (NMRI = 1.6). Incidents identified during on-treatment quality management were also more severe (NMRI = 1.7), and the specific process steps of reviewing portal and CBCT images tended to catch highest-severity incidents. On average, safety barriers caught 46% of all incidents, most frequently at physics chart review, therapist's chart check, and the review of portal images; however, most of the incidents that pass through a particular safety barrier are not designed to be capable of being captured at that barrier. Incident learning systems can be used to assess the most common points of error origination and detection in radiation oncology. This can help tailor safety improvement efforts and target the highest impact portions of the workflow. The most severe near-miss events tend to originate during simulation, with the most severe near-miss events detected at the time of patient treatment. Safety barriers can be improved to allow earlier detection of near-miss events.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Novak, Avrey; Nyflot, Matthew J.; Ermoian, Ralph P.

Purpose: Radiation treatment planning involves a complex workflow that has multiple potential points of vulnerability. This study utilizes an incident reporting system to identify the origination and detection points of near-miss errors, in order to guide their departmental safety improvement efforts. Previous studies have examined where errors arise, but not where they are detected or applied a near-miss risk index (NMRI) to gauge severity. Methods: From 3/2012 to 3/2014, 1897 incidents were analyzed from a departmental incident learning system. All incidents were prospectively reviewed weekly by a multidisciplinary team and assigned a NMRI score ranging from 0 to 4 reflectingmore » potential harm to the patient (no potential harm to potential critical harm). Incidents were classified by point of incident origination and detection based on a 103-step workflow. The individual steps were divided among nine broad workflow categories (patient assessment, imaging for radiation therapy (RT) planning, treatment planning, pretreatment plan review, treatment delivery, on-treatment quality management, post-treatment completion, equipment/software quality management, and other). The average NMRI scores of incidents originating or detected within each broad workflow area were calculated. Additionally, out of 103 individual process steps, 35 were classified as safety barriers, the process steps whose primary function is to catch errors. The safety barriers which most frequently detected incidents were identified and analyzed. Finally, the distance between event origination and detection was explored by grouping events by the number of broad workflow area events passed through before detection, and average NMRI scores were compared. Results: Near-miss incidents most commonly originated within treatment planning (33%). However, the incidents with the highest average NMRI scores originated during imaging for RT planning (NMRI = 2.0, average NMRI of all events = 1.5), specifically during the documentation of patient positioning and localization of the patient. Incidents were most frequently detected during treatment delivery (30%), and incidents identified at this point also had higher severity scores than other workflow areas (NMRI = 1.6). Incidents identified during on-treatment quality management were also more severe (NMRI = 1.7), and the specific process steps of reviewing portal and CBCT images tended to catch highest-severity incidents. On average, safety barriers caught 46% of all incidents, most frequently at physics chart review, therapist’s chart check, and the review of portal images; however, most of the incidents that pass through a particular safety barrier are not designed to be capable of being captured at that barrier. Conclusions: Incident learning systems can be used to assess the most common points of error origination and detection in radiation oncology. This can help tailor safety improvement efforts and target the highest impact portions of the workflow. The most severe near-miss events tend to originate during simulation, with the most severe near-miss events detected at the time of patient treatment. Safety barriers can be improved to allow earlier detection of near-miss events.« less

OIPAV: an integrated software system for ophthalmic image processing, analysis and visualization

NASA Astrophysics Data System (ADS)

Zhang, Lichun; Xiang, Dehui; Jin, Chao; Shi, Fei; Yu, Kai; Chen, Xinjian

2018-03-01

OIPAV (Ophthalmic Images Processing, Analysis and Visualization) is a cross-platform software which is specially oriented to ophthalmic images. It provides a wide range of functionalities including data I/O, image processing, interaction, ophthalmic diseases detection, data analysis and visualization to help researchers and clinicians deal with various ophthalmic images such as optical coherence tomography (OCT) images and color photo of fundus, etc. It enables users to easily access to different ophthalmic image data manufactured from different imaging devices, facilitate workflows of processing ophthalmic images and improve quantitative evaluations. In this paper, we will present the system design and functional modules of the platform and demonstrate various applications. With a satisfying function scalability and expandability, we believe that the software can be widely applied in ophthalmology field.

PACS-Based Computer-Aided Detection and Diagnosis

NASA Astrophysics Data System (ADS)

Huang, H. K. (Bernie); Liu, Brent J.; Le, Anh HongTu; Documet, Jorge

The ultimate goal of Picture Archiving and Communication System (PACS)-based Computer-Aided Detection and Diagnosis (CAD) is to integrate CAD results into daily clinical practice so that it becomes a second reader to aid the radiologist's diagnosis. Integration of CAD and Hospital Information System (HIS), Radiology Information System (RIS) or PACS requires certain basic ingredients from Health Level 7 (HL7) standard for textual data, Digital Imaging and Communications in Medicine (DICOM) standard for images, and Integrating the Healthcare Enterprise (IHE) workflow profiles in order to comply with the Health Insurance Portability and Accountability Act (HIPAA) requirements to be a healthcare information system. Among the DICOM standards and IHE workflow profiles, DICOM Structured Reporting (DICOM-SR); and IHE Key Image Note (KIN), Simple Image and Numeric Report (SINR) and Post-processing Work Flow (PWF) are utilized in CAD-HIS/RIS/PACS integration. These topics with examples are presented in this chapter.

Anti-nuclear antibody screening using HEp-2 cells.

PubMed

Buchner, Carol; Bryant, Cassandra; Eslami, Anna; Lakos, Gabriella

2014-06-23

The American College of Rheumatology position statement on ANA testing stipulates the use of IIF as the gold standard method for ANA screening(1). Although IIF is an excellent screening test in expert hands, the technical difficulties of processing and reading IIF slides--such as the labor intensive slide processing, manual reading, the need for experienced, trained technologists and the use of dark room--make the IIF method difficult to fit in the workflow of modern, automated laboratories. The first and crucial step towards high quality ANA screening is careful slide processing. This procedure is labor intensive, and requires full understanding of the process, as well as attention to details and experience. Slide reading is performed by fluorescent microscopy in dark rooms, and is done by trained technologists who are familiar with the various patterns, in the context of cell cycle and the morphology of interphase and dividing cells. Provided that IIF is the first line screening tool for SARD, understanding the steps to correctly perform this technique is critical. Recently, digital imaging systems have been developed for the automated reading of IIF slides. These systems, such as the NOVA View Automated Fluorescent Microscope, are designed to streamline the routine IIF workflow. NOVA View acquires and stores high resolution digital images of the wells, thereby separating image acquisition from interpretation; images are viewed an interpreted on high resolution computer monitors. It stores images for future reference and supports the operator's interpretation by providing fluorescent light intensity data on the images. It also preliminarily categorizes results as positive or negative, and provides pattern recognition for positive samples. In summary, it eliminates the need for darkroom, and automates and streamlines the IIF reading/interpretation workflow. Most importantly, it increases consistency between readers and readings. Moreover, with the use of barcoded slides, transcription errors are eliminated by providing sample traceability and positive patient identification. This results in increased patient data integrity and safety. The overall goal of this video is to demonstrate the IIF procedure, including slide processing, identification of common IIF patterns, and the introduction of new advancements to simplify and harmonize this technique.

Radiology Workflow Dynamics: How Workflow Patterns Impact Radiologist Perceptions of Workplace Satisfaction.

PubMed

Lee, Matthew H; Schemmel, Andrew J; Pooler, B Dustin; Hanley, Taylor; Kennedy, Tabassum; Field, Aaron; Wiegmann, Douglas; Yu, John-Paul J

2017-04-01

The study aimed to assess perceptions of reading room workflow and the impact separating image-interpretive and nonimage-interpretive task workflows can have on radiologist perceptions of workplace disruptions, workload, and overall satisfaction. A 14-question survey instrument was developed to measure radiologist perceptions of workplace interruptions, satisfaction, and workload prior to and following implementation of separate image-interpretive and nonimage-interpretive reading room workflows. The results were collected over 2 weeks preceding the intervention and 2 weeks following the end of the intervention. The results were anonymized and analyzed using univariate analysis. A total of 18 people responded to the preintervention survey: 6 neuroradiology fellows and 12 attending neuroradiologists. Fifteen people who were then present for the 1-month intervention period responded to the postintervention survey. Perceptions of workplace disruptions, image interpretation, quality of trainee education, ability to perform nonimage-interpretive tasks, and quality of consultations (P < 0.0001) all improved following the intervention. Mental effort and workload also improved across all assessment domains, as did satisfaction with quality of image interpretation and consultative work. Implementation of parallel dedicated image-interpretive and nonimage-interpretive workflows may improve markers of radiologist perceptions of workplace satisfaction. Copyright © 2017 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

Multidimensional Interactive Radiology Report and Analysis: standardization of workflow and reporting for renal mass tracking and quantification

NASA Astrophysics Data System (ADS)

Hwang, Darryl H.; Ma, Kevin; Yepes, Fernando; Nadamuni, Mridula; Nayyar, Megha; Liu, Brent; Duddalwar, Vinay; Lepore, Natasha

2015-12-01

A conventional radiology report primarily consists of a large amount of unstructured text, and lacks clear, concise, consistent and content-rich information. Hence, an area of unmet clinical need consists of developing better ways to communicate radiology findings and information specific to each patient. Here, we design a new workflow and reporting system that combines and integrates advances in engineering technology with those from the medical sciences, the Multidimensional Interactive Radiology Report and Analysis (MIRRA). Until recently, clinical standards have primarily relied on 2D images for the purpose of measurement, but with the advent of 3D processing, many of the manually measured metrics can be automated, leading to better reproducibility and less subjective measurement placement. Hence, we make use this newly available 3D processing in our workflow. Our pipeline is used here to standardize the labeling, tracking, and quantifying of metrics for renal masses.

STAR Data Reconstruction at NERSC/Cori, an adaptable Docker container approach for HPC

NASA Astrophysics Data System (ADS)

Mustafa, Mustafa; Balewski, Jan; Lauret, Jérôme; Porter, Jefferson; Canon, Shane; Gerhardt, Lisa; Hajdu, Levente; Lukascsyk, Mark

2017-10-01

As HPC facilities grow their resources, adaptation of classic HEP/NP workflows becomes a need. Linux containers may very well offer a way to lower the bar to exploiting such resources and at the time, help collaboration to reach vast elastic resources on such facilities and address their massive current and future data processing challenges. In this proceeding, we showcase STAR data reconstruction workflow at Cori HPC system at NERSC. STAR software is packaged in a Docker image and runs at Cori in Shifter containers. We highlight two of the typical end-to-end optimization challenges for such pipelines: 1) data transfer rate which was carried over ESnet after optimizing end points and 2) scalable deployment of conditions database in an HPC environment. Our tests demonstrate equally efficient data processing workflows on Cori/HPC, comparable to standard Linux clusters.

Big Data Challenges in Global Seismic 'Adjoint Tomography' (Invited)

NASA Astrophysics Data System (ADS)

Tromp, J.; Bozdag, E.; Krischer, L.; Lefebvre, M.; Lei, W.; Smith, J.

2013-12-01

The challenge of imaging Earth's interior on a global scale is closely linked to the challenge of handling large data sets. The related iterative workflow involves five distinct phases, namely, 1) data gathering and culling, 2) synthetic seismogram calculations, 3) pre-processing (time-series analysis and time-window selection), 4) data assimilation and adjoint calculations, 5) post-processing (pre-conditioning, regularization, model update). In order to implement this workflow on modern high-performance computing systems, a new seismic data format is being developed. The Adaptable Seismic Data Format (ASDF) is designed to replace currently used data formats with a more flexible format that allows for fast parallel I/O. The metadata is divided into abstract categories, such as "source" and "receiver", along with provenance information for complete reproducibility. The structure of ASDF is designed keeping in mind three distinct applications: earthquake seismology, seismic interferometry, and exploration seismology. Existing time-series analysis tool kits, such as SAC and ObsPy, can be easily interfaced with ASDF so that seismologists can use robust, previously developed software packages. ASDF accommodates an automated, efficient workflow for global adjoint tomography. Manually managing the large number of simulations associated with the workflow can rapidly become a burden, especially with increasing numbers of earthquakes and stations. Therefore, it is of importance to investigate the possibility of automating the entire workflow. Scientific Workflow Management Software (SWfMS) allows users to execute workflows almost routinely. SWfMS provides additional advantages. In particular, it is possible to group independent simulations in a single job to fit the available computational resources. They also give a basic level of fault resilience as the workflow can be resumed at the correct state preceding a failure. Some of the best candidates for our particular workflow are Kepler and Swift, and the latter appears to be the most serious candidate for a large-scale workflow on a single supercomputer, remaining sufficiently simple to accommodate further modifications and improvements.

Tectonic Inversion Along the Algerian and Ligurian Margins: On the Insight Provided By Latest Seismic Processing Techniques Applied to Recent and Vintage 2D Offshore Multichannel Seismic Data

NASA Astrophysics Data System (ADS)

Schenini, L.; Beslier, M. O.; Sage, F.; Badji, R.; Galibert, P. Y.; Lepretre, A.; Dessa, J. X.; Aidi, C.; Watremez, L.

2014-12-01

Recent studies on the Algerian and the North-Ligurian margins in the Western Mediterranean have evidenced inversion-related superficial structures, such as folds and asymmetric sedimentary perched basins whose geometry hints at deep compressive structures dipping towards the continent. Deep seismic imaging of these margins is difficult due to steep slope and superficial multiples, and, in the Mediterranean context, to the highly diffractive Messinian evaporitic series in the basin. During the Algerian-French SPIRAL survey (2009, R/V Atalante), 2D marine multi-channel seismic (MCS) reflection data were collected along the Algerian Margin using a 4.5 km, 360 channel digital streamer and a 3040 cu. in. air-gun array. An advanced processing workflow has been laid out using Geocluster CGG software, which includes noise attenuation, 2D SRME multiple attenuation, surface consistent deconvolution, Kirchhoff pre-stack time migration. This processing produces satisfactory seismic images of the whole sedimentary cover, and of southward dipping reflectors in the acoustic basement along the central part of the margin offshore Great Kabylia, that are interpreted as inversion-related blind thrusts as part of flat-ramp systems. We applied this successful processing workflow to old 2D marine MCS data acquired on the North-Ligurian Margin (Malis survey, 1995, R/V Le Nadir), using a 2.5 km, 96 channel streamer and a 1140 cu. in. air-gun array. Particular attention was paid to multiple attenuation in adapting our workflow. The resulting reprocessed seismic images, interpreted with a coincident velocity model obtained by wide-angle data tomography, provide (1) enhanced imaging of the sedimentary cover down to the top of the acoustic basement, including the base of the Messinian evaporites and the sub-salt Miocene series, which appear to be tectonized as far as in the mid-basin, and (2) new evidence of deep crustal structures in the margin which the initial processing had failed to reveal.

Analyzing microtomography data with Python and the scikit-image library.

PubMed

Gouillart, Emmanuelle; Nunez-Iglesias, Juan; van der Walt, Stéfan

2017-01-01

The exploration and processing of images is a vital aspect of the scientific workflows of many X-ray imaging modalities. Users require tools that combine interactivity, versatility, and performance. scikit-image is an open-source image processing toolkit for the Python language that supports a large variety of file formats and is compatible with 2D and 3D images. The toolkit exposes a simple programming interface, with thematic modules grouping functions according to their purpose, such as image restoration, segmentation, and measurements. scikit-image users benefit from a rich scientific Python ecosystem that contains many powerful libraries for tasks such as visualization or machine learning. scikit-image combines a gentle learning curve, versatile image processing capabilities, and the scalable performance required for the high-throughput analysis of X-ray imaging data.

MO-B-BRC-01: Introduction [Brachytherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prisciandaro, J.

2016-06-15

Brachytherapy has proven to be an effective treatment option for prostate cancer. Initially, prostate brachytherapy was delivered through permanently implanted low dose rate (LDR) radioactive sources; however, high dose rate (HDR) temporary brachytherapy for prostate cancer is gaining popularity. Needle insertion during prostate brachytherapy is most commonly performed under ultrasound (U/S) guidance; however, treatment planning may be performed utilizing several imaging modalities either in an intra- or post-operative setting. During intra-operative prostate HDR, the needles are imaged during implantation, and planning may be performed in real time. At present, the most common imaging modality utilized for intra-operative prostate HDR ismore » U/S. Alternatively, in the post-operative setting, following needle implantation, patients may be simulated with computed tomography (CT) or magnetic resonance imaging (MRI). Each imaging modality and workflow provides its share of benefits and limitations. Prostate HDR has been adopted in a number of cancer centers across the nation. In this educational session, we will explore the role of U/S, CT, and MRI in HDR prostate brachytherapy. Example workflows and operational details will be shared, and we will discuss how to establish a prostate HDR program in a clinical setting. Learning Objectives: Review prostate HDR techniques based on the imaging modality Discuss the challenges and pitfalls introduced by the three imagebased options for prostate HDR brachytherapy Review the QA process and learn about the development of clinical workflows for these imaging options at different institutions.« less

MO-B-BRC-04: MRI-Based Prostate HDR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mourtada, F.

2016-06-15

Brachytherapy has proven to be an effective treatment option for prostate cancer. Initially, prostate brachytherapy was delivered through permanently implanted low dose rate (LDR) radioactive sources; however, high dose rate (HDR) temporary brachytherapy for prostate cancer is gaining popularity. Needle insertion during prostate brachytherapy is most commonly performed under ultrasound (U/S) guidance; however, treatment planning may be performed utilizing several imaging modalities either in an intra- or post-operative setting. During intra-operative prostate HDR, the needles are imaged during implantation, and planning may be performed in real time. At present, the most common imaging modality utilized for intra-operative prostate HDR ismore » U/S. Alternatively, in the post-operative setting, following needle implantation, patients may be simulated with computed tomography (CT) or magnetic resonance imaging (MRI). Each imaging modality and workflow provides its share of benefits and limitations. Prostate HDR has been adopted in a number of cancer centers across the nation. In this educational session, we will explore the role of U/S, CT, and MRI in HDR prostate brachytherapy. Example workflows and operational details will be shared, and we will discuss how to establish a prostate HDR program in a clinical setting. Learning Objectives: Review prostate HDR techniques based on the imaging modality Discuss the challenges and pitfalls introduced by the three imagebased options for prostate HDR brachytherapy Review the QA process and learn about the development of clinical workflows for these imaging options at different institutions.« less

MO-B-BRC-02: Ultrasound Based Prostate HDR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Z.

2016-06-15

Brachytherapy has proven to be an effective treatment option for prostate cancer. Initially, prostate brachytherapy was delivered through permanently implanted low dose rate (LDR) radioactive sources; however, high dose rate (HDR) temporary brachytherapy for prostate cancer is gaining popularity. Needle insertion during prostate brachytherapy is most commonly performed under ultrasound (U/S) guidance; however, treatment planning may be performed utilizing several imaging modalities either in an intra- or post-operative setting. During intra-operative prostate HDR, the needles are imaged during implantation, and planning may be performed in real time. At present, the most common imaging modality utilized for intra-operative prostate HDR ismore » U/S. Alternatively, in the post-operative setting, following needle implantation, patients may be simulated with computed tomography (CT) or magnetic resonance imaging (MRI). Each imaging modality and workflow provides its share of benefits and limitations. Prostate HDR has been adopted in a number of cancer centers across the nation. In this educational session, we will explore the role of U/S, CT, and MRI in HDR prostate brachytherapy. Example workflows and operational details will be shared, and we will discuss how to establish a prostate HDR program in a clinical setting. Learning Objectives: Review prostate HDR techniques based on the imaging modality Discuss the challenges and pitfalls introduced by the three imagebased options for prostate HDR brachytherapy Review the QA process and learn about the development of clinical workflows for these imaging options at different institutions.« less

Semi-automatic object geometry estimation for image personalization

NASA Astrophysics Data System (ADS)

Ding, Hengzhou; Bala, Raja; Fan, Zhigang; Eschbach, Reiner; Bouman, Charles A.; Allebach, Jan P.

2010-01-01

Digital printing brings about a host of benefits, one of which is the ability to create short runs of variable, customized content. One form of customization that is receiving much attention lately is in photofinishing applications, whereby personalized calendars, greeting cards, and photo books are created by inserting text strings into images. It is particularly interesting to estimate the underlying geometry of the surface and incorporate the text into the image content in an intelligent and natural way. Current solutions either allow fixed text insertion schemes into preprocessed images, or provide manual text insertion tools that are time consuming and aimed only at the high-end graphic designer. It would thus be desirable to provide some level of automation in the image personalization process. We propose a semi-automatic image personalization workflow which includes two scenarios: text insertion and text replacement. In both scenarios, the underlying surfaces are assumed to be planar. A 3-D pinhole camera model is used for rendering text, whose parameters are estimated by analyzing existing structures in the image. Techniques in image processing and computer vison such as the Hough transform, the bilateral filter, and connected component analysis are combined, along with necessary user inputs. In particular, the semi-automatic workflow is implemented as an image personalization tool, which is presented in our companion paper.1 Experimental results including personalized images for both scenarios are shown, which demonstrate the effectiveness of our algorithms.

What Not To Do: Anti-patterns for Developing Scientific Workflow Software Components

NASA Astrophysics Data System (ADS)

Futrelle, J.; Maffei, A. R.; Sosik, H. M.; Gallager, S. M.; York, A.

2013-12-01

Scientific workflows promise to enable efficient scaling-up of researcher code to handle large datasets and workloads, as well as documentation of scientific processing via standardized provenance records, etc. Workflow systems and related frameworks for coordinating the execution of otherwise separate components are limited, however, in their ability to overcome software engineering design problems commonly encountered in pre-existing components, such as scripts developed externally by scientists in their laboratories. In practice, this often means that components must be rewritten or replaced in a time-consuming, expensive process. In the course of an extensive workflow development project involving large-scale oceanographic image processing, we have begun to identify and codify 'anti-patterns'--problematic design characteristics of software--that make components fit poorly into complex automated workflows. We have gone on to develop and document low-effort solutions and best practices that efficiently address the anti-patterns we have identified. The issues, solutions, and best practices can be used to evaluate and improve existing code, as well as guiding the development of new components. For example, we have identified a common anti-pattern we call 'batch-itis' in which a script fails and then cannot perform more work, even if that work is not precluded by the failure. The solution we have identified--removing unnecessary looping over independent units of work--is often easier to code than the anti-pattern, as it eliminates the need for complex control flow logic in the component. Other anti-patterns we have identified are similarly easy to identify and often easy to fix. We have drawn upon experience working with three science teams at Woods Hole Oceanographic Institution, each of which has designed novel imaging instruments and associated image analysis code. By developing use cases and prototypes within these teams, we have undertaken formal evaluations of software components developed by programmers with widely varying levels of expertise, and have been able to discover and characterize a number of anti-patterns. Our evaluation methodology and testbed have also enabled us to assess the efficacy of strategies to address these anti-patterns according to scientifically relevant metrics, such as ability of algorithms to perform faster than the rate of data acquisition and the accuracy of workflow component output relative to ground truth. The set of anti-patterns and solutions we have identified augments of the body of more well-known software engineering anti-patterns by addressing additional concerns that obtain when a software component has to function as part of a workflow assembled out of independently-developed codebases. Our experience shows that identifying and resolving these anti-patterns reduces development time and improves performance without reducing component reusability.

Bridging the provenance gap: opportunities and challenges tracking in and ex silico provenance in sUAS workflows

NASA Astrophysics Data System (ADS)

Thomer, A.

2017-12-01

Data provenance - the record of the varied processes that went into the creation of a dataset, as well as the relationships between resulting data objects - is necessary to support the reusability, reproducibility and reliability of earth science data. In sUAS-based research, capturing provenance can be particularly challenging because of the breadth and distributed nature of the many platforms used to collect, process and analyze data. In any given project, multiple drones, controllers, computers, software systems, sensors, cameras, imaging processing algorithms and data processing workflows are used over sometimes long periods of time. These platforms and processing result in dozens - if not hundreds - of data products in varying stages of readiness-for-analysis and sharing. Provenance tracking mechanisms are needed to make the relationships between these many data products explicit, and therefore more reusable and shareable. In this talk, I discuss opportunities and challenges in tracking provenance in sUAS-based research, and identify gaps in current workflow-capture technologies. I draw on prior work conducted as part of the IMLS-funded Site-Based Data Curation project in which we developed methods of documenting in and ex silico (that is, computational and non-computation) workflows, and demonstrate this approaches applicability to research with sUASes. I conclude with a discussion of ontologies and other semantic technologies that have potential application in sUAS research.

Reproducible Bioconductor workflows using browser-based interactive notebooks and containers.

PubMed

Almugbel, Reem; Hung, Ling-Hong; Hu, Jiaming; Almutairy, Abeer; Ortogero, Nicole; Tamta, Yashaswi; Yeung, Ka Yee

2018-01-01

Bioinformatics publications typically include complex software workflows that are difficult to describe in a manuscript. We describe and demonstrate the use of interactive software notebooks to document and distribute bioinformatics research. We provide a user-friendly tool, BiocImageBuilder, that allows users to easily distribute their bioinformatics protocols through interactive notebooks uploaded to either a GitHub repository or a private server. We present four different interactive Jupyter notebooks using R and Bioconductor workflows to infer differential gene expression, analyze cross-platform datasets, process RNA-seq data and KinomeScan data. These interactive notebooks are available on GitHub. The analytical results can be viewed in a browser. Most importantly, the software contents can be executed and modified. This is accomplished using Binder, which runs the notebook inside software containers, thus avoiding the need to install any software and ensuring reproducibility. All the notebooks were produced using custom files generated by BiocImageBuilder. BiocImageBuilder facilitates the publication of workflows with a point-and-click user interface. We demonstrate that interactive notebooks can be used to disseminate a wide range of bioinformatics analyses. The use of software containers to mirror the original software environment ensures reproducibility of results. Parameters and code can be dynamically modified, allowing for robust verification of published results and encouraging rapid adoption of new methods. Given the increasing complexity of bioinformatics workflows, we anticipate that these interactive software notebooks will become as necessary for documenting software methods as traditional laboratory notebooks have been for documenting bench protocols, and as ubiquitous. © The Author 2017. Published by Oxford University Press on behalf of the American Medical Informatics Association. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Enhancing and Customizing Laboratory Information Systems to Improve/Enhance Pathologist Workflow.

PubMed

Hartman, Douglas J

2015-06-01

Optimizing pathologist workflow can be difficult because it is affected by many variables. Surgical pathologists must complete many tasks that culminate in a final pathology report. Several software systems can be used to enhance/improve pathologist workflow. These include voice recognition software, pre-sign-out quality assurance, image utilization, and computerized provider order entry. Recent changes in the diagnostic coding and the more prominent role of centralized electronic health records represent potential areas for increased ways to enhance/improve the workflow for surgical pathologists. Additional unforeseen changes to the pathologist workflow may accompany the introduction of whole-slide imaging technology to the routine diagnostic work. Copyright © 2015 Elsevier Inc. All rights reserved.

Enhancing and Customizing Laboratory Information Systems to Improve/Enhance Pathologist Workflow.

PubMed

Hartman, Douglas J

2016-03-01

Optimizing pathologist workflow can be difficult because it is affected by many variables. Surgical pathologists must complete many tasks that culminate in a final pathology report. Several software systems can be used to enhance/improve pathologist workflow. These include voice recognition software, pre-sign-out quality assurance, image utilization, and computerized provider order entry. Recent changes in the diagnostic coding and the more prominent role of centralized electronic health records represent potential areas for increased ways to enhance/improve the workflow for surgical pathologists. Additional unforeseen changes to the pathologist workflow may accompany the introduction of whole-slide imaging technology to the routine diagnostic work. Copyright © 2016 Elsevier Inc. All rights reserved.

Rapid analysis and exploration of fluorescence microscopy images.

PubMed

Pavie, Benjamin; Rajaram, Satwik; Ouyang, Austin; Altschuler, Jason M; Steininger, Robert J; Wu, Lani F; Altschuler, Steven J

2014-03-19

Despite rapid advances in high-throughput microscopy, quantitative image-based assays still pose significant challenges. While a variety of specialized image analysis tools are available, most traditional image-analysis-based workflows have steep learning curves (for fine tuning of analysis parameters) and result in long turnaround times between imaging and analysis. In particular, cell segmentation, the process of identifying individual cells in an image, is a major bottleneck in this regard. Here we present an alternate, cell-segmentation-free workflow based on PhenoRipper, an open-source software platform designed for the rapid analysis and exploration of microscopy images. The pipeline presented here is optimized for immunofluorescence microscopy images of cell cultures and requires minimal user intervention. Within half an hour, PhenoRipper can analyze data from a typical 96-well experiment and generate image profiles. Users can then visually explore their data, perform quality control on their experiment, ensure response to perturbations and check reproducibility of replicates. This facilitates a rapid feedback cycle between analysis and experiment, which is crucial during assay optimization. This protocol is useful not just as a first pass analysis for quality control, but also may be used as an end-to-end solution, especially for screening. The workflow described here scales to large data sets such as those generated by high-throughput screens, and has been shown to group experimental conditions by phenotype accurately over a wide range of biological systems. The PhenoBrowser interface provides an intuitive framework to explore the phenotypic space and relate image properties to biological annotations. Taken together, the protocol described here will lower the barriers to adopting quantitative analysis of image based screens.

Impact of digital radiography on clinical workflow.

PubMed

May, G A; Deer, D D; Dackiewicz, D

2000-05-01

It is commonly accepted that digital radiography (DR) improves workflow and patient throughput compared with traditional film radiography or computed radiography (CR). DR eliminates the film development step and the time to acquire the image from a CR reader. In addition, the wide dynamic range of DR is such that the technologist can perform the quality-control (QC) step directly at the modality in a few seconds, rather than having to transport the newly acquired image to a centralized QC station for review. Furthermore, additional workflow efficiencies can be achieved with DR by employing tight radiology information system (RIS) integration. In the DR imaging environment, this provides for patient demographic information to be automatically downloaded from the RIS to populate the DR Digital Imaging and Communications in Medicine (DICOM) image header. To learn more about this workflow efficiency improvement, we performed a comparative study of workflow steps under three different conditions: traditional film/screen x-ray, DR without RIS integration (ie, manual entry of patient demographics), and DR with RIS integration. This study was performed at the Cleveland Clinic Foundation (Cleveland, OH) using a newly acquired amorphous silicon flat-panel DR system from Canon Medical Systems (Irvine, CA). Our data show that DR without RIS results in substantial workflow savings over traditional film/screen practice. There is an additional 30% reduction in total examination time using DR with RIS integration.

Workflow oriented software support for image guided radiofrequency ablation of focal liver malignancies

NASA Astrophysics Data System (ADS)

Weihusen, Andreas; Ritter, Felix; Kröger, Tim; Preusser, Tobias; Zidowitz, Stephan; Peitgen, Heinz-Otto

2007-03-01

Image guided radiofrequency (RF) ablation has taken a significant part in the clinical routine as a minimally invasive method for the treatment of focal liver malignancies. Medical imaging is used in all parts of the clinical workflow of an RF ablation, incorporating treatment planning, interventional targeting and result assessment. This paper describes a software application, which has been designed to support the RF ablation workflow under consideration of the requirements of clinical routine, such as easy user interaction and a high degree of robust and fast automatic procedures, in order to keep the physician from spending too much time at the computer. The application therefore provides a collection of specialized image processing and visualization methods for treatment planning and result assessment. The algorithms are adapted to CT as well as to MR imaging. The planning support contains semi-automatic methods for the segmentation of liver tumors and the surrounding vascular system as well as an interactive virtual positioning of RF applicators and a concluding numerical estimation of the achievable heat distribution. The assessment of the ablation result is supported by the segmentation of the coagulative necrosis and an interactive registration of pre- and post-interventional image data for the comparison of tumor and necrosis segmentation masks. An automatic quantification of surface distances is performed to verify the embedding of the tumor area into the thermal lesion area. The visualization methods support representations in the commonly used orthogonal 2D view as well as in 3D scenes.

Techniques for Interventional MRI Guidance in Closed-Bore Systems.

PubMed

Busse, Harald; Kahn, Thomas; Moche, Michael

2018-02-01

Efficient image guidance is the basis for minimally invasive interventions. In comparison with X-ray, computed tomography (CT), or ultrasound imaging, magnetic resonance imaging (MRI) provides the best soft tissue contrast without ionizing radiation and is therefore predestined for procedural control. But MRI is also characterized by spatial constraints, electromagnetic interactions, long imaging times, and resulting workflow issues. Although many technical requirements have been met over the years-most notably magnetic resonance (MR) compatibility of tools, interventional pulse sequences, and powerful processing hardware and software-there is still a large variety of stand-alone devices and systems for specific procedures only.Stereotactic guidance with the table outside the magnet is common and relies on proper registration of the guiding grids or manipulators to the MR images. Instrument tracking, often by optical sensing, can be added to provide the physicians with proper eye-hand coordination during their navigated approach. Only in very short wide-bore systems, needles can be advanced at the extended arm under near real-time imaging. In standard magnets, control and workflow may be improved by remote operation using robotic or manual driving elements.This work highlights a number of devices and techniques for different interventional settings with a focus on percutaneous, interstitial procedures in different organ regions. The goal is to identify technical and procedural elements that might be relevant for interventional guidance in a broader context, independent of the clinical application given here. Key challenges remain the seamless integration into the interventional workflow, safe clinical translation, and proper cost effectiveness.

Workflow management systems in radiology

NASA Astrophysics Data System (ADS)

Wendler, Thomas; Meetz, Kirsten; Schmidt, Joachim

1998-07-01

In a situation of shrinking health care budgets, increasing cost pressure and growing demands to increase the efficiency and the quality of medical services, health care enterprises are forced to optimize or complete re-design their processes. Although information technology is agreed to potentially contribute to cost reduction and efficiency improvement, the real success factors are the re-definition and automation of processes: Business Process Re-engineering and Workflow Management. In this paper we discuss architectures for the use of workflow management systems in radiology. We propose to move forward from information systems in radiology (RIS, PACS) to Radiology Management Systems, in which workflow functionality (process definitions and process automation) is implemented through autonomous workflow management systems (WfMS). In a workflow oriented architecture, an autonomous workflow enactment service communicates with workflow client applications via standardized interfaces. In this paper, we discuss the need for and the benefits of such an approach. The separation of workflow management system and application systems is emphasized, and the consequences that arise for the architecture of workflow oriented information systems. This includes an appropriate workflow terminology, and the definition of standard interfaces for workflow aware application systems. Workflow studies in various institutions have shown that most of the processes in radiology are well structured and suited for a workflow management approach. Numerous commercially available Workflow Management Systems (WfMS) were investigated, and some of them, which are process- oriented and application independent, appear suitable for use in radiology.

A Foundation for Enterprise Imaging: HIMSS-SIIM Collaborative White Paper.

PubMed

Roth, Christopher J; Lannum, Louis M; Persons, Kenneth R

2016-10-01

Care providers today routinely obtain valuable clinical multimedia with mobile devices, scope cameras, ultrasound, and many other modalities at the point of care. Image capture and storage workflows may be heterogeneous across an enterprise, and as a result, they often are not well incorporated in the electronic health record. Enterprise Imaging refers to a set of strategies, initiatives, and workflows implemented across a healthcare enterprise to consistently and optimally capture, index, manage, store, distribute, view, exchange, and analyze all clinical imaging and multimedia content to enhance the electronic health record. This paper is intended to introduce Enterprise Imaging as an important initiative to clinical and informatics leadership, and outline its key elements of governance, strategy, infrastructure, common multimedia content, acquisition workflows, enterprise image viewers, and image exchange services.

Building asynchronous geospatial processing workflows with web services

NASA Astrophysics Data System (ADS)

Zhao, Peisheng; Di, Liping; Yu, Genong

2012-02-01

Geoscience research and applications often involve a geospatial processing workflow. This workflow includes a sequence of operations that use a variety of tools to collect, translate, and analyze distributed heterogeneous geospatial data. Asynchronous mechanisms, by which clients initiate a request and then resume their processing without waiting for a response, are very useful for complicated workflows that take a long time to run. Geospatial contents and capabilities are increasingly becoming available online as interoperable Web services. This online availability significantly enhances the ability to use Web service chains to build distributed geospatial processing workflows. This paper focuses on how to orchestrate Web services for implementing asynchronous geospatial processing workflows. The theoretical bases for asynchronous Web services and workflows, including asynchrony patterns and message transmission, are examined to explore different asynchronous approaches to and architecture of workflow code for the support of asynchronous behavior. A sample geospatial processing workflow, issued by the Open Geospatial Consortium (OGC) Web Service, Phase 6 (OWS-6), is provided to illustrate the implementation of asynchronous geospatial processing workflows and the challenges in using Web Services Business Process Execution Language (WS-BPEL) to develop them.

Large field of view quantitative phase imaging of induced pluripotent stem cells and optical pathlength reference materials

NASA Astrophysics Data System (ADS)

Kwee, Edward; Peterson, Alexander; Stinson, Jeffrey; Halter, Michael; Yu, Liya; Majurski, Michael; Chalfoun, Joe; Bajcsy, Peter; Elliott, John

2018-02-01

Induced pluripotent stem cells (iPSCs) are reprogrammed cells that can have heterogeneous biological potential. Quality assurance metrics of reprogrammed iPSCs will be critical to ensure reliable use in cell therapies and personalized diagnostic tests. We present a quantitative phase imaging (QPI) workflow which includes acquisition, processing, and stitching multiple adjacent image tiles across a large field of view (LFOV) of a culture vessel. Low magnification image tiles (10x) were acquired with a Phasics SID4BIO camera on a Zeiss microscope. iPSC cultures were maintained using a custom stage incubator on an automated stage. We implement an image acquisition strategy that compensates for non-flat illumination wavefronts to enable imaging of an entire well plate, including the meniscus region normally obscured in Zernike phase contrast imaging. Polynomial fitting and background mode correction was implemented to enable comparability and stitching between multiple tiles. LFOV imaging of reference materials indicated that image acquisition and processing strategies did not affect quantitative phase measurements across the LFOV. Analysis of iPSC colony images demonstrated mass doubling time was significantly different than area doubling time. These measurements were benchmarked with prototype microsphere beads and etched-glass gratings with specified spatial dimensions designed to be QPI reference materials with optical pathlength shifts suitable for cell microscopy. This QPI workflow and the use of reference materials can provide non-destructive traceable imaging method for novel iPSC heterogeneity characterization.

Parallel and Efficient Sensitivity Analysis of Microscopy Image Segmentation Workflows in Hybrid Systems

PubMed Central

Barreiros, Willian; Teodoro, George; Kurc, Tahsin; Kong, Jun; Melo, Alba C. M. A.; Saltz, Joel

2017-01-01

We investigate efficient sensitivity analysis (SA) of algorithms that segment and classify image features in a large dataset of high-resolution images. Algorithm SA is the process of evaluating variations of methods and parameter values to quantify differences in the output. A SA can be very compute demanding because it requires re-processing the input dataset several times with different parameters to assess variations in output. In this work, we introduce strategies to efficiently speed up SA via runtime optimizations targeting distributed hybrid systems and reuse of computations from runs with different parameters. We evaluate our approach using a cancer image analysis workflow on a hybrid cluster with 256 nodes, each with an Intel Phi and a dual socket CPU. The SA attained a parallel efficiency of over 90% on 256 nodes. The cooperative execution using the CPUs and the Phi available in each node with smart task assignment strategies resulted in an additional speedup of about 2×. Finally, multi-level computation reuse lead to an additional speedup of up to 2.46× on the parallel version. The level of performance attained with the proposed optimizations will allow the use of SA in large-scale studies. PMID:29081725

Seamless online science workflow development and collaboration using IDL and the ENVI Services Engine

NASA Astrophysics Data System (ADS)

Harris, A. T.; Ramachandran, R.; Maskey, M.

2013-12-01

The Exelis-developed IDL and ENVI software are ubiquitous tools in Earth science research environments. The IDL Workbench is used by the Earth science community for programming custom data analysis and visualization modules. ENVI is a software solution for processing and analyzing geospatial imagery that combines support for multiple Earth observation scientific data types (optical, thermal, multi-spectral, hyperspectral, SAR, LiDAR) with advanced image processing and analysis algorithms. The ENVI & IDL Services Engine (ESE) is an Earth science data processing engine that allows researchers to use open standards to rapidly create, publish and deploy advanced Earth science data analytics within any existing enterprise infrastructure. Although powerful in many ways, the tools lack collaborative features out-of-box. Thus, as part of the NASA funded project, Collaborative Workbench to Accelerate Science Algorithm Development, researchers at the University of Alabama in Huntsville and Exelis have developed plugins that allow seamless research collaboration from within IDL workbench. Such additional features within IDL workbench are possible because IDL workbench is built using the Eclipse Rich Client Platform (RCP). RCP applications allow custom plugins to be dropped in for extended functionalities. Specific functionalities of the plugins include creating complex workflows based on IDL application source code, submitting workflows to be executed by ESE in the cloud, and sharing and cloning of workflows among collaborators. All these functionalities are available to scientists without leaving their IDL workbench. Because ESE can interoperate with any middleware, scientific programmers can readily string together IDL processing tasks (or tasks written in other languages like C++, Java or Python) to create complex workflows for deployment within their current enterprise architecture (e.g. ArcGIS Server, GeoServer, Apache ODE or SciFlo from JPL). Using the collaborative IDL Workbench, coupled with ESE for execution in the cloud, asynchronous workflows could be executed in batch mode on large data in the cloud. We envision that a scientist will initially develop a scientific workflow locally on a small set of data. Once tested, the scientist will deploy the workflow to the cloud for execution. Depending on the results, the scientist may share the workflow and results, allowing them to be stored in a community catalog and instantly loaded into the IDL Workbench of other scientists. Thereupon, scientists can clone and modify or execute the workflow with different input parameters. The Collaborative Workbench will provide a platform for collaboration in the cloud, helping Earth scientists solve big-data problems in the Earth and planetary sciences.

SU-E-J-15: Automatically Detect Patient Treatment Position and Orientation in KV Portal Images

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qiu, J; Yang, D

2015-06-15

Purpose: In the course of radiation therapy, the complex information processing workflow will Result in potential errors, such as incorrect or inaccurate patient setups. With automatic image check and patient identification, such errors could be effectively reduced. For this purpose, we developed a simple and rapid image processing method, to automatically detect the patient position and orientation in 2D portal images, so to allow automatic check of positions and orientations for patient daily RT treatments. Methods: Based on the principle of portal image formation, a set of whole body DRR images were reconstructed from multiple whole body CT volume datasets,more » and fused together to be used as the matching template. To identify the patient setup position and orientation shown in a 2D portal image, the 2D portal image was preprocessed (contrast enhancement, down-sampling and couch table detection), then matched to the template image so to identify the laterality (left or right), position, orientation and treatment site. Results: Five day’s clinical qualified portal images were gathered randomly, then were processed by the automatic detection and matching method without any additional information. The detection results were visually checked by physicists. 182 images were correct detection in a total of 200kV portal images. The correct rate was 91%. Conclusion: The proposed method can detect patient setup and orientation quickly and automatically. It only requires the image intensity information in KV portal images. This method can be useful in the framework of Electronic Chart Check (ECCK) to reduce the potential errors in workflow of radiation therapy and so to improve patient safety. In addition, the auto-detection results, as the patient treatment site position and patient orientation, could be useful to guide the sequential image processing procedures, e.g. verification of patient daily setup accuracy. This work was partially supported by research grant from Varian Medical System.« less

Combining transrectal ultrasound and CT for image-guided adaptive brachytherapy of cervical cancer: Proof of concept.

PubMed

Nesvacil, Nicole; Schmid, Maximilian P; Pötter, Richard; Kronreif, Gernot; Kirisits, Christian

To investigate the feasibility of a treatment planning workflow for three-dimensional image-guided cervix cancer brachytherapy, combining volumetric transrectal ultrasound (TRUS) for target definition with CT for dose optimization to organs at risk (OARs), for settings with no access to MRI. A workflow for TRUS/CT-based volumetric treatment planning was developed, based on a customized system including ultrasound probe, stepper unit, and software for image volume acquisition. A full TRUS/CT-based workflow was simulated in a clinical case and compared with MR- or CT-only delineation. High-risk clinical target volume was delineated on TRUS, and OARs were delineated on CT. Manually defined tandem/ring applicator positions on TRUS and CT were used as a reference for rigid registration of the image volumes. Treatment plan optimization for TRUS target and CT organ volumes was performed and compared to MRI and CT target contours. TRUS/CT-based contouring, applicator reconstruction, image fusion, and treatment planning were feasible, and the full workflow could be successfully demonstrated. The TRUS/CT plan fulfilled all clinical planning aims. Dose-volume histogram evaluation of the TRUS/CT-optimized plan (high-risk clinical target volume D 90 , OARs D 2cm³ for) on different image modalities showed good agreement between dose values reported for TRUS/CT and MRI-only reference contours and large deviations for CT-only target parameters. A TRUS/CT-based workflow for full three-dimensional image-guided cervix brachytherapy treatment planning seems feasible and may be clinically comparable to MRI-based treatment planning. Further development to solve challenges with applicator definition in the TRUS volume is required before systematic applicability of this workflow. Copyright © 2016 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

Wireless remote control clinical image workflow: utilizing a PDA for offsite distribution

NASA Astrophysics Data System (ADS)

Liu, Brent J.; Documet, Luis; Documet, Jorge; Huang, H. K.; Muldoon, Jean

2004-04-01

Last year we presented in RSNA an application to perform wireless remote control of PACS image distribution utilizing a handheld device such as a Personal Digital Assistant (PDA). This paper describes the clinical experiences including workflow scenarios of implementing the PDA application to route exams from the clinical PACS archive server to various locations for offsite distribution of clinical PACS exams. By utilizing this remote control application, radiologists can manage image workflow distribution with a single wireless handheld device without impacting their clinical workflow on diagnostic PACS workstations. A PDA application was designed and developed to perform DICOM Query and C-Move requests by a physician from a clinical PACS Archive to a CD-burning device for automatic burning of PACS data for the distribution to offsite. In addition, it was also used for convenient routing of historical PACS exams to the local web server, local workstations, and teleradiology systems. The application was evaluated by radiologists as well as other clinical staff who need to distribute PACS exams to offsite referring physician"s offices and offsite radiologists. An application for image workflow management utilizing wireless technology was implemented in a clinical environment and evaluated. A PDA application was successfully utilized to perform DICOM Query and C-Move requests from the clinical PACS archive to various offsite exam distribution devices. Clinical staff can utilize the PDA to manage image workflow and PACS exam distribution conveniently for offsite consultations by referring physicians and radiologists. This solution allows the radiologist to expand their effectiveness in health care delivery both within the radiology department as well as offisite by improving their clinical workflow.

An optimized workflow for the integration of biological information into radiotherapy planning: experiences with T1w DCE-MRI

NASA Astrophysics Data System (ADS)

Neff, T.; Kiessling, F.; Brix, G.; Baudendistel, K.; Zechmann, C.; Giesel, F. L.; Bendl, R.

2005-09-01

Planning of radiotherapy is often difficult due to restrictions on morphological images. New imaging techniques enable the integration of biological information into treatment planning and help to improve the detection of vital and aggressive tumour areas. This might improve clinical outcome. However, nowadays morphological data sets are still the gold standard in the planning of radiotherapy. In this paper, we introduce an in-house software platform enabling us to combine images from different imaging modalities yielding biological and morphological information in a workflow driven approach. This is demonstrated for the combination of morphological CT, MRI, functional DCE-MRI and PET data. Data of patients with a tumour of the prostate and with a meningioma were examined with DCE-MRI by applying pharmacokinetic two-compartment models for post-processing. The results were compared with the clinical plans for radiation therapy. Generated parameter maps give additional information about tumour spread, which can be incorporated in the definition of safety margins.

Deep Sky Imaging: Workflow 2

NASA Astrophysics Data System (ADS)

Schedler, Johannes

As astrophotographers we are living in a golden age. In recent years CCD technology and the quality of amateur telescopes have reached a level of perfection, giving amateurs the chance to produce images rivaling those taken from mountaintops by large professional systems as recently as two decades ago. However hardware and good imaging location is only a part of the game. A high level of skill with image processing can offer amateurs an edge and provide a chance to compensate for the limited aperture of our telescopes.

Workflow continuity--moving beyond business continuity in a multisite 24-7 healthcare organization.

PubMed

Kolowitz, Brian J; Lauro, Gonzalo Romero; Barkey, Charles; Black, Harry; Light, Karen; Deible, Christopher

2012-12-01

As hospitals move towards providing in-house 24 × 7 services, there is an increasing need for information systems to be available around the clock. This study investigates one organization's need for a workflow continuity solution that provides around the clock availability for information systems that do not provide highly available services. The organization investigated is a large multifacility healthcare organization that consists of 20 hospitals and more than 30 imaging centers. A case analysis approach was used to investigate the organization's efforts. The results show an overall reduction in downtimes where radiologists could not continue their normal workflow on the integrated Picture Archiving and Communications System (PACS) solution by 94 % from 2008 to 2011. The impact of unplanned downtimes was reduced by 72 % while the impact of planned downtimes was reduced by 99.66 % over the same period. Additionally more than 98 h of radiologist impact due to a PACS upgrade in 2008 was entirely eliminated in 2011 utilizing the system created by the workflow continuity approach. Workflow continuity differs from high availability and business continuity in its design process and available services. Workflow continuity only ensures that critical workflows are available when the production system is unavailable due to scheduled or unscheduled downtimes. Workflow continuity works in conjunction with business continuity and highly available system designs. The results of this investigation revealed that this approach can add significant value to organizations because impact on users is minimized if not eliminated entirely.

Spatial Data Exploring by Satellite Image Distributed Processing

NASA Astrophysics Data System (ADS)

Mihon, V. D.; Colceriu, V.; Bektas, F.; Allenbach, K.; Gvilava, M.; Gorgan, D.

2012-04-01

Our society needs and environmental predictions encourage the applications development, oriented on supervising and analyzing different Earth Science related phenomena. Satellite images could be explored for discovering information concerning land cover, hydrology, air quality, and water and soil pollution. Spatial and environment related data could be acquired by imagery classification consisting of data mining throughout the multispectral bands. The process takes in account a large set of variables such as satellite image types (e.g. MODIS, Landsat), particular geographic area, soil composition, vegetation cover, and generally the context (e.g. clouds, snow, and season). All these specific and variable conditions require flexible tools and applications to support an optimal search for the appropriate solutions, and high power computation resources. The research concerns with experiments on solutions of using the flexible and visual descriptions of the satellite image processing over distributed infrastructures (e.g. Grid, Cloud, and GPU clusters). This presentation highlights the Grid based implementation of the GreenLand application. The GreenLand application development is based on simple, but powerful, notions of mathematical operators and workflows that are used in distributed and parallel executions over the Grid infrastructure. Currently it is used in three major case studies concerning with Istanbul geographical area, Rioni River in Georgia, and Black Sea catchment region. The GreenLand application offers a friendly user interface for viewing and editing workflows and operators. The description involves the basic operators provided by GRASS [1] library as well as many other image related operators supported by the ESIP platform [2]. The processing workflows are represented as directed graphs giving the user a fast and easy way to describe complex parallel algorithms, without having any prior knowledge of any programming language or application commands. Also this Web application does not require any kind of install for what the house-hold user is concerned. It is a remote application which may be accessed over the Internet. Currently the GreenLand application is available through the BSC-OS Portal provided by the enviroGRIDS FP7 project [3]. This presentation aims to highlight the challenges and issues of flexible description of the Grid based processing of satellite images, interoperability with other software platforms available in the portal, as well as the particular requirements of the Black Sea related use cases.

A simple and unsupervised semi-automatic workflow to detect shallow landslides in Alpine areas based on VHR remote sensing data

NASA Astrophysics Data System (ADS)

Amato, Gabriele; Eisank, Clemens; Albrecht, Florian

2017-04-01

Landslide detection from Earth observation imagery is an important preliminary work for landslide mapping, landslide inventories and landslide hazard assessment. In this context, the object-based image analysis (OBIA) concept has been increasingly used over the last decade. Within the framework of the Land@Slide project (Earth observation based landslide mapping: from methodological developments to automated web-based information delivery) a simple, unsupervised, semi-automatic and object-based approach for the detection of shallow landslides has been developed and implemented in the InterIMAGE open-source software. The method was applied to an Alpine case study in western Austria, exploiting spectral information from pansharpened 4-bands WorldView-2 satellite imagery (0.5 m spatial resolution) in combination with digital elevation models. First, we divided the image into sub-images, i.e. tiles, and then we applied the workflow to each of them without changing the parameters. The workflow was implemented as top-down approach: at the image tile level, an over-classification of the potential landslide area was produced; the over-estimated area was re-segmented and re-classified by several processing cycles until most false positive objects have been eliminated. In every step a Baatz algorithm based segmentation generates polygons "candidates" to be landslides. At the same time, the average values of normalized difference vegetation index (NDVI) and brightness are calculated for these polygons; after that, these values are used as thresholds to perform an objects selection in order to improve the quality of the classification results. In combination, also empirically determined values of slope and roughness are used in the selection process. Results for each tile were merged to obtain the landslide map for the test area. For final validation, the landslide map was compared to a geological map and a supervised landslide classification in order to estimate its accuracy. Results for the test area showed that the proposed method is capable of accurately distinguishing landslides from roofs and trees. Implementation of the workflow into InterIMAGE was straightforward. We conclude that the method is able to extract landslides in forested areas, but that there is still room for improvements concerning the extraction in non-forested high-alpine regions.

Intuitive presentation of clinical forensic data using anonymous and person-specific 3D reference manikins.

PubMed

Urschler, Martin; Höller, Johannes; Bornik, Alexander; Paul, Tobias; Giretzlehner, Michael; Bischof, Horst; Yen, Kathrin; Scheurer, Eva

2014-08-01

The increasing use of CT/MR devices in forensic analysis motivates the need to present forensic findings from different sources in an intuitive reference visualization, with the aim of combining 3D volumetric images along with digital photographs of external findings into a 3D computer graphics model. This model allows a comprehensive presentation of forensic findings in court and enables comparative evaluation studies correlating data sources. The goal of this work was to investigate different methods to generate anonymous and patient-specific 3D models which may be used as reference visualizations. The issue of registering 3D volumetric as well as 2D photographic data to such 3D models is addressed to provide an intuitive context for injury documentation from arbitrary modalities. We present an image processing and visualization work-flow, discuss the major parts of this work-flow, compare the different investigated reference models, and show a number of cases studies that underline the suitability of the proposed work-flow for presenting forensically relevant information in 3D visualizations. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Semi-automatic mapping of fault rocks on a Digital Outcrop Model, Gole Larghe Fault Zone (Southern Alps, Italy)

NASA Astrophysics Data System (ADS)

Vho, Alice; Bistacchi, Andrea

2015-04-01

A quantitative analysis of fault-rock distribution is of paramount importance for studies of fault zone architecture, fault and earthquake mechanics, and fluid circulation along faults at depth. Here we present a semi-automatic workflow for fault-rock mapping on a Digital Outcrop Model (DOM). This workflow has been developed on a real case of study: the strike-slip Gole Larghe Fault Zone (GLFZ). It consists of a fault zone exhumed from ca. 10 km depth, hosted in granitoid rocks of Adamello batholith (Italian Southern Alps). Individual seismogenic slip surfaces generally show green cataclasites (cemented by the precipitation of epidote and K-feldspar from hydrothermal fluids) and more or less well preserved pseudotachylytes (black when well preserved, greenish to white when altered). First of all, a digital model for the outcrop is reconstructed with photogrammetric techniques, using a large number of high resolution digital photographs, processed with VisualSFM software. By using high resolution photographs the DOM can have a much higher resolution than with LIDAR surveys, up to 0.2 mm/pixel. Then, image processing is performed to map the fault-rock distribution with the ImageJ-Fiji package. Green cataclasites and epidote/K-feldspar veins can be quite easily separated from the host rock (tonalite) using spectral analysis. Particularly, band ratio and principal component analysis have been tested successfully. The mapping of black pseudotachylyte veins is more tricky because the differences between the pseudotachylyte and biotite spectral signature are not appreciable. For this reason we have tested different morphological processing tools aimed at identifying (and subtracting) the tiny biotite grains. We propose a solution based on binary images involving a combination of size and circularity thresholds. Comparing the results with manually segmented images, we noticed that major problems occur only when pseudotachylyte veins are very thin and discontinuous. After having tested and refined the image analysis processing for some typical images, we have recorded a macro with ImageJ-Fiji allowing to process all the images for a given DOM. As a result, the three different types of rocks can be semi-automatically mapped on large DOMs using a simple and efficient procedure. This allows to develop quantitative analyses of fault rock distribution and thickness, fault trace roughness/curvature and length, fault zone architecture, and alteration halos due to hydrothermal fluid-rock interaction. To improve our workflow, additional or different morphological operators could be integrated in our procedure to yield a better resolution on small and thin pseudotachylyte veins (e.g. perimeter/area ratio).

Commercial applications for optical data storage

NASA Astrophysics Data System (ADS)

Tas, Jeroen

1991-03-01

Optical data storage has spurred the market for document imaging systems. These systems are increasingly being used to electronically manage the processing, storage and retrieval of documents. Applications range from straightforward archives to sophisticated workflow management systems. The technology is developing rapidly and within a few years optical imaging facilities will be incorporated in most of the office information systems. This paper gives an overview of the status of the market, the applications and the trends of optical imaging systems.

SimITK: visual programming of the ITK image-processing library within Simulink.

PubMed

Dickinson, Andrew W L; Abolmaesumi, Purang; Gobbi, David G; Mousavi, Parvin

2014-04-01

The Insight Segmentation and Registration Toolkit (ITK) is a software library used for image analysis, visualization, and image-guided surgery applications. ITK is a collection of C++ classes that poses the challenge of a steep learning curve should the user not have appropriate C++ programming experience. To remove the programming complexities and facilitate rapid prototyping, an implementation of ITK within a higher-level visual programming environment is presented: SimITK. ITK functionalities are automatically wrapped into "blocks" within Simulink, the visual programming environment of MATLAB, where these blocks can be connected to form workflows: visual schematics that closely represent the structure of a C++ program. The heavily templated C++ nature of ITK does not facilitate direct interaction between Simulink and ITK; an intermediary is required to convert respective data types and allow intercommunication. As such, a SimITK "Virtual Block" has been developed that serves as a wrapper around an ITK class which is capable of resolving the ITK data types to native Simulink data types. Part of the challenge surrounding this implementation involves automatically capturing and storing the pertinent class information that need to be refined from an initial state prior to being reflected within the final block representation. The primary result from the SimITK wrapping procedure is multiple Simulink block libraries. From these libraries, blocks are selected and interconnected to demonstrate two examples: a 3D segmentation workflow and a 3D multimodal registration workflow. Compared to their pure-code equivalents, the workflows highlight ITK usability through an alternative visual interpretation of the code that abstracts away potentially confusing technicalities.

Five task clusters that enable efficient and effective digitization of biological collections

PubMed Central

Nelson, Gil; Paul, Deborah; Riccardi, Gregory; Mast, Austin R.

2012-01-01

Abstract This paper describes and illustrates five major clusters of related tasks (herein referred to as task clusters) that are common to efficient and effective practices in the digitization of biological specimen data and media. Examples of these clusters come from the observation of diverse digitization processes. The staff of iDigBio (The U.S. National Science Foundation’s National Resource for Advancing Digitization of Biological Collections) visited active biological and paleontological collections digitization programs for the purpose of documenting and assessing current digitization practices and tools. These observations identified five task clusters that comprise the digitization process leading up to data publication: (1) pre-digitization curation and staging, (2) specimen image capture, (3) specimen image processing, (4) electronic data capture, and (5) georeferencing locality descriptions. While not all institutions are completing each of these task clusters for each specimen, these clusters describe a composite picture of digitization of biological and paleontological specimens across the programs that were observed. We describe these clusters, three workflow patterns that dominate the implemention of these clusters, and offer a set of workflow recommendations for digitization programs. PMID:22859876

nmsBuilder: Freeware to create subject-specific musculoskeletal models for OpenSim.

PubMed

Valente, Giordano; Crimi, Gianluigi; Vanella, Nicola; Schileo, Enrico; Taddei, Fulvia

2017-12-01

Musculoskeletal modeling and simulations of movement have been increasingly used in orthopedic and neurological scenarios, with increased attention to subject-specific applications. In general, musculoskeletal modeling applications have been facilitated by the development of dedicated software tools; however, subject-specific studies have been limited also by time-consuming modeling workflows and high skilled expertise required. In addition, no reference tools exist to standardize the process of musculoskeletal model creation and make it more efficient. Here we present a freely available software application, nmsBuilder 2.0, to create musculoskeletal models in the file format of OpenSim, a widely-used open-source platform for musculoskeletal modeling and simulation. nmsBuilder 2.0 is the result of a major refactoring of a previous implementation that moved a first step toward an efficient workflow for subject-specific model creation. nmsBuilder includes a graphical user interface that provides access to all functionalities, based on a framework for computer-aided medicine written in C++. The operations implemented can be used in a workflow to create OpenSim musculoskeletal models from 3D surfaces. A first step includes data processing to create supporting objects necessary to create models, e.g. surfaces, anatomical landmarks, reference systems; and a second step includes the creation of OpenSim objects, e.g. bodies, joints, muscles, and the corresponding model. We present a case study using nmsBuilder 2.0: the creation of an MRI-based musculoskeletal model of the lower limb. The model included four rigid bodies, five degrees of freedom and 43 musculotendon actuators, and was created from 3D surfaces of the segmented images of a healthy subject through the modeling workflow implemented in the software application. We have presented nmsBuilder 2.0 for the creation of musculoskeletal OpenSim models from image-based data, and made it freely available via nmsbuilder.org. This application provides an efficient workflow for model creation and helps standardize the process. We hope this would help promote personalized applications in musculoskeletal biomechanics, including larger sample size studies, and might also represent a basis for future developments for specific applications. Copyright © 2017 Elsevier B.V. All rights reserved.

Analysis of acute brain slices by electron microscopy: a correlative light-electron microscopy workflow based on Tokuyasu cryo-sectioning.

PubMed

Loussert Fonta, Celine; Leis, Andrew; Mathisen, Cliff; Bouvier, David S; Blanchard, Willy; Volterra, Andrea; Lich, Ben; Humbel, Bruno M

2015-01-01

Acute brain slices are slices of brain tissue that are kept vital in vitro for further recordings and analyses. This tool is of major importance in neurobiology and allows the study of brain cells such as microglia, astrocytes, neurons and their inter/intracellular communications via ion channels or transporters. In combination with light/fluorescence microscopies, acute brain slices enable the ex vivo analysis of specific cells or groups of cells inside the slice, e.g. astrocytes. To bridge ex vivo knowledge of a cell with its ultrastructure, we developed a correlative microscopy approach for acute brain slices. The workflow begins with sampling of the tissue and precise trimming of a region of interest, which contains GFP-tagged astrocytes that can be visualised by fluorescence microscopy of ultrathin sections. The astrocytes and their surroundings are then analysed by high resolution scanning transmission electron microscopy (STEM). An important aspect of this workflow is the modification of a commercial cryo-ultramicrotome to observe the fluorescent GFP signal during the trimming process. It ensured that sections contained at least one GFP astrocyte. After cryo-sectioning, a map of the GFP-expressing astrocytes is established and transferred to correlation software installed on a focused ion beam scanning electron microscope equipped with a STEM detector. Next, the areas displaying fluorescence are selected for high resolution STEM imaging. An overview area (e.g. a whole mesh of the grid) is imaged with an automated tiling and stitching process. In the final stitched image, the local organisation of the brain tissue can be surveyed or areas of interest can be magnified to observe fine details, e.g. vesicles or gold labels on specific proteins. The robustness of this workflow is contingent on the quality of sample preparation, based on Tokuyasu's protocol. This method results in a reasonable compromise between preservation of morphology and maintenance of antigenicity. Finally, an important feature of this approach is that the fluorescence of the GFP signal is preserved throughout the entire preparation process until the last step before electron microscopy. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Mapping Eroded Areas on Mountain Grassland with Terrestrial Photogrammetry and Object-Based Image Analysis

NASA Astrophysics Data System (ADS)

Mayr, Andreas; Rutzinger, Martin; Bremer, Magnus; Geitner, Clemens

2016-06-01

In the Alps as well as in other mountain regions steep grassland is frequently affected by shallow erosion. Often small landslides or snow movements displace the vegetation together with soil and/or unconsolidated material. This results in bare earth surface patches within the grass covered slope. Close-range and remote sensing techniques are promising for both mapping and monitoring these eroded areas. This is essential for a better geomorphological process understanding, to assess past and recent developments, and to plan mitigation measures. Recent developments in image matching techniques make it feasible to produce high resolution orthophotos and digital elevation models from terrestrial oblique images. In this paper we propose to delineate the boundary of eroded areas for selected scenes of a study area, using close-range photogrammetric data. Striving for an efficient, objective and reproducible workflow for this task, we developed an approach for automated classification of the scenes into the classes grass and eroded. We propose an object-based image analysis (OBIA) workflow which consists of image segmentation and automated threshold selection for classification using the Excess Green Vegetation Index (ExG). The automated workflow is tested with ten different scenes. Compared to a manual classification, grass and eroded areas are classified with an overall accuracy between 90.7% and 95.5%, depending on the scene. The methods proved to be insensitive to differences in illumination of the scenes and greenness of the grass. The proposed workflow reduces user interaction and is transferable to other study areas. We conclude that close-range photogrammetry is a valuable low-cost tool for mapping this type of eroded areas in the field with a high level of detail and quality. In future, the output will be used as ground truth for an area-wide mapping of eroded areas in coarser resolution aerial orthophotos acquired at the same time.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ushizima, Daniela M.; Bianchi, Andrea G. C.; DeBianchi, Christina

We introduce a computational analysis workflow to access properties of solid objects using nondestructive imaging techniques that rely on X-ray imaging. The goal is to process and quantify structures from material science sample cross sections. The algorithms can differentiate the porous media (high density material) from the void (background, low density media) using a Boolean classifier, so that we can extract features, such as volume, surface area, granularity spectrum, porosity, among others. Our workflow, Quant-CT, leverages several algorithms from ImageJ, such as statistical region merging and 3D object counter. It also includes schemes for bilateral filtering that use a 3Dmore » kernel, for parallel processing of sub-stacks, and for handling over-segmentation using histogram similarities. The Quant-CT supports fast user interaction, providing the ability for the user to train the algorithm via subsamples to feed its core algorithms with automated parameterization. Quant-CT plugin is currently available for testing by personnel at the Advanced Light Source and Earth Sciences Divisions and Energy Frontier Research Center (EFRC), LBNL, as part of their research on porous materials. The goal is to understand the processes in fluid-rock systems for the geologic sequestration of CO2, and to develop technology for the safe storage of CO2 in deep subsurface rock formations. We describe our implementation, and demonstrate our plugin on porous material images. This paper targets end-users, with relevant information for developers to extend its current capabilities.« less

Conceptual-level workflow modeling of scientific experiments using NMR as a case study

PubMed Central

Verdi, Kacy K; Ellis, Heidi JC; Gryk, Michael R

2007-01-01

Background Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration. Results We propose a structured process to capture scientific workflows at the conceptual level that allows workflows to be documented efficiently, results in concise models of the workflow and more-correct workflow implementations, and provides insight into the scientific process itself. The approach uses three modeling techniques to model the structural, data flow, and control flow aspects of the workflow. The domain of biomolecular structure determination using Nuclear Magnetic Resonance spectroscopy is used to demonstrate the process. Specifically, we show the application of the approach to capture the workflow for the process of conducting biomolecular analysis using Nuclear Magnetic Resonance (NMR) spectroscopy. Conclusion Using the approach, we were able to accurately document, in a short amount of time, numerous steps in the process of conducting an experiment using NMR spectroscopy. The resulting models are correct and precise, as outside validation of the models identified only minor omissions in the models. In addition, the models provide an accurate visual description of the control flow for conducting biomolecular analysis using NMR spectroscopy experiment. PMID:17263870

Conceptual-level workflow modeling of scientific experiments using NMR as a case study.

PubMed

Verdi, Kacy K; Ellis, Heidi Jc; Gryk, Michael R

2007-01-30

Scientific workflows improve the process of scientific experiments by making computations explicit, underscoring data flow, and emphasizing the participation of humans in the process when intuition and human reasoning are required. Workflows for experiments also highlight transitions among experimental phases, allowing intermediate results to be verified and supporting the proper handling of semantic mismatches and different file formats among the various tools used in the scientific process. Thus, scientific workflows are important for the modeling and subsequent capture of bioinformatics-related data. While much research has been conducted on the implementation of scientific workflows, the initial process of actually designing and generating the workflow at the conceptual level has received little consideration. We propose a structured process to capture scientific workflows at the conceptual level that allows workflows to be documented efficiently, results in concise models of the workflow and more-correct workflow implementations, and provides insight into the scientific process itself. The approach uses three modeling techniques to model the structural, data flow, and control flow aspects of the workflow. The domain of biomolecular structure determination using Nuclear Magnetic Resonance spectroscopy is used to demonstrate the process. Specifically, we show the application of the approach to capture the workflow for the process of conducting biomolecular analysis using Nuclear Magnetic Resonance (NMR) spectroscopy. Using the approach, we were able to accurately document, in a short amount of time, numerous steps in the process of conducting an experiment using NMR spectroscopy. The resulting models are correct and precise, as outside validation of the models identified only minor omissions in the models. In addition, the models provide an accurate visual description of the control flow for conducting biomolecular analysis using NMR spectroscopy experiment.

A practical workflow for making anatomical atlases for biological research.

PubMed

Wan, Yong; Lewis, A Kelsey; Colasanto, Mary; van Langeveld, Mark; Kardon, Gabrielle; Hansen, Charles

2012-01-01

The anatomical atlas has been at the intersection of science and art for centuries. These atlases are essential to biological research, but high-quality atlases are often scarce. Recent advances in imaging technology have made high-quality 3D atlases possible. However, until now there has been a lack of practical workflows using standard tools to generate atlases from images of biological samples. With certain adaptations, CG artists' workflow and tools, traditionally used in the film industry, are practical for building high-quality biological atlases. Researchers have developed a workflow for generating a 3D anatomical atlas using accessible artists' tools. They used this workflow to build a mouse limb atlas for studying the musculoskeletal system's development. This research aims to raise the awareness of using artists' tools in scientific research and promote interdisciplinary collaborations between artists and scientists. This video (http://youtu.be/g61C-nia9ms) demonstrates a workflow for creating an anatomical atlas.

DEWEY: the DICOM-enabled workflow engine system.

PubMed

Erickson, Bradley J; Langer, Steve G; Blezek, Daniel J; Ryan, William J; French, Todd L

2014-06-01

Workflow is a widely used term to describe the sequence of steps to accomplish a task. The use of workflow technology in medicine and medical imaging in particular is limited. In this article, we describe the application of a workflow engine to improve workflow in a radiology department. We implemented a DICOM-enabled workflow engine system in our department. We designed it in a way to allow for scalability, reliability, and flexibility. We implemented several workflows, including one that replaced an existing manual workflow and measured the number of examinations prepared in time without and with the workflow system. The system significantly increased the number of examinations prepared in time for clinical review compared to human effort. It also met the design goals defined at its outset. Workflow engines appear to have value as ways to efficiently assure that complex workflows are completed in a timely fashion.

A stereoscopic lens for digital cinema cameras

NASA Astrophysics Data System (ADS)

Lipton, Lenny; Rupkalvis, John

2015-03-01

Live-action stereoscopic feature films are, for the most part, produced using a costly post-production process to convert planar cinematography into stereo-pair images and are only occasionally shot stereoscopically using bulky dual-cameras that are adaptations of the Ramsdell rig. The stereoscopic lens design described here might very well encourage more live-action image capture because it uses standard digital cinema cameras and workflow to save time and money.

Radiology information system: a workflow-based approach.

PubMed

Zhang, Jinyan; Lu, Xudong; Nie, Hongchao; Huang, Zhengxing; van der Aalst, W M P

2009-09-01

Introducing workflow management technology in healthcare seems to be prospective in dealing with the problem that the current healthcare Information Systems cannot provide sufficient support for the process management, although several challenges still exist. The purpose of this paper is to study the method of developing workflow-based information system in radiology department as a use case. First, a workflow model of typical radiology process was established. Second, based on the model, the system could be designed and implemented as a group of loosely coupled components. Each component corresponded to one task in the process and could be assembled by the workflow management system. The legacy systems could be taken as special components, which also corresponded to the tasks and were integrated through transferring non-work- flow-aware interfaces to the standard ones. Finally, a workflow dashboard was designed and implemented to provide an integral view of radiology processes. The workflow-based Radiology Information System was deployed in the radiology department of Zhejiang Chinese Medicine Hospital in China. The results showed that it could be adjusted flexibly in response to the needs of changing process, and enhance the process management in the department. It can also provide a more workflow-aware integration method, comparing with other methods such as IHE-based ones. The workflow-based approach is a new method of developing radiology information system with more flexibility, more functionalities of process management and more workflow-aware integration. The work of this paper is an initial endeavor for introducing workflow management technology in healthcare.

Overview of geostationary ocean color imager (GOCI) and GOCI data processing system (GDPS)

NASA Astrophysics Data System (ADS)

Ryu, Joo-Hyung; Han, Hee-Jeong; Cho, Seongick; Park, Young-Je; Ahn, Yu-Hwan

2012-09-01

GOCI, the world's first geostationary ocean color satellite, provides images with a spatial resolution of 500 m at hourly intervals up to 8 times a day, allowing observations of short-term changes in the Northeast Asian region. The GOCI Data Processing System (GDPS), a specialized data processing software for GOCI, was developed for real-time generation of various products. This paper describes GOCI characteristics and GDPS workflow/products, so as to enable the efficient utilization of GOCI. To provide quality images and data, atmospheric correction and data analysis algorithms must be improved through continuous Cal/Val. GOCI-II will be developed by 2018 to facilitate in-depth studies on geostationary ocean color satellites.

Going fully digital: Perspective of a Dutch academic pathology lab

PubMed Central

Stathonikos, Nikolas; Veta, Mitko; Huisman, André; van Diest, Paul J.

2013-01-01

During the last years, whole slide imaging has become more affordable and widely accepted in pathology labs. Digital slides are increasingly being used for digital archiving of routinely produced clinical slides, remote consultation and tumor boards, and quantitative image analysis for research purposes and in education. However, the implementation of a fully digital Pathology Department requires an in depth look into the suitability of digital slides for routine clinical use (the image quality of the produced digital slides and the factors that affect it) and the required infrastructure to support such use (the storage requirements and integration with lab management and hospital information systems). Optimization of digital pathology workflow requires communication between several systems, which can be facilitated by the use of open standards for digital slide storage and scanner management. Consideration of these aspects along with appropriate validation of the use of digital slides for routine pathology can pave the way for pathology departments to go “fully digital.” In this paper, we summarize our experiences so far in the process of implementing a fully digital workflow at our Pathology Department and the steps that are needed to complete this process. PMID:23858390

Several considerations with respect to the future of digital photography and photographic printing

NASA Astrophysics Data System (ADS)

Tuijn, Chris; Mahy, Marc F.

2000-12-01

Digital cameras are no longer exotic gadgets being used by a privileged group of early adopters. More and more people realize that there are obvious advantages to the digital solution over the conventional film-based workflow. Claiming that prints on paper are no longer necessary in the digit workflow, however, would be similar to reviving the myth of the paperless office. Often, people still like to share their memories on paper and this for a variety of reasons. There are still some hurdles to be taken in order to make the digital dream com true. In this paper, we will give a survey of the different workflows in digital photography. The local, semi-local and Internet solutions will be discussed as well as the preferred output systems for each of these solutions. When discussing output system, we immediately think of appropriate color management solutions. In the second part of this paper, we will discuss the major color management issues appearing in digital photography. A clear separation between the image acquisition and the image rendering phases will be made. After a quick survey of the different image restoration and enhancement techniques, we will make some reflections on the ideal color exchange space; the enhanced image should be delivered in this exchange space and, from there, the standard color management transformations can be applied to transfer the image from this exchange space to the native color space of the output device. We will also discus some color gamut characteristics and color management problems of different types of photographic printers that can occur during this conversion process.

Standards to support information systems integration in anatomic pathology.

PubMed

Daniel, Christel; García Rojo, Marcial; Bourquard, Karima; Henin, Dominique; Schrader, Thomas; Della Mea, Vincenzo; Gilbertson, John; Beckwith, Bruce A

2009-11-01

Integrating anatomic pathology information- text and images-into electronic health care records is a key challenge for enhancing clinical information exchange between anatomic pathologists and clinicians. The aim of the Integrating the Healthcare Enterprise (IHE) international initiative is precisely to ensure interoperability of clinical information systems by using existing widespread industry standards such as Digital Imaging and Communication in Medicine (DICOM) and Health Level Seven (HL7). To define standard-based informatics transactions to integrate anatomic pathology information to the Healthcare Enterprise. We used the methodology of the IHE initiative. Working groups from IHE, HL7, and DICOM, with special interest in anatomic pathology, defined consensual technical solutions to provide end-users with improved access to consistent information across multiple information systems. The IHE anatomic pathology technical framework describes a first integration profile, "Anatomic Pathology Workflow," dedicated to the diagnostic process including basic image acquisition and reporting solutions. This integration profile relies on 10 transactions based on HL7 or DICOM standards. A common specimen model was defined to consistently identify and describe specimens in both HL7 and DICOM transactions. The IHE anatomic pathology working group has defined standard-based informatics transactions to support the basic diagnostic workflow in anatomic pathology laboratories. In further stages, the technical framework will be completed to manage whole-slide images and semantically rich structured reports in the diagnostic workflow and to integrate systems used for patient care and those used for research activities (such as tissue bank databases or tissue microarrayers).

Sensor-based architecture for medical imaging workflow analysis.

PubMed

Silva, Luís A Bastião; Campos, Samuel; Costa, Carlos; Oliveira, José Luis

2014-08-01

The growing use of computer systems in medical institutions has been generating a tremendous quantity of data. While these data have a critical role in assisting physicians in the clinical practice, the information that can be extracted goes far beyond this utilization. This article proposes a platform capable of assembling multiple data sources within a medical imaging laboratory, through a network of intelligent sensors. The proposed integration framework follows a SOA hybrid architecture based on an information sensor network, capable of collecting information from several sources in medical imaging laboratories. Currently, the system supports three types of sensors: DICOM repository meta-data, network workflows and examination reports. Each sensor is responsible for converting unstructured information from data sources into a common format that will then be semantically indexed in the framework engine. The platform was deployed in the Cardiology department of a central hospital, allowing identification of processes' characteristics and users' behaviours that were unknown before the utilization of this solution.

Digital stereo photogrammetry for grain-scale monitoring of fluvial surfaces: Error evaluation and workflow optimisation

NASA Astrophysics Data System (ADS)

Bertin, Stephane; Friedrich, Heide; Delmas, Patrice; Chan, Edwin; Gimel'farb, Georgy

2015-03-01

Grain-scale monitoring of fluvial morphology is important for the evaluation of river system dynamics. Significant progress in remote sensing and computer performance allows rapid high-resolution data acquisition, however, applications in fluvial environments remain challenging. Even in a controlled environment, such as a laboratory, the extensive acquisition workflow is prone to the propagation of errors in digital elevation models (DEMs). This is valid for both of the common surface recording techniques: digital stereo photogrammetry and terrestrial laser scanning (TLS). The optimisation of the acquisition process, an effective way to reduce the occurrence of errors, is generally limited by the use of commercial software. Therefore, the removal of evident blunders during post processing is regarded as standard practice, although this may introduce new errors. This paper presents a detailed evaluation of a digital stereo-photogrammetric workflow developed for fluvial hydraulic applications. The introduced workflow is user-friendly and can be adapted to various close-range measurements: imagery is acquired with two Nikon D5100 cameras and processed using non-proprietary "on-the-job" calibration and dense scanline-based stereo matching algorithms. Novel ground truth evaluation studies were designed to identify the DEM errors, which resulted from a combination of calibration errors, inaccurate image rectifications and stereo-matching errors. To ensure optimum DEM quality, we show that systematic DEM errors must be minimised by ensuring a good distribution of control points throughout the image format during calibration. DEM quality is then largely dependent on the imagery utilised. We evaluated the open access multi-scale Retinex algorithm to facilitate the stereo matching, and quantified its influence on DEM quality. Occlusions, inherent to any roughness element, are still a major limiting factor to DEM accuracy. We show that a careful selection of the camera-to-object and baseline distance reduces errors in occluded areas and that realistic ground truths help to quantify those errors.

Technical Note: scuda: A software platform for cumulative dose assessment.

PubMed

Park, Seyoun; McNutt, Todd; Plishker, William; Quon, Harry; Wong, John; Shekhar, Raj; Lee, Junghoon

2016-10-01

Accurate tracking of anatomical changes and computation of actually delivered dose to the patient are critical for successful adaptive radiation therapy (ART). Additionally, efficient data management and fast processing are practically important for the adoption in clinic as ART involves a large amount of image and treatment data. The purpose of this study was to develop an accurate and efficient Software platform for CUmulative Dose Assessment (scuda) that can be seamlessly integrated into the clinical workflow. scuda consists of deformable image registration (DIR), segmentation, dose computation modules, and a graphical user interface. It is connected to our image PACS and radiotherapy informatics databases from which it automatically queries/retrieves patient images, radiotherapy plan, beam data, and daily treatment information, thus providing an efficient and unified workflow. For accurate registration of the planning CT and daily CBCTs, the authors iteratively correct CBCT intensities by matching local intensity histograms during the DIR process. Contours of the target tumor and critical structures are then propagated from the planning CT to daily CBCTs using the computed deformations. The actual delivered daily dose is computed using the registered CT and patient setup information by a superposition/convolution algorithm, and accumulated using the computed deformation fields. Both DIR and dose computation modules are accelerated by a graphics processing unit. The cumulative dose computation process has been validated on 30 head and neck (HN) cancer cases, showing 3.5 ± 5.0 Gy (mean±STD) absolute mean dose differences between the planned and the actually delivered doses in the parotid glands. On average, DIR, dose computation, and segmentation take 20 s/fraction and 17 min for a 35-fraction treatment including additional computation for dose accumulation. The authors developed a unified software platform that provides accurate and efficient monitoring of anatomical changes and computation of actually delivered dose to the patient, thus realizing an efficient cumulative dose computation workflow. Evaluation on HN cases demonstrated the utility of our platform for monitoring the treatment quality and detecting significant dosimetric variations that are keys to successful ART.

Selectively active markers for solving of the partial occlusion problem in matchmoving and chromakeying workflow

NASA Astrophysics Data System (ADS)

Mazurek, Przemysław

2013-09-01

Matchmoving (Match Moving) is the process used for the estimation of camera movements for further integration of acquired video image with computer graphics. The estimation of movements is possible using pattern recognition, 2D and 3D tracking algorithms. The main problem for the workflow is the partial occlusion of markers by the actor, because manual rotoscoping is necessary for fixing of the chroma-keyed footage. In the paper, the partial occlusion problem is solved using the invented, selectively active electronic markers. The sensor network with multiple infrared links detects occlusion state (no-occlusion, partial, full) and switch LED's based markers.

High-Performance Compute Infrastructure in Astronomy: 2020 Is Only Months Away

NASA Astrophysics Data System (ADS)

Berriman, B.; Deelman, E.; Juve, G.; Rynge, M.; Vöckler, J. S.

2012-09-01

By 2020, astronomy will be awash with as much as 60 PB of public data. Full scientific exploitation of such massive volumes of data will require high-performance computing on server farms co-located with the data. Development of this computing model will be a community-wide enterprise that has profound cultural and technical implications. Astronomers must be prepared to develop environment-agnostic applications that support parallel processing. The community must investigate the applicability and cost-benefit of emerging technologies such as cloud computing to astronomy, and must engage the Computer Science community to develop science-driven cyberinfrastructure such as workflow schedulers and optimizers. We report here the results of collaborations between a science center, IPAC, and a Computer Science research institute, ISI. These collaborations may be considered pathfinders in developing a high-performance compute infrastructure in astronomy. These collaborations investigated two exemplar large-scale science-driver workflow applications: 1) Calculation of an infrared atlas of the Galactic Plane at 18 different wavelengths by placing data from multiple surveys on a common plate scale and co-registering all the pixels; 2) Calculation of an atlas of periodicities present in the public Kepler data sets, which currently contain 380,000 light curves. These products have been generated with two workflow applications, written in C for performance and designed to support parallel processing on multiple environments and platforms, but with different compute resource needs: the Montage image mosaic engine is I/O-bound, and the NASA Star and Exoplanet Database periodogram code is CPU-bound. Our presentation will report cost and performance metrics and lessons-learned for continuing development. Applicability of Cloud Computing: Commercial Cloud providers generally charge for all operations, including processing, transfer of input and output data, and for storage of data, and so the costs of running applications vary widely according to how they use resources. The cloud is well suited to processing CPU-bound (and memory bound) workflows such as the periodogram code, given the relatively low cost of processing in comparison with I/O operations. I/O-bound applications such as Montage perform best on high-performance clusters with fast networks and parallel file-systems. Science-driven Cyberinfrastructure: Montage has been widely used as a driver application to develop workflow management services, such as task scheduling in distributed environments, designing fault tolerance techniques for job schedulers, and developing workflow orchestration techniques. Running Parallel Applications Across Distributed Cloud Environments: Data processing will eventually take place in parallel distributed across cyber infrastructure environments having different architectures. We have used the Pegasus Work Management System (WMS) to successfully run applications across three very different environments: TeraGrid, OSG (Open Science Grid), and FutureGrid. Provisioning resources across different grids and clouds (also referred to as Sky Computing), involves establishing a distributed environment, where issues of, e.g, remote job submission, data management, and security need to be addressed. This environment also requires building virtual machine images that can run in different environments. Usually, each cloud provides basic images that can be customized with additional software and services. In most of our work, we provisioned compute resources using a custom application, called Wrangler. Pegasus WMS abstracts the architectures of the compute environments away from the end-user, and can be considered a first-generation tool suitable for scientists to run their applications on disparate environments.

Automation and workflow considerations for embedding Digimarc Barcodes at scale

NASA Astrophysics Data System (ADS)

Rodriguez, Tony; Haaga, Don; Calhoon, Sean

2015-03-01

The Digimarc® Barcode is a digital watermark applied to packages and variable data labels that carries GS1 standard GTIN-14 data traditionally carried by a 1-D barcode. The Digimarc Barcode can be read with smartphones and imaging-based barcode readers commonly used in grocery and retail environments. Using smartphones, consumers can engage with products and retailers can materially increase the speed of check-out, increasing store margins and providing a better experience for shoppers. Internal testing has shown an average of 53% increase in scanning throughput, enabling 100's of millions of dollars in cost savings [1] for retailers when deployed at scale. To get to scale, the process of embedding a digital watermark must be automated and integrated within existing workflows. Creating the tools and processes to do so represents a new challenge for the watermarking community. This paper presents a description and an analysis of the workflow implemented by Digimarc to deploy the Digimarc Barcode at scale. An overview of the tools created and lessons learned during the introduction of technology to the market are provided.

RESTFul based heterogeneous Geoprocessing workflow interoperation for Sensor Web Service

NASA Astrophysics Data System (ADS)

Yang, Chao; Chen, Nengcheng; Di, Liping

2012-10-01

Advanced sensors on board satellites offer detailed Earth observations. A workflow is one approach for designing, implementing and constructing a flexible and live link between these sensors' resources and users. It can coordinate, organize and aggregate the distributed sensor Web services to meet the requirement of a complex Earth observation scenario. A RESTFul based workflow interoperation method is proposed to integrate heterogeneous workflows into an interoperable unit. The Atom protocols are applied to describe and manage workflow resources. The XML Process Definition Language (XPDL) and Business Process Execution Language (BPEL) workflow standards are applied to structure a workflow that accesses sensor information and one that processes it separately. Then, a scenario for nitrogen dioxide (NO2) from a volcanic eruption is used to investigate the feasibility of the proposed method. The RESTFul based workflows interoperation system can describe, publish, discover, access and coordinate heterogeneous Geoprocessing workflows.

Parallel processing considerations for image recognition tasks

NASA Astrophysics Data System (ADS)

Simske, Steven J.

2011-01-01

Many image recognition tasks are well-suited to parallel processing. The most obvious example is that many imaging tasks require the analysis of multiple images. From this standpoint, then, parallel processing need be no more complicated than assigning individual images to individual processors. However, there are three less trivial categories of parallel processing that will be considered in this paper: parallel processing (1) by task; (2) by image region; and (3) by meta-algorithm. Parallel processing by task allows the assignment of multiple workflows-as diverse as optical character recognition [OCR], document classification and barcode reading-to parallel pipelines. This can substantially decrease time to completion for the document tasks. For this approach, each parallel pipeline is generally performing a different task. Parallel processing by image region allows a larger imaging task to be sub-divided into a set of parallel pipelines, each performing the same task but on a different data set. This type of image analysis is readily addressed by a map-reduce approach. Examples include document skew detection and multiple face detection and tracking. Finally, parallel processing by meta-algorithm allows different algorithms to be deployed on the same image simultaneously. This approach may result in improved accuracy.

Impact of digital imaging and communications in medicine workflow on the integration of patient demographics and ophthalmic test data.

PubMed

Pandit, Ravi R; Boland, Michael V

2015-02-01

To determine the impact of a Digital Imaging and Communications in Medicine (DICOM) workflow on the linkage of demographic information to ophthalmic testing data. Evaluation of technology. Six hundred ninety-nine visual field testing encounters performed by 6 ophthalmic technicians and the transfer error queue of 37 442 ophthalmic test results. At 3 months before and 6 and 18 months after implementation of a DICOM workflow, technicians recorded the work required to enter, confirm, or edit patient demographics in each visual field device. We also determined the proportion of imaging tests sent to an error queue for manual reconciliation because of incorrect demographic information before and 3, 6, and 18 months after the DICOM workflow was established. The proportion of testing encounters for which staff had to enter, edit, or merge patient demographics and the proportion of misfiled images. Staff entered, edited, or merged data for 48% of patients before implementation (n = 237). This decreased to 24% within 6 months and 20% within 18 months of implementing the DICOM archive (n = 230 and n = 232, respectively). Staff could locate a patient in a DICOM work list for 97% of encounters at 3 months and 99% at 18 months. Before implementation, 9.2% of the images required additional intervention to be associated with the correct patient (n = 3581). This decreased by 85% over 6 months to 1.4% (n = 9979; P < 0.01). There was an increase in the percentage of misfiled images between 6 and 18 months from 1.4% to 2.2% (n = 24 549; P < 0.01), representing an overall 76% decrease over 18 months relative to the pre-DICOM period. Implementation of a DICOM-compatible workflow in an ophthalmology clinic reduced the need to enter or edit patient demographic information into imaging or testing devices by more than 50% and reduced the need to manage misfiled images by 76%. In a clinical environment that demands both efficiency and patient safety, the DICOM workflow is an important update to current practice. Copyright © 2015 American Academy of Ophthalmology. Published by Elsevier Inc. All rights reserved.

Canine neuroanatomy: Development of a 3D reconstruction and interactive application for undergraduate veterinary education

PubMed Central

Raffan, Hazel; Guevar, Julien; Poyade, Matthieu; Rea, Paul M.

2017-01-01

Current methods used to communicate and present the complex arrangement of vasculature related to the brain and spinal cord is limited in undergraduate veterinary neuroanatomy training. Traditionally it is taught with 2-dimensional (2D) diagrams, photographs and medical imaging scans which show a fixed viewpoint. 2D representations of 3-dimensional (3D) objects however lead to loss of spatial information, which can present problems when translating this to the patient. Computer-assisted learning packages with interactive 3D anatomical models have become established in medical training, yet equivalent resources are scarce in veterinary education. For this reason, we set out to develop a workflow methodology creating an interactive model depicting the vasculature of the canine brain that could be used in undergraduate education. Using MR images of a dog and several commonly available software programs, we set out to show how combining image editing, segmentation and surface generation, 3D modeling and texturing can result in the creation of a fully interactive application for veterinary training. In addition to clearly identifying a workflow methodology for the creation of this dataset, we have also demonstrated how an interactive tutorial and self-assessment tool can be incorporated into this. In conclusion, we present a workflow which has been successful in developing a 3D reconstruction of the canine brain and associated vasculature through segmentation, surface generation and post-processing of readily available medical imaging data. The reconstructed model was implemented into an interactive application for veterinary education that has been designed to target the problems associated with learning neuroanatomy, primarily the inability to visualise complex spatial arrangements from 2D resources. The lack of similar resources in this field suggests this workflow is original within a veterinary context. There is great potential to explore this method, and introduce a new dimension into veterinary education and training. PMID:28192461

Canine neuroanatomy: Development of a 3D reconstruction and interactive application for undergraduate veterinary education.

PubMed

Raffan, Hazel; Guevar, Julien; Poyade, Matthieu; Rea, Paul M

2017-01-01

Current methods used to communicate and present the complex arrangement of vasculature related to the brain and spinal cord is limited in undergraduate veterinary neuroanatomy training. Traditionally it is taught with 2-dimensional (2D) diagrams, photographs and medical imaging scans which show a fixed viewpoint. 2D representations of 3-dimensional (3D) objects however lead to loss of spatial information, which can present problems when translating this to the patient. Computer-assisted learning packages with interactive 3D anatomical models have become established in medical training, yet equivalent resources are scarce in veterinary education. For this reason, we set out to develop a workflow methodology creating an interactive model depicting the vasculature of the canine brain that could be used in undergraduate education. Using MR images of a dog and several commonly available software programs, we set out to show how combining image editing, segmentation and surface generation, 3D modeling and texturing can result in the creation of a fully interactive application for veterinary training. In addition to clearly identifying a workflow methodology for the creation of this dataset, we have also demonstrated how an interactive tutorial and self-assessment tool can be incorporated into this. In conclusion, we present a workflow which has been successful in developing a 3D reconstruction of the canine brain and associated vasculature through segmentation, surface generation and post-processing of readily available medical imaging data. The reconstructed model was implemented into an interactive application for veterinary education that has been designed to target the problems associated with learning neuroanatomy, primarily the inability to visualise complex spatial arrangements from 2D resources. The lack of similar resources in this field suggests this workflow is original within a veterinary context. There is great potential to explore this method, and introduce a new dimension into veterinary education and training.

Talkoot Portals: Discover, Tag, Share, and Reuse Collaborative Science Workflows

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Ramachandran, R.; Lynnes, C.

2009-05-01

A small but growing number of scientists are beginning to harness Web 2.0 technologies, such as wikis, blogs, and social tagging, as a transformative way of doing science. These technologies provide researchers easy mechanisms to critique, suggest and share ideas, data and algorithms. At the same time, large suites of algorithms for science analysis are being made available as remotely-invokable Web Services, which can be chained together to create analysis workflows. This provides the research community an unprecedented opportunity to collaborate by sharing their workflows with one another, reproducing and analyzing research results, and leveraging colleagues' expertise to expedite the process of scientific discovery. However, wikis and similar technologies are limited to text, static images and hyperlinks, providing little support for collaborative data analysis. A team of information technology and Earth science researchers from multiple institutions have come together to improve community collaboration in science analysis by developing a customizable "software appliance" to build collaborative portals for Earth Science services and analysis workflows. The critical requirement is that researchers (not just information technologists) be able to build collaborative sites around service workflows within a few hours. We envision online communities coming together, much like Finnish "talkoot" (a barn raising), to build a shared research space. Talkoot extends a freely available, open source content management framework with a series of modules specific to Earth Science for registering, creating, managing, discovering, tagging and sharing Earth Science web services and workflows for science data processing, analysis and visualization. Users will be able to author a "science story" in shareable web notebooks, including plots or animations, backed up by an executable workflow that directly reproduces the science analysis. New services and workflows of interest will be discoverable using tag search, and advertised using "service casts" and "interest casts" (Atom feeds). Multiple science workflow systems will be plugged into the system, with initial support for UAH's Mining Workflow Composer and the open-source Active BPEL engine, and JPL's SciFlo engine and the VizFlow visual programming interface. With the ability to share and execute analysis workflows, Talkoot portals can be used to do collaborative science in addition to communicate ideas and results. It will be useful for different science domains, mission teams, research projects and organizations. Thus, it will help to solve the "sociological" problem of bringing together disparate groups of researchers, and the technical problem of advertising, discovering, developing, documenting, and maintaining inter-agency science workflows. The presentation will discuss the goals of and barriers to Science 2.0, the social web technologies employed in the Talkoot software appliance (e.g. CMS, social tagging, personal presence, advertising by feeds, etc.), illustrate the resulting collaborative capabilities, and show early prototypes of the web interfaces (e.g. embedded workflows).

The InSAR Scientific Computing Environment (ISCE): An Earth Science SAR Processing Framework, Toolbox, and Foundry

NASA Astrophysics Data System (ADS)

Agram, P. S.; Gurrola, E. M.; Lavalle, M.; Sacco, G. F.; Rosen, P. A.

2016-12-01

The InSAR Scientific Computing Environment (ISCE) provides both a modular, flexible, and extensible framework for building software components and applications that work together seamlessly as well as a toolbox for processing InSAR data into higher level geodetic image products from a diverse array of radar satellites and aircraft. ISCE easily scales to serve as the SAR processing engine at the core of the NASA JPL Advanced Rapid Imaging and Analysis (ARIA) Center for Natural Hazards as well as a software toolbox for individual scientists working with SAR data. ISCE is planned as the foundational element in processing NISAR data, enabling a new class of analyses that take greater advantage of the long time and large spatial scales of these data. ISCE in ARIA is also a SAR Foundry for development of new processing components and workflows to meet the needs of both large processing centers and individual users. The ISCE framework contains object-oriented Python components layered to construct Python InSAR components that manage legacy Fortran/C InSAR programs. The Python user interface enables both command-line deployment of workflows as well as an interactive "sand box" (the Python interpreter) where scientists can "play" with the data. Recent developments in ISCE include the addition of components to ingest Sentinel-1A SAR data (both stripmap and TOPS-mode) and a new workflow for processing the TOPS-mode data. New components are being developed to exploit polarimetric-SAR data to provide the ecosystem and land-cover/land-use change communities with rigorous and efficient tools to perform multi-temporal, polarimetric and tomographic analyses in order to generate calibrated, geocoded and mosaicked Level-2 and Level-3 products (e.g., maps of above-ground biomass or forest disturbance). ISCE has been downloaded by over 200 users by a license for WinSAR members through the Unavco.org website. Others may apply directly to JPL for a license at download.jpl.nasa.gov.

Semi-automted analysis of high-resolution aerial images to quantify docks in Upper Midwest glacial lakes

USGS Publications Warehouse

Beck, Marcus W.; Vondracek, Bruce C.; Hatch, Lorin K.; Vinje, Jason

2013-01-01

Lake resources can be negatively affected by environmental stressors originating from multiple sources and different spatial scales. Shoreline development, in particular, can negatively affect lake resources through decline in habitat quality, physical disturbance, and impacts on fisheries. The development of remote sensing techniques that efficiently characterize shoreline development in a regional context could greatly improve management approaches for protecting and restoring lake resources. The goal of this study was to develop an approach using high-resolution aerial photographs to quantify and assess docks as indicators of shoreline development. First, we describe a dock analysis workflow that can be used to quantify the spatial extent of docks using aerial images. Our approach incorporates pixel-based classifiers with object-based techniques to effectively analyze high-resolution digital imagery. Second, we apply the analysis workflow to quantify docks for 4261 lakes managed by the Minnesota Department of Natural Resources. Overall accuracy of the analysis results was 98.4% (87.7% based on ) after manual post-processing. The analysis workflow was also 74% more efficient than the time required for manual digitization of docks. These analyses have immediate relevance for resource planning in Minnesota, whereas the dock analysis workflow could be used to quantify shoreline development in other regions with comparable imagery. These data can also be used to better understand the effects of shoreline development on aquatic resources and to evaluate the effects of shoreline development relative to other stressors.

Performance of an Automated Versus a Manual Whole-Body Magnetic Resonance Imaging Workflow.

PubMed

Stocker, Daniel; Finkenstaedt, Tim; Kuehn, Bernd; Nanz, Daniel; Klarhoefer, Markus; Guggenberger, Roman; Andreisek, Gustav; Kiefer, Berthold; Reiner, Caecilia S

2018-04-24

The aim of this study was to evaluate the performance of an automated workflow for whole-body magnetic resonance imaging (WB-MRI), which reduces user interaction compared with the manual WB-MRI workflow. This prospective study was approved by the local ethics committee. Twenty patients underwent WB-MRI for myopathy evaluation on a 3 T MRI scanner. Ten patients (7 women; age, 52 ± 13 years; body weight, 69.9 ± 13.3 kg; height, 173 ± 9.3 cm; body mass index, 23.2 ± 3.0) were examined with a prototypical automated WB-MRI workflow, which automatically segments the whole body, and 10 patients (6 women; age, 35.9 ± 12.4 years; body weight, 72 ± 21 kg; height, 169.2 ± 10.4 cm; body mass index, 24.9 ± 5.6) with a manual scan. Overall image quality (IQ; 5-point scale: 5, excellent; 1, poor) and coverage of the study volume were assessed by 2 readers for each sequence (coronal T2-weighted turbo inversion recovery magnitude [TIRM] and axial contrast-enhanced T1-weighted [ce-T1w] gradient dual-echo sequence). Interreader agreement was evaluated with intraclass correlation coefficients. Examination time, number of user interactions, and MR technicians' acceptance rating (1, highest; 10, lowest) was compared between both groups. Total examination time was significantly shorter for automated WB-MRI workflow versus manual WB-MRI workflow (30.0 ± 4.2 vs 41.5 ± 3.4 minutes, P < 0.0001) with significantly shorter planning time (2.5 ± 0.8 vs 14.0 ± 7.0 minutes, P < 0.0001). Planning took 8% of the total examination time with automated versus 34% with manual WB-MRI workflow (P < 0.0001). The number of user interactions with automated WB-MRI workflow was significantly lower compared with manual WB-MRI workflow (10.2 ± 4.4 vs 48.2 ± 17.2, P < 0.0001). Planning efforts were rated significantly lower by the MR technicians for the automated WB-MRI workflow than for the manual WB-MRI workflow (2.20 ± 0.92 vs 4.80 ± 2.39, respectively; P = 0.005). Overall IQ was similar between automated and manual WB-MRI workflow (TIRM: 4.00 ± 0.94 vs 3.45 ± 1.19, P = 0.264; ce-T1w: 4.20 ± 0.88 vs 4.55 ± .55, P = 0.423). Interreader agreement for overall IQ was excellent for TIRM and ce-T1w with an intraclass correlation coefficient of 0.95 (95% confidence interval, 0.86-0.98) and 0.88 (95% confidence interval, 0.70-0.95). Incomplete coverage of the thoracic compartment in the ce-T1w sequence occurred more often in the automated WB-MRI workflow (P = 0.008) for reader 2. No other significant differences in the study volume coverage were found. In conclusion, the automated WB-MRI scanner workflow showed a significant reduction of the examination time and the user interaction compared with the manual WB-MRI workflow. Image quality and the coverage of the study volume were comparable in both groups.

Development of a user-friendly system for image processing of electron microscopy by integrating a web browser and PIONE with Eos.

PubMed

Tsukamoto, Takafumi; Yasunaga, Takuo

2014-11-01

Eos (Extensible object-oriented system) is one of the powerful applications for image processing of electron micrographs. In usual cases, Eos works with only character user interfaces (CUI) under the operating systems (OS) such as OS-X or Linux, not user-friendly. Thus, users of Eos need to be expert at image processing of electron micrographs, and have a little knowledge of computer science, as well. However, all the persons who require Eos does not an expert for CUI. Thus we extended Eos to a web system independent of OS with graphical user interfaces (GUI) by integrating web browser.Advantage to use web browser is not only to extend Eos with GUI, but also extend Eos to work under distributed computational environment. Using Ajax (Asynchronous JavaScript and XML) technology, we implemented more comfortable user-interface on web browser. Eos has more than 400 commands related to image processing for electron microscopy, and the usage of each command is different from each other. Since the beginning of development, Eos has managed their user-interface by using the interface definition file of "OptionControlFile" written in CSV (Comma-Separated Value) format, i.e., Each command has "OptionControlFile", which notes information for interface and its usage generation. Developed GUI system called "Zephyr" (Zone for Easy Processing of HYpermedia Resources) also accessed "OptionControlFIle" and produced a web user-interface automatically, because its mechanism is mature and convenient,The basic actions of client side system was implemented properly and can supply auto-generation of web-form, which has functions of execution, image preview, file-uploading to a web server. Thus the system can execute Eos commands with unique options for each commands, and process image analysis. There remain problems of image file format for visualization and workspace for analysis: The image file format information is useful to check whether the input/output file is correct and we also need to provide common workspace for analysis because the client is physically separated from a server. We solved the file format problem by extension of rules of OptionControlFile of Eos. Furthermore, to solve workspace problems, we have developed two type of system. The first system is to use only local environments. The user runs a web server provided by Eos, access to a web client through a web browser, and manipulate the local files with GUI on the web browser. The second system is employing PIONE (Process-rule for Input/Output Negotiation Environment), which is our developing platform that works under heterogenic distributed environment. The users can put their resources, such as microscopic images, text files and so on, into the server-side environment supported by PIONE, and so experts can write PIONE rule definition, which defines a workflow of image processing. PIONE run each image processing on suitable computers, following the defined rule. PIONE has the ability of interactive manipulation, and user is able to try a command with various setting values. In this situation, we contribute to auto-generation of GUI for a PIONE workflow.As advanced functions, we have developed a module to log user actions. The logs include information such as setting values in image processing, procedure of commands and so on. If we use the logs effectively, we can get a lot of advantages. For example, when an expert may discover some know-how of image processing, other users can also share logs including his know-hows and so we may obtain recommendation workflow of image analysis, if we analyze logs. To implement social platform of image processing for electron microscopists, we have developed system infrastructure, as well. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Refining the Workflow of UV Camera Measurements: Data Collection from Low Emission Rate Volcanoes under Variable Conditions

NASA Astrophysics Data System (ADS)

Brewer, I. D.; Werner, C. A.; Nadeau, P. A.

2010-12-01

UV camera systems are gaining popularity worldwide for quantifying SO2 column abundances and emission rates from volcanoes, which serve as primary measures of volcanic hazard and aid in eruption forecasting. To date many of the investigations have focused on fairly active and routinely monitored volcanoes under optimal conditions. Some recent studies have begun to recommend protocols and procedures for data collection, but additional questions still need to be addressed. In this study we attempt to answer these questions, and also present results from volcanoes that are rarely monitored. Conditions at these volcanoes are typically sub-optimal for UV camera measurements. Discussion of such data is essential in the assessment of the wider applicability of UV camera measurements for SO2 monitoring purposes. Data discussed herein consists of plume images from volcanoes with relatively low emission rates, with varying weather conditions and from various distances (2-12 km). These include Karangatang Volcano (Indonesia), Mount St. Helens (Washington, USA), and Augustine and Redoubt Volcanoes (Alaska, USA). High emission rate data were also collected at Kilauea Volcano (Hawaii, USA), and blue sky test images with no plume were collected at Mammoth Mountain (California, USA). All data were collected between 2008 and 2010 using both single-filter (307 nm) and dual-filter (307 nm/326 nm) systems and were accompanied by FLYSPEC measurements. With the dual-filter systems, both a filter wheel setup and a synchronous-imaging dual-camera setup were employed. Data collection and processing questions included (1) what is the detection limit of the camera, (2) how large is the variability in raw camera output, (3) how do camera optics affect the measurements and how can this be corrected, (4) how much variability is observed in calibration under various conditions, (5) what is the optimal workflow for image collection and processing, and (6) what is the range of camera operating conditions? Besides emission rates from these infrequently monitored volcanoes, the results of this study include a recommended workflow and procedure for image collection and calibration, and a MATLAB-based algorithm for batch processing, thereby enabling accurate emission rates at 1 Hz when a synchronous-imaging dual-camera setup is used.

[Evaluating the maturity of IT-supported clinical imaging and diagnosis using the Digital Imaging Adoption Model : Are your clinical imaging processes ready for the digital era?

PubMed

Studzinski, J

2017-06-01

The Digital Imaging Adoption Model (DIAM) has been jointly developed by HIMSS Analytics and the European Society of Radiology (ESR). It helps evaluate the maturity of IT-supported processes in medical imaging, particularly in radiology. This eight-stage maturity model drives your organisational, strategic and tactical alignment towards imaging-IT planning. The key audience for the model comprises hospitals with imaging centers, as well as external imaging centers that collaborate with hospitals. The assessment focuses on different dimensions relevant to digital imaging, such as software infrastructure and usage, workflow security, clinical documentation and decision support, data exchange and analytical capabilities. With its standardised approach, it enables regional, national and international benchmarking. All DIAM participants receive a structured report that can be used as a basis for presenting, e.g. budget planning and investment decisions at management level.

Camera-augmented mobile C-arm (CamC): A feasibility study of augmented reality imaging in the operating room.

PubMed

von der Heide, Anna Maria; Fallavollita, Pascal; Wang, Lejing; Sandner, Philipp; Navab, Nassir; Weidert, Simon; Euler, Ekkehard

2018-04-01

In orthopaedic trauma surgery, image-guided procedures are mostly based on fluoroscopy. The reduction of radiation exposure is an important goal. The purpose of this work was to investigate the impact of a camera-augmented mobile C-arm (CamC) on radiation exposure and the surgical workflow during a first clinical trial. Applying a workflow-oriented approach, 10 general workflow steps were defined to compare the CamC to traditional C-arms. The surgeries included were arbitrarily identified and assigned to the study. The evaluation criteria were radiation exposure and operation time for each workflow step and the entire surgery. The evaluation protocol was designed and conducted in a single-centre study. The radiation exposure was remarkably reduced by 18 X-ray shots 46% using the CamC while keeping similar surgery times. The intuitiveness of the system, its easy integration into the surgical workflow, and its great potential to reduce radiation have been demonstrated. Copyright © 2017 John Wiley & Sons, Ltd.

Integration of prior CT into CBCT reconstruction for improved image quality via reconstruction of difference: first patient studies

NASA Astrophysics Data System (ADS)

Zhang, Hao; Gang, Grace J.; Lee, Junghoon; Wong, John; Stayman, J. Webster

2017-03-01

Purpose: There are many clinical situations where diagnostic CT is used for an initial diagnosis or treatment planning, followed by one or more CBCT scans that are part of an image-guided intervention. Because the high-quality diagnostic CT scan is a rich source of patient-specific anatomical knowledge, this provides an opportunity to incorporate the prior CT image into subsequent CBCT reconstruction for improved image quality. We propose a penalized-likelihood method called reconstruction of difference (RoD), to directly reconstruct differences between the CBCT scan and the CT prior. In this work, we demonstrate the efficacy of RoD with clinical patient datasets. Methods: We introduce a data processing workflow using the RoD framework to reconstruct anatomical changes between the prior CT and current CBCT. This workflow includes processing steps to account for non-anatomical differences between the two scans including 1) scatter correction for CBCT datasets due to increased scatter fractions in CBCT data; 2) histogram matching for attenuation variations between CT and CBCT; and 3) registration for different patient positioning. CBCT projection data and CT planning volumes for two radiotherapy patients - one abdominal study and one head-and-neck study - were investigated. Results: In comparisons between the proposed RoD framework and more traditional FDK and penalized-likelihood reconstructions, we find a significant improvement in image quality when prior CT information is incorporated into the reconstruction. RoD is able to provide additional low-contrast details while correctly incorporating actual physical changes in patient anatomy. Conclusions: The proposed framework provides an opportunity to either improve image quality or relax data fidelity constraints for CBCT imaging when prior CT studies of the same patient are available. Possible clinical targets include CBCT image-guided radiotherapy and CBCT image-guided surgeries.

From Panoramic Photos to a Low-Cost Photogrammetric Workflow for Cultural Heritage 3d Documentation

NASA Astrophysics Data System (ADS)

D'Annibale, E.; Tassetti, A. N.; Malinverni, E. S.

2013-07-01

The research aims to optimize a workflow of architecture documentation: starting from panoramic photos, tackling available instruments and technologies to propose an integrated, quick and low-cost solution of Virtual Architecture. The broader research background shows how to use spherical panoramic images for the architectural metric survey. The input data (oriented panoramic photos), the level of reliability and Image-based Modeling methods constitute an integrated and flexible 3D reconstruction approach: from the professional survey of cultural heritage to its communication in virtual museum. The proposed work results from the integration and implementation of different techniques (Multi-Image Spherical Photogrammetry, Structure from Motion, Imagebased Modeling) with the aim to achieve high metric accuracy and photorealistic performance. Different documentation chances are possible within the proposed workflow: from the virtual navigation of spherical panoramas to complex solutions of simulation and virtual reconstruction. VR tools make for the integration of different technologies and the development of new solutions for virtual navigation. Image-based Modeling techniques allow 3D model reconstruction with photo realistic and high-resolution texture. High resolution of panoramic photo and algorithms of panorama orientation and photogrammetric restitution vouch high accuracy and high-resolution texture. Automated techniques and their following integration are subject of this research. Data, advisably processed and integrated, provide different levels of analysis and virtual reconstruction joining the photogrammetric accuracy to the photorealistic performance of the shaped surfaces. Lastly, a new solution of virtual navigation is tested. Inside the same environment, it proposes the chance to interact with high resolution oriented spherical panorama and 3D reconstructed model at once.

Workflow Challenges of Enterprise Imaging: HIMSS-SIIM Collaborative White Paper.

PubMed

Towbin, Alexander J; Roth, Christopher J; Bronkalla, Mark; Cram, Dawn

2016-10-01

With the advent of digital cameras, there has been an explosion in the number of medical specialties using images to diagnose or document disease and guide interventions. In many specialties, these images are not added to the patient's electronic medical record and are not distributed so that other providers caring for the patient can view them. As hospitals begin to develop enterprise imaging strategies, they have found that there are multiple challenges preventing the implementation of systems to manage image capture, image upload, and image management. This HIMSS-SIIM white paper will describe the key workflow challenges related to enterprise imaging and offer suggestions for potential solutions to these challenges.

SEM AutoAnalysis: enhancing photomask and NIL defect disposition and review

NASA Astrophysics Data System (ADS)

Schulz, Kristian; Egodage, Kokila; Tabbone, Gilles; Ehrlich, Christian; Garetto, Anthony

2017-06-01

For defect disposition and repair verification regarding printability, AIMS™ is the state of the art measurement tool in industry. With its unique capability of capturing aerial images of photomasks it is the one method that comes closest to emulating the printing behaviour of a scanner. However for nanoimprint lithography (NIL) templates aerial images cannot be applied to evaluate the success of a repair process. Hence, for NIL defect dispositioning scanning, electron microscopy (SEM) imaging is the method of choice. In addition, it has been a standard imaging method for further root cause analysis of defects and defect review on optical photomasks which enables 2D or even 3D mask profiling at high resolutions. In recent years a trend observed in mask shops has been the automation of processes that traditionally were driven by operators. This of course has brought many advantages one of which is freeing cost intensive labour from conducting repetitive and tedious work. Furthermore, it reduces variability in processes due to different operator skill and experience levels which at the end contributes to eliminating the human factor. Taking these factors into consideration, one of the software based solutions available under the FAVOR® brand to support customer needs is the aerial image evaluation software, AIMS™ AutoAnalysis (AAA). It provides fully automated analysis of AIMS™ images and runs in parallel to measurements. This is enabled by its direct connection and communication with the AIMS™tools. As one of many positive outcomes, generating automated result reports is facilitated, standardizing the mask manufacturing workflow. Today, AAA has been successfully introduced into production at multiple customers and is supporting the workflow as described above. These trends indeed have triggered the demand for similar automation with respect to SEM measurements leading to the development of SEM AutoAnalysis (SAA). It aims towards a fully automated SEM image evaluation process utilizing a completely different algorithm due to the different nature of SEM images and aerial images. Both AAA and SAA are the building blocks towards an image evaluation suite in the mask shop industry.

Separating Business Logic from Medical Knowledge in Digital Clinical Workflows Using Business Process Model and Notation and Arden Syntax.

PubMed

de Bruin, Jeroen S; Adlassnig, Klaus-Peter; Leitich, Harald; Rappelsberger, Andrea

2018-01-01

Evidence-based clinical guidelines have a major positive effect on the physician's decision-making process. Computer-executable clinical guidelines allow for automated guideline marshalling during a clinical diagnostic process, thus improving the decision-making process. Implementation of a digital clinical guideline for the prevention of mother-to-child transmission of hepatitis B as a computerized workflow, thereby separating business logic from medical knowledge and decision-making. We used the Business Process Model and Notation language system Activiti for business logic and workflow modeling. Medical decision-making was performed by an Arden-Syntax-based medical rule engine, which is part of the ARDENSUITE software. We succeeded in creating an electronic clinical workflow for the prevention of mother-to-child transmission of hepatitis B, where institution-specific medical decision-making processes could be adapted without modifying the workflow business logic. Separation of business logic and medical decision-making results in more easily reusable electronic clinical workflows.

A PDA study management tool (SMT) utilizing wireless broadband and full DICOM viewing capability

NASA Astrophysics Data System (ADS)

Documet, Jorge; Liu, Brent; Zhou, Zheng; Huang, H. K.; Documet, Luis

2007-03-01

During the last 4 years IPI (Image Processing and Informatics) Laboratory has been developing a web-based Study Management Tool (SMT) application that allows Radiologists, Film librarians and PACS-related (Picture Archiving and Communication System) users to dynamically and remotely perform Query/Retrieve operations in a PACS network. The users utilizing a regular PDA (Personal Digital Assistant) can remotely query a PACS archive to distribute any study to an existing DICOM (Digital Imaging and Communications in Medicine) node. This application which has proven to be convenient to manage the Study Workflow [1, 2] has been extended to include a DICOM viewing capability in the PDA. With this new feature, users can take a quick view of DICOM images providing them mobility and convenience at the same time. In addition, we are extending this application to Metropolitan-Area Wireless Broadband Networks. This feature requires Smart Phones that are capable of working as a PDA and have access to Broadband Wireless Services. With the extended application to wireless broadband technology and the preview of DICOM images, the Study Management Tool becomes an even more powerful tool for clinical workflow management.

Defining the value of magnetic resonance imaging in prostate brachytherapy using time-driven activity-based costing.

PubMed

Thaker, Nikhil G; Orio, Peter F; Potters, Louis

Magnetic resonance imaging (MRI) simulation and planning for prostate brachytherapy (PBT) may deliver potential clinical benefits but at an unknown cost to the provider and healthcare system. Time-driven activity-based costing (TDABC) is an innovative bottom-up costing tool in healthcare that can be used to measure the actual consumption of resources required over the full cycle of care. TDABC analysis was conducted to compare patient-level costs for an MRI-based versus traditional PBT workflow. TDABC cost was only 1% higher for the MRI-based workflow, and utilization of MRI allowed for cost shifting from other imaging modalities, such as CT and ultrasound, to MRI during the PBT process. Future initiatives will be required to follow the costs of care over longer periods of time to determine if improvements in outcomes and toxicities with an MRI-based approach lead to lower resource utilization and spending over the long-term. Understanding provider costs will become important as healthcare reform transitions to value-based purchasing and other alternative payment models. Copyright © 2016 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

Computer-assisted image processing to detect spores from the fungus Pandora neoaphidis.

PubMed

Korsnes, Reinert; Westrum, Karin; Fløistad, Erling; Klingen, Ingeborg

2016-01-01

This contribution demonstrates an example of experimental automatic image analysis to detect spores prepared on microscope slides derived from trapping. The application is to monitor aerial spore counts of the entomopathogenic fungus Pandora neoaphidis which may serve as a biological control agent for aphids. Automatic detection of such spores can therefore play a role in plant protection. The present approach for such detection is a modification of traditional manual microscopy of prepared slides, where autonomous image recording precedes computerised image analysis. The purpose of the present image analysis is to support human visual inspection of imagery data - not to replace it. The workflow has three components:•Preparation of slides for microscopy.•Image recording.•Computerised image processing where the initial part is, as usual, segmentation depending on the actual data product. Then comes identification of blobs, calculation of principal axes of blobs, symmetry operations and projection on a three parameter egg shape space.

Research and Implementation of Key Technologies in Multi-Agent System to Support Distributed Workflow

NASA Astrophysics Data System (ADS)

Pan, Tianheng

2018-01-01

In recent years, the combination of workflow management system and Multi-agent technology is a hot research field. The problem of lack of flexibility in workflow management system can be improved by introducing multi-agent collaborative management. The workflow management system adopts distributed structure. It solves the problem that the traditional centralized workflow structure is fragile. In this paper, the agent of Distributed workflow management system is divided according to its function. The execution process of each type of agent is analyzed. The key technologies such as process execution and resource management are analyzed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mendonsa, D; Nekoogar, F; Martz, H

This document describes the functionality of every component in the DHS/IDD archival and storage hardware system shown in Fig. 1. The document describes steps by step process of image data being received at LLNL then being processed and made available to authorized personnel and collaborators. Throughout this document references will be made to one of two figures, Fig. 1 describing the elements of the architecture and the Fig. 2 describing the workflow and how the project utilizes the available hardware.

Quantitative Image Feature Engine (QIFE): an Open-Source, Modular Engine for 3D Quantitative Feature Extraction from Volumetric Medical Images.

PubMed

Echegaray, Sebastian; Bakr, Shaimaa; Rubin, Daniel L; Napel, Sandy

2017-10-06

The aim of this study was to develop an open-source, modular, locally run or server-based system for 3D radiomics feature computation that can be used on any computer system and included in existing workflows for understanding associations and building predictive models between image features and clinical data, such as survival. The QIFE exploits various levels of parallelization for use on multiprocessor systems. It consists of a managing framework and four stages: input, pre-processing, feature computation, and output. Each stage contains one or more swappable components, allowing run-time customization. We benchmarked the engine using various levels of parallelization on a cohort of CT scans presenting 108 lung tumors. Two versions of the QIFE have been released: (1) the open-source MATLAB code posted to Github, (2) a compiled version loaded in a Docker container, posted to DockerHub, which can be easily deployed on any computer. The QIFE processed 108 objects (tumors) in 2:12 (h/mm) using 1 core, and 1:04 (h/mm) hours using four cores with object-level parallelization. We developed the Quantitative Image Feature Engine (QIFE), an open-source feature-extraction framework that focuses on modularity, standards, parallelism, provenance, and integration. Researchers can easily integrate it with their existing segmentation and imaging workflows by creating input and output components that implement their existing interfaces. Computational efficiency can be improved by parallelizing execution at the cost of memory usage. Different parallelization levels provide different trade-offs, and the optimal setting will depend on the size and composition of the dataset to be processed.

Talkoot Portals: Discover, Tag, Share, and Reuse Collaborative Science Workflows (Invited)

NASA Astrophysics Data System (ADS)

Wilson, B. D.; Ramachandran, R.; Lynnes, C.

2009-12-01

A small but growing number of scientists are beginning to harness Web 2.0 technologies, such as wikis, blogs, and social tagging, as a transformative way of doing science. These technologies provide researchers easy mechanisms to critique, suggest and share ideas, data and algorithms. At the same time, large suites of algorithms for science analysis are being made available as remotely-invokable Web Services, which can be chained together to create analysis workflows. This provides the research community an unprecedented opportunity to collaborate by sharing their workflows with one another, reproducing and analyzing research results, and leveraging colleagues’ expertise to expedite the process of scientific discovery. However, wikis and similar technologies are limited to text, static images and hyperlinks, providing little support for collaborative data analysis. A team of information technology and Earth science researchers from multiple institutions have come together to improve community collaboration in science analysis by developing a customizable “software appliance” to build collaborative portals for Earth Science services and analysis workflows. The critical requirement is that researchers (not just information technologists) be able to build collaborative sites around service workflows within a few hours. We envision online communities coming together, much like Finnish “talkoot” (a barn raising), to build a shared research space. Talkoot extends a freely available, open source content management framework with a series of modules specific to Earth Science for registering, creating, managing, discovering, tagging and sharing Earth Science web services and workflows for science data processing, analysis and visualization. Users will be able to author a “science story” in shareable web notebooks, including plots or animations, backed up by an executable workflow that directly reproduces the science analysis. New services and workflows of interest will be discoverable using tag search, and advertised using “service casts” and “interest casts” (Atom feeds). Multiple science workflow systems will be plugged into the system, with initial support for UAH’s Mining Workflow Composer and the open-source Active BPEL engine, and JPL’s SciFlo engine and the VizFlow visual programming interface. With the ability to share and execute analysis workflows, Talkoot portals can be used to do collaborative science in addition to communicate ideas and results. It will be useful for different science domains, mission teams, research projects and organizations. Thus, it will help to solve the “sociological” problem of bringing together disparate groups of researchers, and the technical problem of advertising, discovering, developing, documenting, and maintaining inter-agency science workflows. The presentation will discuss the goals of and barriers to Science 2.0, the social web technologies employed in the Talkoot software appliance (e.g. CMS, social tagging, personal presence, advertising by feeds, etc.), illustrate the resulting collaborative capabilities, and show early prototypes of the web interfaces (e.g. embedded workflows).

A processing work-flow for measuring erythrocytes velocity in extended vascular networks from wide field high-resolution optical imaging data.

PubMed

Deneux, Thomas; Takerkart, Sylvain; Grinvald, Amiram; Masson, Guillaume S; Vanzetta, Ivo

2012-02-01

Comprehensive information on the spatio-temporal dynamics of the vascular response is needed to underpin the signals used in hemodynamics-based functional imaging. It has recently been shown that red blood cells (RBCs) velocity and its changes can be extracted from wide-field optical imaging recordings of intrinsic absorption changes in cortex. Here, we describe a complete processing work-flow for reliable RBC velocity estimation in cortical networks. Several pre-processing steps are implemented: image co-registration, necessary to correct for small movements of the vasculature, semi-automatic image segmentation for fast and reproducible vessel selection, reconstruction of RBC trajectories patterns for each micro-vessel, and spatio-temporal filtering to enhance the desired data characteristics. The main analysis step is composed of two robust algorithms for estimating the RBCs' velocity field. Vessel diameter and its changes are also estimated, as well as local changes in backscattered light intensity. This full processing chain is implemented with a software suite that is freely distributed. The software uses efficient data management for handling the very large data sets obtained with in vivo optical imaging. It offers a complete and user-friendly graphical user interface with visualization tools for displaying and exploring data and results. A full data simulation framework is also provided in order to optimize the performances of the algorithm with respect to several characteristics of the data. We illustrate the performance of our method in three different cases of in vivo data. We first document the massive RBC speed response evoked by a spreading depression in anesthetized rat somato-sensory cortex. Second, we show the velocity response elicited by a visual stimulation in anesthetized cat visual cortex. Finally, we report, for the first time, visually-evoked RBC speed responses in an extended vascular network in awake monkey extrastriate cortex. Copyright © 2011 Elsevier Inc. All rights reserved.

NeuroManager: a workflow analysis based simulation management engine for computational neuroscience

PubMed Central

Stockton, David B.; Santamaria, Fidel

2015-01-01

We developed NeuroManager, an object-oriented simulation management software engine for computational neuroscience. NeuroManager automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. The object-oriented approach (1) provides flexibility to adapt to a variety of neuroscience simulators, (2) simplifies the use of heterogeneous computational resources, from desktops to super computer clusters, and (3) improves tracking of simulator/simulation evolution. We implemented NeuroManager in MATLAB, a widely used engineering and scientific language, for its signal and image processing tools, prevalence in electrophysiology analysis, and increasing use in college Biology education. To design and develop NeuroManager we analyzed the workflow of simulation submission for a variety of simulators, operating systems, and computational resources, including the handling of input parameters, data, models, results, and analyses. This resulted in 22 stages of simulation submission workflow. The software incorporates progress notification, automatic organization, labeling, and time-stamping of data and results, and integrated access to MATLAB's analysis and visualization tools. NeuroManager provides users with the tools to automate daily tasks, and assists principal investigators in tracking and recreating the evolution of research projects performed by multiple people. Overall, NeuroManager provides the infrastructure needed to improve workflow, manage multiple simultaneous simulations, and maintain provenance of the potentially large amounts of data produced during the course of a research project. PMID:26528175

NeuroManager: a workflow analysis based simulation management engine for computational neuroscience.

PubMed

Stockton, David B; Santamaria, Fidel

2015-01-01

We developed NeuroManager, an object-oriented simulation management software engine for computational neuroscience. NeuroManager automates the workflow of simulation job submissions when using heterogeneous computational resources, simulators, and simulation tasks. The object-oriented approach (1) provides flexibility to adapt to a variety of neuroscience simulators, (2) simplifies the use of heterogeneous computational resources, from desktops to super computer clusters, and (3) improves tracking of simulator/simulation evolution. We implemented NeuroManager in MATLAB, a widely used engineering and scientific language, for its signal and image processing tools, prevalence in electrophysiology analysis, and increasing use in college Biology education. To design and develop NeuroManager we analyzed the workflow of simulation submission for a variety of simulators, operating systems, and computational resources, including the handling of input parameters, data, models, results, and analyses. This resulted in 22 stages of simulation submission workflow. The software incorporates progress notification, automatic organization, labeling, and time-stamping of data and results, and integrated access to MATLAB's analysis and visualization tools. NeuroManager provides users with the tools to automate daily tasks, and assists principal investigators in tracking and recreating the evolution of research projects performed by multiple people. Overall, NeuroManager provides the infrastructure needed to improve workflow, manage multiple simultaneous simulations, and maintain provenance of the potentially large amounts of data produced during the course of a research project.

Uncertainty in training image-based inversion of hydraulic head data constrained to ERT data: Workflow and case study

NASA Astrophysics Data System (ADS)

Hermans, Thomas; Nguyen, Frédéric; Caers, Jef

2015-07-01

In inverse problems, investigating uncertainty in the posterior distribution of model parameters is as important as matching data. In recent years, most efforts have focused on techniques to sample the posterior distribution with reasonable computational costs. Within a Bayesian context, this posterior depends on the prior distribution. However, most of the studies ignore modeling the prior with realistic geological uncertainty. In this paper, we propose a workflow inspired by a Popper-Bayes philosophy that data should first be used to falsify models, then only be considered for matching. We propose a workflow consisting of three steps: (1) in defining the prior, we interpret multiple alternative geological scenarios from literature (architecture of facies) and site-specific data (proportions of facies). Prior spatial uncertainty is modeled using multiple-point geostatistics, where each scenario is defined using a training image. (2) We validate these prior geological scenarios by simulating electrical resistivity tomography (ERT) data on realizations of each scenario and comparing them to field ERT in a lower dimensional space. In this second step, the idea is to probabilistically falsify scenarios with ERT, meaning that scenarios which are incompatible receive an updated probability of zero while compatible scenarios receive a nonzero updated belief. (3) We constrain the hydrogeological model with hydraulic head and ERT using a stochastic search method. The workflow is applied to a synthetic and a field case studies in an alluvial aquifer. This study highlights the importance of considering and estimating prior uncertainty (without data) through a process of probabilistic falsification.

Sentinel-2 ArcGIS Tool for Environmental Monitoring

NASA Astrophysics Data System (ADS)

Plesoianu, Alin; Cosmin Sandric, Ionut; Anca, Paula; Vasile, Alexandru; Calugaru, Andreea; Vasile, Cristian; Zavate, Lucian

2017-04-01

This paper addresses one of the biggest challenges regarding Sentinel-2 data, related to the need of an efficient tool to access and process the large collection of images that are available. Consequently, developing a tool for the automation of Sentinel-2 data analysis is the most immediate need. We developed a series of tools for the automation of Sentinel-2 data download and processing for vegetation health monitoring. The tools automatically perform the following operations: downloading image tiles from ESA's Scientific Hub or other venders (Amazon), pre-processing of the images to extract the 10-m bands, creating image composites, applying a series of vegetation indexes (NDVI, OSAVI, etc.) and performing change detection analyses on different temporal data sets. All of these tools run in a dynamic way in the ArcGIS Platform, without the need of creating intermediate datasets (rasters, layers), as the images are processed on-the-fly in order to avoid data duplication. Finally, they allow complete integration with the ArcGIS environment and workflows

WE-H-207B-00: MRgRT

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

2016-06-15

In recent years, steady progress has been made towards the implementation of MRI in external beam radiation therapy for processes ranging from treatment simulation to in-room guidance. Novel procedures relying mostly on MR data are currently implemented in the clinic. This session will cover topics such as (a) commissioning and quality control of the MR in-room imagers and simulators specific to RT, (b) treatment planning requirements, constraints and challenges when dealing with various MR data, (c) quantification of organ motion with an emphasis on treatment delivery guidance, and (d) MR-driven strategies for adaptive RT workflows. The content of the sessionmore » was chosen to address both educational and practical key aspects of MR guidance. Learning Objectives: Good understanding of MR testing recommended for in-room MR imaging as well as image data validation for RT chain (e.g. image transfer, filtering for consistency, spatial accuracy, manipulation for task specific); Familiarity with MR-based planning procedures: motivation, core workflow requirements, current status, challenges; Overview of the current methods for the quantification of organ motion; Discussion on approaches for adaptive treatment planning and delivery. T. Stanescu - License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image system-related distortions.; T. Stanescu, N/A.« less

WE-H-207B-03: MRI Guidance in the Radiation Therapy Clinic: Site-Specific Discussions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shang, C.

2016-06-15

In recent years, steady progress has been made towards the implementation of MRI in external beam radiation therapy for processes ranging from treatment simulation to in-room guidance. Novel procedures relying mostly on MR data are currently implemented in the clinic. This session will cover topics such as (a) commissioning and quality control of the MR in-room imagers and simulators specific to RT, (b) treatment planning requirements, constraints and challenges when dealing with various MR data, (c) quantification of organ motion with an emphasis on treatment delivery guidance, and (d) MR-driven strategies for adaptive RT workflows. The content of the sessionmore » was chosen to address both educational and practical key aspects of MR guidance. Learning Objectives: Good understanding of MR testing recommended for in-room MR imaging as well as image data validation for RT chain (e.g. image transfer, filtering for consistency, spatial accuracy, manipulation for task specific); Familiarity with MR-based planning procedures: motivation, core workflow requirements, current status, challenges; Overview of the current methods for the quantification of organ motion; Discussion on approaches for adaptive treatment planning and delivery. T. Stanescu - License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image system-related distortions.; T. Stanescu, N/A.« less

WE-H-207B-04: Strategies for Adaptive RT

DOE Office of Scientific and Technical Information (OSTI.GOV)

Green, O.

2016-06-15

In recent years, steady progress has been made towards the implementation of MRI in external beam radiation therapy for processes ranging from treatment simulation to in-room guidance. Novel procedures relying mostly on MR data are currently implemented in the clinic. This session will cover topics such as (a) commissioning and quality control of the MR in-room imagers and simulators specific to RT, (b) treatment planning requirements, constraints and challenges when dealing with various MR data, (c) quantification of organ motion with an emphasis on treatment delivery guidance, and (d) MR-driven strategies for adaptive RT workflows. The content of the sessionmore » was chosen to address both educational and practical key aspects of MR guidance. Learning Objectives: Good understanding of MR testing recommended for in-room MR imaging as well as image data validation for RT chain (e.g. image transfer, filtering for consistency, spatial accuracy, manipulation for task specific); Familiarity with MR-based planning procedures: motivation, core workflow requirements, current status, challenges; Overview of the current methods for the quantification of organ motion; Discussion on approaches for adaptive treatment planning and delivery. T. Stanescu - License agreement with Modus Medical Devices to develop a phantom for the quantification of MR image system-related distortions.; T. Stanescu, N/A.« less

The standard-based open workflow system in GeoBrain (Invited)

NASA Astrophysics Data System (ADS)

Di, L.; Yu, G.; Zhao, P.; Deng, M.

2013-12-01

GeoBrain is an Earth science Web-service system developed and operated by the Center for Spatial Information Science and Systems, George Mason University. In GeoBrain, a standard-based open workflow system has been implemented to accommodate the automated processing of geospatial data through a set of complex geo-processing functions for advanced production generation. The GeoBrain models the complex geoprocessing at two levels, the conceptual and concrete. At the conceptual level, the workflows exist in the form of data and service types defined by ontologies. The workflows at conceptual level are called geo-processing models and cataloged in GeoBrain as virtual product types. A conceptual workflow is instantiated into a concrete, executable workflow when a user requests a product that matches a virtual product type. Both conceptual and concrete workflows are encoded in Business Process Execution Language (BPEL). A BPEL workflow engine, called BPELPower, has been implemented to execute the workflow for the product generation. A provenance capturing service has been implemented to generate the ISO 19115-compliant complete product provenance metadata before and after the workflow execution. The generation of provenance metadata before the workflow execution allows users to examine the usability of the final product before the lengthy and expensive execution takes place. The three modes of workflow executions defined in the ISO 19119, transparent, translucent, and opaque, are available in GeoBrain. A geoprocessing modeling portal has been developed to allow domain experts to develop geoprocessing models at the type level with the support of both data and service/processing ontologies. The geoprocessing models capture the knowledge of the domain experts and are become the operational offering of the products after a proper peer review of models is conducted. An automated workflow composition has been experimented successfully based on ontologies and artificial intelligence technology. The GeoBrain workflow system has been used in multiple Earth science applications, including the monitoring of global agricultural drought, the assessment of flood damage, the derivation of national crop condition and progress information, and the detection of nuclear proliferation facilities and events.

Technical Note: SCUDA: A software platform for cumulative dose assessment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, Seyoun; McNutt, Todd; Quon, Harry

Purpose: Accurate tracking of anatomical changes and computation of actually delivered dose to the patient are critical for successful adaptive radiation therapy (ART). Additionally, efficient data management and fast processing are practically important for the adoption in clinic as ART involves a large amount of image and treatment data. The purpose of this study was to develop an accurate and efficient Software platform for CUmulative Dose Assessment (SCUDA) that can be seamlessly integrated into the clinical workflow. Methods: SCUDA consists of deformable image registration (DIR), segmentation, dose computation modules, and a graphical user interface. It is connected to our imagemore » PACS and radiotherapy informatics databases from which it automatically queries/retrieves patient images, radiotherapy plan, beam data, and daily treatment information, thus providing an efficient and unified workflow. For accurate registration of the planning CT and daily CBCTs, the authors iteratively correct CBCT intensities by matching local intensity histograms during the DIR process. Contours of the target tumor and critical structures are then propagated from the planning CT to daily CBCTs using the computed deformations. The actual delivered daily dose is computed using the registered CT and patient setup information by a superposition/convolution algorithm, and accumulated using the computed deformation fields. Both DIR and dose computation modules are accelerated by a graphics processing unit. Results: The cumulative dose computation process has been validated on 30 head and neck (HN) cancer cases, showing 3.5 ± 5.0 Gy (mean±STD) absolute mean dose differences between the planned and the actually delivered doses in the parotid glands. On average, DIR, dose computation, and segmentation take 20 s/fraction and 17 min for a 35-fraction treatment including additional computation for dose accumulation. Conclusions: The authors developed a unified software platform that provides accurate and efficient monitoring of anatomical changes and computation of actually delivered dose to the patient, thus realizing an efficient cumulative dose computation workflow. Evaluation on HN cases demonstrated the utility of our platform for monitoring the treatment quality and detecting significant dosimetric variations that are keys to successful ART.« less

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters.

PubMed

Cheng, Gong; Lu, Quan; Ma, Ling; Zhang, Guocai; Xu, Liang; Zhou, Zongshan

2017-01-01

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily.

BGDMdocker: a Docker workflow for data mining and visualization of bacterial pan-genomes and biosynthetic gene clusters

PubMed Central

Cheng, Gong; Zhang, Guocai; Xu, Liang

2017-01-01

Recently, Docker technology has received increasing attention throughout the bioinformatics community. However, its implementation has not yet been mastered by most biologists; accordingly, its application in biological research has been limited. In order to popularize this technology in the field of bioinformatics and to promote the use of publicly available bioinformatics tools, such as Dockerfiles and Images from communities, government sources, and private owners in the Docker Hub Registry and other Docker-based resources, we introduce here a complete and accurate bioinformatics workflow based on Docker. The present workflow enables analysis and visualization of pan-genomes and biosynthetic gene clusters of bacteria. This provides a new solution for bioinformatics mining of big data from various publicly available biological databases. The present step-by-step guide creates an integrative workflow through a Dockerfile to allow researchers to build their own Image and run Container easily. PMID:29204317

The Nasa-Isro SAR Mission Science Data Products and Processing Workflows

NASA Astrophysics Data System (ADS)

Rosen, P. A.; Agram, P. S.; Lavalle, M.; Cohen, J.; Buckley, S.; Kumar, R.; Misra-Ray, A.; Ramanujam, V.; Agarwal, K. M.

2017-12-01

The NASA-ISRO SAR (NISAR) Mission is currently in the development phase and in the process of specifying its suite of data products and algorithmic workflows, responding to inputs from the NISAR Science and Applications Team. NISAR will provide raw data (Level 0), full-resolution complex imagery (Level 1), and interferometric and polarimetric image products (Level 2) for the entire data set, in both natural radar and geocoded coordinates. NASA and ISRO are coordinating the formats, meta-data layers, and algorithms for these products, for both the NASA-provided L-band radar and the ISRO-provided S-band radar. Higher level products will be also be generated for the purpose of calibration and validation, over large areas of Earth, including tectonic plate boundaries, ice sheets and sea-ice, and areas of ecosystem disturbance and change. This level of comprehensive product generation has been unprecedented for SAR missions in the past, and leads to storage processing challenges for the production system and the archive center. Further, recognizing the potential to support applications that require low latency product generation and delivery, the NISAR team is optimizing the entire end-to-end ground data system for such response, including exploring the advantages of cloud-based processing, algorithmic acceleration using GPUs, and on-demand processing schemes that minimize computational and transport costs, but allow rapid delivery to science and applications users. This paper will review the current products, workflows, and discuss the scientific and operational trade-space of mission capabilities.

Accessible high performance computing solutions for near real-time image processing for time critical applications

NASA Astrophysics Data System (ADS)

Bielski, Conrad; Lemoine, Guido; Syryczynski, Jacek

2009-09-01

High Performance Computing (HPC) hardware solutions such as grid computing and General Processing on a Graphics Processing Unit (GPGPU) are now accessible to users with general computing needs. Grid computing infrastructures in the form of computing clusters or blades are becoming common place and GPGPU solutions that leverage the processing power of the video card are quickly being integrated into personal workstations. Our interest in these HPC technologies stems from the need to produce near real-time maps from a combination of pre- and post-event satellite imagery in support of post-disaster management. Faster processing provides a twofold gain in this situation: 1. critical information can be provided faster and 2. more elaborate automated processing can be performed prior to providing the critical information. In our particular case, we test the use of the PANTEX index which is based on analysis of image textural measures extracted using anisotropic, rotation-invariant GLCM statistics. The use of this index, applied in a moving window, has been shown to successfully identify built-up areas in remotely sensed imagery. Built-up index image masks are important input to the structuring of damage assessment interpretation because they help optimise the workload. The performance of computing the PANTEX workflow is compared on two different HPC hardware architectures: (1) a blade server with 4 blades, each having dual quad-core CPUs and (2) a CUDA enabled GPU workstation. The reference platform is a dual CPU-quad core workstation and the PANTEX workflow total computing time is measured. Furthermore, as part of a qualitative evaluation, the differences in setting up and configuring various hardware solutions and the related software coding effort is presented.

SU-F-T-251: The Quality Assurance for the Heavy Patient Load Department in the Developing Country: The Primary Experience of An Entire Workflow QA Process Management in Radiotherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xie, J; Wang, J; Peng, J

Purpose: To implement an entire workflow quality assurance (QA) process in the radiotherapy department and to reduce the error rates of radiotherapy based on the entire workflow management in the developing country. Methods: The entire workflow QA process management starts from patient registration to the end of last treatment including all steps through the entire radiotherapy process. Error rate of chartcheck is used to evaluate the the entire workflow QA process. Two to three qualified senior medical physicists checked the documents before the first treatment fraction of every patient. Random check of the treatment history during treatment was also performed.more » A total of around 6000 patients treatment data before and after implementing the entire workflow QA process were compared from May, 2014 to December, 2015. Results: A systemic checklist was established. It mainly includes patient’s registration, treatment plan QA, information exporting to OIS(Oncology Information System), documents of treatment QAand QA of the treatment history. The error rate derived from the chart check decreases from 1.7% to 0.9% after our the entire workflow QA process. All checked errors before the first treatment fraction were corrected as soon as oncologist re-confirmed them and reinforce staff training was accordingly followed to prevent those errors. Conclusion: The entire workflow QA process improved the safety, quality of radiotherapy in our department and we consider that our QA experience can be applicable for the heavily-loaded radiotherapy departments in developing country.« less

BPELPower—A BPEL execution engine for geospatial web services

NASA Astrophysics Data System (ADS)

Yu, Genong (Eugene); Zhao, Peisheng; Di, Liping; Chen, Aijun; Deng, Meixia; Bai, Yuqi

2012-10-01

The Business Process Execution Language (BPEL) has become a popular choice for orchestrating and executing workflows in the Web environment. As one special kind of scientific workflow, geospatial Web processing workflows are data-intensive, deal with complex structures in data and geographic features, and execute automatically with limited human intervention. To enable the proper execution and coordination of geospatial workflows, a specially enhanced BPEL execution engine is required. BPELPower was designed, developed, and implemented as a generic BPEL execution engine with enhancements for executing geospatial workflows. The enhancements are especially in its capabilities in handling Geography Markup Language (GML) and standard geospatial Web services, such as the Web Processing Service (WPS) and the Web Feature Service (WFS). BPELPower has been used in several demonstrations over the decade. Two scenarios were discussed in detail to demonstrate the capabilities of BPELPower. That study showed a standard-compliant, Web-based approach for properly supporting geospatial processing, with the only enhancement at the implementation level. Pattern-based evaluation and performance improvement of the engine are discussed: BPELPower directly supports 22 workflow control patterns and 17 workflow data patterns. In the future, the engine will be enhanced with high performance parallel processing and broad Web paradigms.

A characterization of workflow management systems for extreme-scale applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ferreira da Silva, Rafael; Filgueira, Rosa; Pietri, Ilia

We present that the automation of the execution of computational tasks is at the heart of improving scientific productivity. Over the last years, scientific workflows have been established as an important abstraction that captures data processing and computation of large and complex scientific applications. By allowing scientists to model and express entire data processing steps and their dependencies, workflow management systems relieve scientists from the details of an application and manage its execution on a computational infrastructure. As the resource requirements of today’s computational and data science applications that process vast amounts of data keep increasing, there is a compellingmore » case for a new generation of advances in high-performance computing, commonly termed as extreme-scale computing, which will bring forth multiple challenges for the design of workflow applications and management systems. This paper presents a novel characterization of workflow management systems using features commonly associated with extreme-scale computing applications. We classify 15 popular workflow management systems in terms of workflow execution models, heterogeneous computing environments, and data access methods. Finally, the paper also surveys workflow applications and identifies gaps for future research on the road to extreme-scale workflows and management systems.« less

A characterization of workflow management systems for extreme-scale applications

DOE PAGES

Ferreira da Silva, Rafael; Filgueira, Rosa; Pietri, Ilia; ...

2017-02-16

We present that the automation of the execution of computational tasks is at the heart of improving scientific productivity. Over the last years, scientific workflows have been established as an important abstraction that captures data processing and computation of large and complex scientific applications. By allowing scientists to model and express entire data processing steps and their dependencies, workflow management systems relieve scientists from the details of an application and manage its execution on a computational infrastructure. As the resource requirements of today’s computational and data science applications that process vast amounts of data keep increasing, there is a compellingmore » case for a new generation of advances in high-performance computing, commonly termed as extreme-scale computing, which will bring forth multiple challenges for the design of workflow applications and management systems. This paper presents a novel characterization of workflow management systems using features commonly associated with extreme-scale computing applications. We classify 15 popular workflow management systems in terms of workflow execution models, heterogeneous computing environments, and data access methods. Finally, the paper also surveys workflow applications and identifies gaps for future research on the road to extreme-scale workflows and management systems.« less

MO-E-BRC-01: Online Adaptive MR-Guided RT: Workflow and Clinical Implementation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kashani, R.

Online adaptive radiation therapy has the potential to ensure delivery of optimal treatment to the patient by accounting for anatomical and potentially functional changes that occur from one fraction to the next and over the course of treatment. While on-line adaptive RT (ART) has been a topic of many publications, discussions, and research, it has until very recently remained largely a concept and not a practical implementation. However, recent advances in on-table imaging, use of deformable image registration for contour generation and dose tracking, faster and more efficient plan optimization, as well as fast quality assurance method has enabled themore » implementation of ART in the clinic in the past couple of years. The introduction of these tools into routine clinical use requires many considerations and progressive knowledge to understand how processes that have historically taken hours/days to complete can now be done in less than 30 minutes. This session will discuss considerations to perform real time contouring, planning and patient specific QA, as well as a practical workflow and the required resources. Learning Objectives: To understand the difficulties, challenges and available technologies for online adaptive RT. To understand how to implement online adaptive therapy in a clinical environment and to understand the workflow and resources required. To understand the limitations and sources of uncertainty in the online adaptive process I have research funding from ViewRay Inc. and Philips Medical Systems.; R. Kashani, I have research funding from ViewRay Inc. and Philips Medical Systems.; X. Li, Research supported by Elekta Inc.« less

Quality Metadata Management for Geospatial Scientific Workflows: from Retrieving to Assessing with Online Tools

NASA Astrophysics Data System (ADS)

Leibovici, D. G.; Pourabdollah, A.; Jackson, M.

2011-12-01

Experts and decision-makers use or develop models to monitor global and local changes of the environment. Their activities require the combination of data and processing services in a flow of operations and spatial data computations: a geospatial scientific workflow. The seamless ability to generate, re-use and modify a geospatial scientific workflow is an important requirement but the quality of outcomes is equally much important [1]. Metadata information attached to the data and processes, and particularly their quality, is essential to assess the reliability of the scientific model that represents a workflow [2]. Managing tools, dealing with qualitative and quantitative metadata measures of the quality associated with a workflow, are, therefore, required for the modellers. To ensure interoperability, ISO and OGC standards [3] are to be adopted, allowing for example one to define metadata profiles and to retrieve them via web service interfaces. However these standards need a few extensions when looking at workflows, particularly in the context of geoprocesses metadata. We propose to fill this gap (i) at first through the provision of a metadata profile for the quality of processes, and (ii) through providing a framework, based on XPDL [4], to manage the quality information. Web Processing Services are used to implement a range of metadata analyses on the workflow in order to evaluate and present quality information at different levels of the workflow. This generates the metadata quality, stored in the XPDL file. The focus is (a) on the visual representations of the quality, summarizing the retrieved quality information either from the standardized metadata profiles of the components or from non-standard quality information e.g., Web 2.0 information, and (b) on the estimated qualities of the outputs derived from meta-propagation of uncertainties (a principle that we have introduced [5]). An a priori validation of the future decision-making supported by the outputs of the workflow once run, is then provided using the meta-propagated qualities, obtained without running the workflow [6], together with the visualization pointing out the need to improve the workflow with better data or better processes on the workflow graph itself. [1] Leibovici, DG, Hobona, G Stock, K Jackson, M (2009) Qualifying geospatial workfow models for adaptive controlled validity and accuracy. In: IEEE 17th GeoInformatics, 1-5 [2] Leibovici, DG, Pourabdollah, A (2010a) Workflow Uncertainty using a Metamodel Framework and Metadata for Data and Processes. OGC TC/PC Meetings, September 2010, Toulouse, France [3] OGC (2011) www.opengeospatial.org [4] XPDL (2008) Workflow Process Definition Interface - XML Process Definition Language.Workflow Management Coalition, Document WfMC-TC-1025, 2008 [5] Leibovici, DG Pourabdollah, A Jackson, M (2011) Meta-propagation of Uncertainties for Scientific Workflow Management in Interoperable Spatial Data Infrastructures. In: Proceedings of the European Geosciences Union (EGU2011), April 2011, Austria [6] Pourabdollah, A Leibovici, DG Jackson, M (2011) MetaPunT: an Open Source tool for Meta-Propagation of uncerTainties in Geospatial Processing. In: Proceedings of OSGIS2011, June 2011, Nottingham, UK

Mathematical imaging methods for mitosis analysis in live-cell phase contrast microscopy.

PubMed

Grah, Joana Sarah; Harrington, Jennifer Alison; Koh, Siang Boon; Pike, Jeremy Andrew; Schreiner, Alexander; Burger, Martin; Schönlieb, Carola-Bibiane; Reichelt, Stefanie

2017-02-15

In this paper we propose a workflow to detect and track mitotic cells in time-lapse microscopy image sequences. In order to avoid the requirement for cell lines expressing fluorescent markers and the associated phototoxicity, phase contrast microscopy is often preferred over fluorescence microscopy in live-cell imaging. However, common specific image characteristics complicate image processing and impede use of standard methods. Nevertheless, automated analysis is desirable due to manual analysis being subjective, biased and extremely time-consuming for large data sets. Here, we present the following workflow based on mathematical imaging methods. In the first step, mitosis detection is performed by means of the circular Hough transform. The obtained circular contour subsequently serves as an initialisation for the tracking algorithm based on variational methods. It is sub-divided into two parts: in order to determine the beginning of the whole mitosis cycle, a backwards tracking procedure is performed. After that, the cell is tracked forwards in time until the end of mitosis. As a result, the average of mitosis duration and ratios of different cell fates (cell death, no division, division into two or more daughter cells) can be measured and statistics on cell morphologies can be obtained. All of the tools are featured in the user-friendly MATLAB®Graphical User Interface MitosisAnalyser. Copyright © 2017. Published by Elsevier Inc.

Wireless-PDA-controlled image workflow from PACS: the next trend in the health care enterprise?

NASA Astrophysics Data System (ADS)

Erberich, Stephan G.; Documet, Jorge; Zhou, Michael Z.; Cao, Fei; Liu, Brent J.; Mogel, Greg T.; Huang, H. K.

2003-05-01

Image workflow in today's Picture Archiving and Communication Systems (PACS) is controlled from fixed Display Workstations (DW) using proprietary control interfaces. A remote access to the Hospital Information System (HIS) and Radiology Information System (RIS) for urgent patient information retrieval does not exist or gradually become available. The lack for remote access and workflow control for HIS and RIS is especially true when it comes to medical images of a PACS on Department or Hospital level. As images become more complex and data sizes expand rapidly with new image techniques like functional MRI, Mammography or routine spiral CT to name a few, the access and manageability becomes an important issue. Long image downloads or incomplete work lists cannot be tolerated in a busy health care environment. In addition, the domain of the PACS is no longer limited to the imaging department and PACS is also being used in the ER and emergency care units. Thus a prompt and secure access and manageability not only by the radiologist, but also from the physician becomes crucial to optimally utilize the PACS in the health care enterprise of the new millennium. The purpose of this paper is to introduce a concept and its implementation of a remote access and workflow control of the PACS combining wireless, Internet and Internet2 technologies. A wireless device, the Personal Digital Assistant (PDA), is used to communicate to a PACS web server that acts as a gateway controlling the commands for which the user has access to the PACS server. The commands implemented for this test-bed are query/retrieve of the patient list and study list including modality, examination, series and image selection and pushing any list items to a selected DW on the PACS network.

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research.

PubMed

Yaniv, Ziv; Lowekamp, Bradley C; Johnson, Hans J; Beare, Richard

2018-06-01

Modern scientific endeavors increasingly require team collaborations to construct and interpret complex computational workflows. This work describes an image-analysis environment that supports the use of computational tools that facilitate reproducible research and support scientists with varying levels of software development skills. The Jupyter notebook web application is the basis of an environment that enables flexible, well-documented, and reproducible workflows via literate programming. Image-analysis software development is made accessible to scientists with varying levels of programming experience via the use of the SimpleITK toolkit, a simplified interface to the Insight Segmentation and Registration Toolkit. Additional features of the development environment include user friendly data sharing using online data repositories and a testing framework that facilitates code maintenance. SimpleITK provides a large number of examples illustrating educational and research-oriented image analysis workflows for free download from GitHub under an Apache 2.0 license: github.com/InsightSoftwareConsortium/SimpleITK-Notebooks .

Approach to implementing a DICOM network: incorporate both economics and workflow adaptation

NASA Astrophysics Data System (ADS)

Beaver, S. Merritt; Sippel-Schmidt, Teresa M.

1995-05-01

This paper describes an approach to aide in the decision-making process for the justification and design of a digital image and information management system. It identifies key technical and clinical issues that need to be addressed by a healthcare institution during this process. Some issues identified here are very controversial and may take months or years for a department to determine solutions which meet their specific staffing, financial, and technical needs.

Navigation concepts for magnetic resonance imaging-guided musculoskeletal interventions.

PubMed

Busse, Harald; Kahn, Thomas; Moche, Michael

2011-08-01

Image-guided musculoskeletal (MSK) interventions are a widely used alternative to open surgical procedures for various pathological findings in different body regions. They traditionally involve one of the established x-ray imaging techniques (radiography, fluoroscopy, computed tomography) or ultrasound scanning. Over the last decades, magnetic resonance imaging (MRI) has evolved into one of the most powerful diagnostic tools for nearly the whole body and has therefore been increasingly considered for interventional guidance as well.The strength of MRI for MSK applications is a combination of well-known general advantages, such as multiplanar and functional imaging capabilities, wide choice of tissue contrasts, and absence of ionizing radiation, as well as a number of MSK-specific factors, for example, the excellent depiction of soft-tissue tumors, nonosteolytic bone changes, and bone marrow lesions. On the downside, the magnetic resonance-compatible equipment needed, restricted space in the magnet, longer imaging times, and the more complex workflow have so far limited the number of MSK procedures under MRI guidance.Navigation solutions are generally a natural extension of any interventional imaging system, in particular, because powerful hardware and software for image processing have become routinely available. They help to identify proper access paths, provide accurate feedback on the instrument positions, facilitate the workflow in an MRI environment, and ultimately contribute to procedural safety and success.The purposes of this work were to describe some basic concepts and devices for MRI guidance of MSK procedures and to discuss technical and clinical achievements and challenges for some selected implementations.

A novel approach to optimize workflow in grid-based teleradiology applications.

PubMed

Yılmaz, Ayhan Ozan; Baykal, Nazife

2016-01-01

This study proposes an infrastructure with a reporting workflow optimization algorithm (RWOA) in order to interconnect facilities, reporting units and radiologists on a single access interface, to increase the efficiency of the reporting process by decreasing the medical report turnaround time and to increase the quality of medical reports by determining the optimum match between the inspection and radiologist in terms of subspecialty, workload and response time. Workflow centric network architecture with an enhanced caching, querying and retrieving mechanism is implemented by seamlessly integrating Grid Agent and Grid Manager to conventional digital radiology systems. The inspection and radiologist attributes are modelled using a hierarchical ontology structure. Attribute preferences rated by radiologists and technical experts are formed into reciprocal matrixes and weights for entities are calculated utilizing Analytic Hierarchy Process (AHP). The assignment alternatives are processed by relation-based semantic matching (RBSM) and Integer Linear Programming (ILP). The results are evaluated based on both real case applications and simulated process data in terms of subspecialty, response time and workload success rates. Results obtained using simulated data are compared with the outcomes obtained by applying Round Robin, Shortest Queue and Random distribution policies. The proposed algorithm is also applied to a real case teleradiology application process data where medical reporting workflow was performed based on manual assignments by the chief radiologist for 6225 inspections. RBSM gives the highest subspecialty success rate and integrating ILP with RBSM ratings as RWOA provides a better response time and workload distribution success rate. RWOA based image delivery also prevents bandwidth, storage or hardware related stuck and latencies. When compared with a real case teleradiology application where inspection assignments were performed manually, the proposed solution was found to increase the experience success rate by 13.25%, workload success rate by 63.76% and response time success rate by 120%. The total response time in the real case application data was improved by 22.39%. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Workflow opportunities using JPEG 2000

NASA Astrophysics Data System (ADS)

Foshee, Scott

2002-11-01

JPEG 2000 is a new image compression standard from ISO/IEC JTC1 SC29 WG1, the Joint Photographic Experts Group (JPEG) committee. Better thought of as a sibling to JPEG rather than descendant, the JPEG 2000 standard offers wavelet based compression as well as companion file formats and related standardized technology. This paper examines the JPEG 2000 standard for features in four specific areas-compression, file formats, client-server, and conformance/compliance that enable image workflows.

Process improvement for the safe delivery of multidisciplinary-executed treatments-A case in Y-90 microspheres therapy.

PubMed

Cai, Bin; Altman, Michael B; Garcia-Ramirez, Jose; LaBrash, Jason; Goddu, S Murty; Mutic, Sasa; Parikh, Parag J; Olsen, Jeffrey R; Saad, Nael; Zoberi, Jacqueline E

To develop a safe and robust workflow for yttrium-90 (Y-90) radioembolization procedures in a multidisciplinary team environment. A generalized Define-Measure-Analyze-Improve-Control (DMAIC)-based approach to process improvement was applied to a Y-90 radioembolization workflow. In the first DMAIC cycle, events with the Y-90 workflow were defined and analyzed. To improve the workflow, a web-based interactive electronic white board (EWB) system was adopted as the central communication platform and information processing hub. The EWB-based Y-90 workflow then underwent a second DMAIC cycle. Out of 245 treatments, three misses that went undetected until treatment initiation were recorded over a period of 21 months, and root-cause-analysis was performed to determine causes of each incident and opportunities for improvement. The EWB-based Y-90 process was further improved via new rules to define reliable sources of information as inputs into the planning process, as well as new check points to ensure this information was communicated correctly throughout the process flow. After implementation of the revised EWB-based Y-90 workflow, after two DMAIC-like cycles, there were zero misses out of 153 patient treatments in 1 year. The DMAIC-based approach adopted here allowed the iterative development of a robust workflow to achieve an adaptable, event-minimizing planning process despite a complex setting which requires the participation of multiple teams for Y-90 microspheres therapy. Implementation of such a workflow using the EWB or similar platform with a DMAIC-based process improvement approach could be expanded to other treatment procedures, especially those requiring multidisciplinary management. Copyright © 2016 American Brachytherapy Society. Published by Elsevier Inc. All rights reserved.

Process-Structure Linkages Using a Data Science Approach: Application to Simulated Additive Manufacturing Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Popova, Evdokia; Rodgers, Theron M.; Gong, Xinyi

A novel data science workflow is developed and demonstrated to extract process-structure linkages (i.e., reduced-order model) for microstructure evolution problems when the final microstructure depends on (simulation or experimental) processing parameters. Our workflow consists of four main steps: data pre-processing, microstructure quantification, dimensionality reduction, and extraction/validation of process-structure linkages. These methods that can be employed within each step vary based on the type and amount of available data. In this paper, this data-driven workflow is applied to a set of synthetic additive manufacturing microstructures obtained using the Potts-kinetic Monte Carlo (kMC) approach. Additive manufacturing techniques inherently produce complex microstructures thatmore » can vary significantly with processing conditions. Using the developed workflow, a low-dimensional data-driven model was established to correlate process parameters with the predicted final microstructure. In addition, the modular workflows developed and presented in this work facilitate easy dissemination and curation by the broader community.« less

Process-Structure Linkages Using a Data Science Approach: Application to Simulated Additive Manufacturing Data

DOE PAGES

Popova, Evdokia; Rodgers, Theron M.; Gong, Xinyi; ...

2017-03-13

A novel data science workflow is developed and demonstrated to extract process-structure linkages (i.e., reduced-order model) for microstructure evolution problems when the final microstructure depends on (simulation or experimental) processing parameters. Our workflow consists of four main steps: data pre-processing, microstructure quantification, dimensionality reduction, and extraction/validation of process-structure linkages. These methods that can be employed within each step vary based on the type and amount of available data. In this paper, this data-driven workflow is applied to a set of synthetic additive manufacturing microstructures obtained using the Potts-kinetic Monte Carlo (kMC) approach. Additive manufacturing techniques inherently produce complex microstructures thatmore » can vary significantly with processing conditions. Using the developed workflow, a low-dimensional data-driven model was established to correlate process parameters with the predicted final microstructure. In addition, the modular workflows developed and presented in this work facilitate easy dissemination and curation by the broader community.« less

Semi-automatic mapping of fault rocks on a Digital Outcrop Model, Gole Larghe Fault Zone (Southern Alps, Italy)

NASA Astrophysics Data System (ADS)

Mittempergher, Silvia; Vho, Alice; Bistacchi, Andrea

2016-04-01

A quantitative analysis of fault-rock distribution in outcrops of exhumed fault zones is of fundamental importance for studies of fault zone architecture, fault and earthquake mechanics, and fluid circulation. We present a semi-automatic workflow for fault-rock mapping on a Digital Outcrop Model (DOM), developed on the Gole Larghe Fault Zone (GLFZ), a well exposed strike-slip fault in the Adamello batholith (Italian Southern Alps). The GLFZ has been exhumed from ca. 8-10 km depth, and consists of hundreds of individual seismogenic slip surfaces lined by green cataclasites (crushed wall rocks cemented by the hydrothermal epidote and K-feldspar) and black pseudotachylytes (solidified frictional melts, considered as a marker for seismic slip). A digital model of selected outcrop exposures was reconstructed with photogrammetric techniques, using a large number of high resolution digital photographs processed with VisualSFM software. The resulting DOM has a resolution up to 0.2 mm/pixel. Most of the outcrop was imaged using images each one covering a 1 x 1 m2 area, while selected structural features, such as sidewall ripouts or stepovers, were covered with higher-resolution images covering 30 x 40 cm2 areas.Image processing algorithms were preliminarily tested using the ImageJ-Fiji package, then a workflow in Matlab was developed to process a large collection of images sequentially. Particularly in detailed 30 x 40 cm images, cataclasites and hydrothermal veins were successfully identified using spectral analysis in RGB and HSV color spaces. This allows mapping the network of cataclasites and veins which provided the pathway for hydrothermal fluid circulation, and also the volume of mineralization, since we are able to measure the thickness of cataclasites and veins on the outcrop surface. The spectral signature of pseudotachylyte veins is indistinguishable from that of biotite grains in the wall rock (tonalite), so we tested morphological analysis tools to discriminate them with respect to biotite. In higher resolution images this could be performed using circularity and size thresholds, however this could not be easily implemented in an automated procedure since the thresholds must be varied by the interpreter almost for each image. In 1 x 1 m images the resolution is generally too low to distinguish cataclasite and pseudotachylyte, so most of the time fault rocks were treated together. For this analysis we developed a fully automated workflow that, after applying noise correction, classification and skeletonization algorithms, returns labeled edge images of fault segments together with vector polylines associated to edge properties. Vector and edge properties represent a useful format to perform further quantitative analysis, for instance for classifying fault segments based on structural criteria, detect continuous fault traces, and detect the kind of termination of faults/fractures. This approach allows to collect statistically relevant datasets useful for further quantitative structural analysis.

The equivalency between logic Petri workflow nets and workflow nets.

PubMed

Wang, Jing; Yu, ShuXia; Du, YuYue

2015-01-01

Logic Petri nets (LPNs) can describe and analyze batch processing functions and passing value indeterminacy in cooperative systems. Logic Petri workflow nets (LPWNs) are proposed based on LPNs in this paper. Process mining is regarded as an important bridge between modeling and analysis of data mining and business process. Workflow nets (WF-nets) are the extension to Petri nets (PNs), and have successfully been used to process mining. Some shortcomings cannot be avoided in process mining, such as duplicate tasks, invisible tasks, and the noise of logs. The online shop in electronic commerce in this paper is modeled to prove the equivalence between LPWNs and WF-nets, and advantages of LPWNs are presented.

The Equivalency between Logic Petri Workflow Nets and Workflow Nets

PubMed Central

Wang, Jing; Yu, ShuXia; Du, YuYue

2015-01-01

Logic Petri nets (LPNs) can describe and analyze batch processing functions and passing value indeterminacy in cooperative systems. Logic Petri workflow nets (LPWNs) are proposed based on LPNs in this paper. Process mining is regarded as an important bridge between modeling and analysis of data mining and business process. Workflow nets (WF-nets) are the extension to Petri nets (PNs), and have successfully been used to process mining. Some shortcomings cannot be avoided in process mining, such as duplicate tasks, invisible tasks, and the noise of logs. The online shop in electronic commerce in this paper is modeled to prove the equivalence between LPWNs and WF-nets, and advantages of LPWNs are presented. PMID:25821845

A real-time phenotyping framework using machine learning for plant stress severity rating in soybean.

PubMed

Naik, Hsiang Sing; Zhang, Jiaoping; Lofquist, Alec; Assefa, Teshale; Sarkar, Soumik; Ackerman, David; Singh, Arti; Singh, Asheesh K; Ganapathysubramanian, Baskar

2017-01-01

Phenotyping is a critical component of plant research. Accurate and precise trait collection, when integrated with genetic tools, can greatly accelerate the rate of genetic gain in crop improvement. However, efficient and automatic phenotyping of traits across large populations is a challenge; which is further exacerbated by the necessity of sampling multiple environments and growing replicated trials. A promising approach is to leverage current advances in imaging technology, data analytics and machine learning to enable automated and fast phenotyping and subsequent decision support. In this context, the workflow for phenotyping (image capture → data storage and curation → trait extraction → machine learning/classification → models/apps for decision support) has to be carefully designed and efficiently executed to minimize resource usage and maximize utility. We illustrate such an end-to-end phenotyping workflow for the case of plant stress severity phenotyping in soybean, with a specific focus on the rapid and automatic assessment of iron deficiency chlorosis (IDC) severity on thousands of field plots. We showcase this analytics framework by extracting IDC features from a set of ~4500 unique canopies representing a diverse germplasm base that have different levels of IDC, and subsequently training a variety of classification models to predict plant stress severity. The best classifier is then deployed as a smartphone app for rapid and real time severity rating in the field. We investigated 10 different classification approaches, with the best classifier being a hierarchical classifier with a mean per-class accuracy of ~96%. We construct a phenotypically meaningful 'population canopy graph', connecting the automatically extracted canopy trait features with plant stress severity rating. We incorporated this image capture → image processing → classification workflow into a smartphone app that enables automated real-time evaluation of IDC scores using digital images of the canopy. We expect this high-throughput framework to help increase the rate of genetic gain by providing a robust extendable framework for other abiotic and biotic stresses. We further envision this workflow embedded onto a high throughput phenotyping ground vehicle and unmanned aerial system that will allow real-time, automated stress trait detection and quantification for plant research, breeding and stress scouting applications.

DIaaS: Data-Intensive workflows as a service - Enabling easy composition and deployment of data-intensive workflows on Virtual Research Environments

NASA Astrophysics Data System (ADS)

Filgueira, R.; Ferreira da Silva, R.; Deelman, E.; Atkinson, M.

2016-12-01

We present the Data-Intensive workflows as a Service (DIaaS) model for enabling easy data-intensive workflow composition and deployment on clouds using containers. DIaaS model backbone is Asterism, an integrated solution for running data-intensive stream-based applications on heterogeneous systems, which combines the benefits of dispel4py with Pegasus workflow systems. The stream-based executions of an Asterism workflow are managed by dispel4py, while the data movement between different e-Infrastructures, and the coordination of the application execution are automatically managed by Pegasus. DIaaS combines Asterism framework with Docker containers to provide an integrated, complete, easy-to-use, portable approach to run data-intensive workflows on distributed platforms. Three containers integrate the DIaaS model: a Pegasus node, and an MPI and an Apache Storm clusters. Container images are described as Dockerfiles (available online at http://github.com/dispel4py/pegasus_dispel4py), linked to Docker Hub for providing continuous integration (automated image builds), and image storing and sharing. In this model, all required software (workflow systems and execution engines) for running scientific applications are packed into the containers, which significantly reduces the effort (and possible human errors) required by scientists or VRE administrators to build such systems. The most common use of DIaaS will be to act as a backend of VREs or Scientific Gateways to run data-intensive applications, deploying cloud resources upon request. We have demonstrated the feasibility of DIaaS using the data-intensive seismic ambient noise cross-correlation application (Figure 1). The application preprocesses (Phase1) and cross-correlates (Phase2) traces from several seismic stations. The application is submitted via Pegasus (Container1), and Phase1 and Phase2 are executed in the MPI (Container2) and Storm (Container3) clusters respectively. Although both phases could be executed within the same environment, this setup demonstrates the flexibility of DIaaS to run applications across e-Infrastructures. In summary, DIaaS delivers specialized software to execute data-intensive applications in a scalable, efficient, and robust manner reducing the engineering time and computational cost.

TheHiveDB image data management and analysis framework.

PubMed

Muehlboeck, J-Sebastian; Westman, Eric; Simmons, Andrew

2014-01-06

The hive database system (theHiveDB) is a web-based brain imaging database, collaboration, and activity system which has been designed as an imaging workflow management system capable of handling cross-sectional and longitudinal multi-center studies. It can be used to organize and integrate existing data from heterogeneous projects as well as data from ongoing studies. It has been conceived to guide and assist the researcher throughout the entire research process, integrating all relevant types of data across modalities (e.g., brain imaging, clinical, and genetic data). TheHiveDB is a modern activity and resource management system capable of scheduling image processing on both private compute resources and the cloud. The activity component supports common image archival and management tasks as well as established pipeline processing (e.g., Freesurfer for extraction of scalar measures from magnetic resonance images). Furthermore, via theHiveDB activity system algorithm developers may grant access to virtual machines hosting versioned releases of their tools to collaborators and the imaging community. The application of theHiveDB is illustrated with a brief use case based on organizing, processing, and analyzing data from the publically available Alzheimer Disease Neuroimaging Initiative.

TheHiveDB image data management and analysis framework

PubMed Central

Muehlboeck, J-Sebastian; Westman, Eric; Simmons, Andrew

2014-01-01

The hive database system (theHiveDB) is a web-based brain imaging database, collaboration, and activity system which has been designed as an imaging workflow management system capable of handling cross-sectional and longitudinal multi-center studies. It can be used to organize and integrate existing data from heterogeneous projects as well as data from ongoing studies. It has been conceived to guide and assist the researcher throughout the entire research process, integrating all relevant types of data across modalities (e.g., brain imaging, clinical, and genetic data). TheHiveDB is a modern activity and resource management system capable of scheduling image processing on both private compute resources and the cloud. The activity component supports common image archival and management tasks as well as established pipeline processing (e.g., Freesurfer for extraction of scalar measures from magnetic resonance images). Furthermore, via theHiveDB activity system algorithm developers may grant access to virtual machines hosting versioned releases of their tools to collaborators and the imaging community. The application of theHiveDB is illustrated with a brief use case based on organizing, processing, and analyzing data from the publically available Alzheimer Disease Neuroimaging Initiative. PMID:24432000

SU-F-J-110: MRI-Guided Single-Session Simulation, Online Adaptation, and Treatment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hill, P; Geurts, M; Mittauer, K

Purpose: To develop a combined simulation and treatment workflow for MRI-guided radiation therapy using the ViewRay treatment planning and delivery system. Methods: Several features of the ViewRay MRIdian planning and treatment workflows are used to simulate and treat patients that require emergent radiotherapy. A simple “pre-plan” is created on diagnostic imaging retrieved from radiology PACS, where conformal fields are created to target a volume defined by a physician based on review of the diagnostic images and chart notes. After initial consult in radiation oncology, the patient is brought to the treatment room, immobilized, and imaged in treatment position with amore » volumetric MR. While the patient rests on the table, the pre-plan is applied to the treatment planning MR and dose is calculated in the treatment geometry. After physician review, modification of the plan may include updating the target definition, redefining fields, or re-balancing beam weights. Once an acceptable treatment plan is finalized and approved, the patient is treated. Results: Careful preparation and judicious choices in the online planning process allow conformal treatment plans to be created and delivered in a single, thirty-minute session. Several advantages have been identified using this process as compared to conventional urgent CT simulation and delivery. Efficiency gains are notable, as physicians appreciate the predictable time commitment and patient waiting time for treatment is decreased. MR guidance in a treatment position offers both enhanced contrast for target delineation and reduction of setup uncertainties. The MRIdian system tools designed for adaptive radiotherapy are particularly useful, enabling plan changes to be made in minutes. Finally, the resulting plans, typically 6 conformal beams, are delivered as quickly as more conventional AP/PA beam arrangements with comparatively superior dose distributions. Conclusion: The ViewRay treatment planning software and delivery system can accommodate a fast simulation and treatment workflow.« less

First Steps Toward Ultrasound-Based Motion Compensation for Imaging and Therapy: Calibration with an Optical System and 4D PET Imaging

PubMed Central

Schwaab, Julia; Kurz, Christopher; Sarti, Cristina; Bongers, André; Schoenahl, Frédéric; Bert, Christoph; Debus, Jürgen; Parodi, Katia; Jenne, Jürgen Walter

2015-01-01

Target motion, particularly in the abdomen, due to respiration or patient movement is still a challenge in many diagnostic and therapeutic processes. Hence, methods to detect and compensate this motion are required. Diagnostic ultrasound (US) represents a non-invasive and dose-free alternative to fluoroscopy, providing more information about internal target motion than respiration belt or optical tracking. The goal of this project is to develop an US-based motion tracking for real-time motion correction in radiation therapy and diagnostic imaging, notably in 4D positron emission tomography (PET). In this work, a workflow is established to enable the transformation of US tracking data to the coordinates of the treatment delivery or imaging system – even if the US probe is moving due to respiration. It is shown that the US tracking signal is equally adequate for 4D PET image reconstruction as the clinically used respiration belt and provides additional opportunities in this concern. Furthermore, it is demonstrated that the US probe being within the PET field of view generally has no relevant influence on the image quality. The accuracy and precision of all the steps in the calibration workflow for US tracking-based 4D PET imaging are found to be in an acceptable range for clinical implementation. Eventually, we show in vitro that an US-based motion tracking in absolute room coordinates with a moving US transducer is feasible. PMID:26649277

Practice patterns of image guided particle therapy in Europe: A 2016 survey of the European Particle Therapy Network (EPTN).

PubMed

Bolsi, Alessandra; Peroni, Marta; Amelio, Dante; Dasu, Alexandru; Stock, Markus; Toma-Dasu, Iuliana; Nyström, Petra Witt; Hoffmann, Aswin

2018-03-28

Image guidance is critical in achieving accurate and precise radiation delivery in particle therapy, even more than in photon therapy. However, equipment, quality assurance procedures and clinical workflows for image-guided particle therapy (IGPT) may vary substantially between centres due to a lack of standardization. A survey was conducted to evaluate the current practice of IGPT in European particle therapy centres. In 2016, a questionnaire was distributed among 19 particle therapy centres in 12 European countries. The questionnaire consisted of 30 open and 37 closed questions related to image guidance in the general clinical workflow, for moving targets, current research activities and future perspectives of IGPT. All centres completed the questionnaire. The IGPT methods used by the 10 treating centres varied substantially. The 9 non-treating centres were in the process to introduce IGPT. Most centres have developed their own IGPT strategies, being tightly connected to their specific technical implementation and dose delivery methods. Insight into the current clinical practice of IGPT in European particle therapy centres was obtained. A variety in IGPT practices and procedures was confirmed, which underlines the need for harmonisation of practice parameters and consensus guidelines. Copyright © 2018 Elsevier B.V. All rights reserved.

Preliminary Evaluation of a Commercial 360 Multi-Camera Rig for Photogrammetric Purposes

NASA Astrophysics Data System (ADS)

Teppati Losè, L.; Chiabrando, F.; Spanò, A.

2018-05-01

The research presented in this paper is focused on a preliminary evaluation of a 360 multi-camera rig: the possibilities to use the images acquired by the system in a photogrammetric workflow and for the creation of spherical images are investigated and different tests and analyses are reported. Particular attention is dedicated to different operative approaches for the estimation of the interior orientation parameters of the cameras, both from an operative and theoretical point of view. The consistency of the six cameras that compose the 360 system was in depth analysed adopting a self-calibration approach in a commercial photogrammetric software solution. A 3D calibration field was projected and created, and several topographic measurements were performed in order to have a set of control points to enhance and control the photogrammetric process. The influence of the interior parameters of the six cameras were analyse both in the different phases of the photogrammetric workflow (reprojection errors on the single tie point, dense cloud generation, geometrical description of the surveyed object, etc.), both in the stitching of the different images into a single spherical panorama (some consideration on the influence of the camera parameters on the overall quality of the spherical image are reported also in these section).

Computer vision and machine learning for robust phenotyping in genome-wide studies

PubMed Central

Zhang, Jiaoping; Naik, Hsiang Sing; Assefa, Teshale; Sarkar, Soumik; Reddy, R. V. Chowda; Singh, Arti; Ganapathysubramanian, Baskar; Singh, Asheesh K.

2017-01-01

Traditional evaluation of crop biotic and abiotic stresses are time-consuming and labor-intensive limiting the ability to dissect the genetic basis of quantitative traits. A machine learning (ML)-enabled image-phenotyping pipeline for the genetic studies of abiotic stress iron deficiency chlorosis (IDC) of soybean is reported. IDC classification and severity for an association panel of 461 diverse plant-introduction accessions was evaluated using an end-to-end phenotyping workflow. The workflow consisted of a multi-stage procedure including: (1) optimized protocols for consistent image capture across plant canopies, (2) canopy identification and registration from cluttered backgrounds, (3) extraction of domain expert informed features from the processed images to accurately represent IDC expression, and (4) supervised ML-based classifiers that linked the automatically extracted features with expert-rating equivalent IDC scores. ML-generated phenotypic data were subsequently utilized for the genome-wide association study and genomic prediction. The results illustrate the reliability and advantage of ML-enabled image-phenotyping pipeline by identifying previously reported locus and a novel locus harboring a gene homolog involved in iron acquisition. This study demonstrates a promising path for integrating the phenotyping pipeline into genomic prediction, and provides a systematic framework enabling robust and quicker phenotyping through ground-based systems. PMID:28272456

Sci-Thur PM - Colourful Interactions: Highlights 04: A Fast Quantitative MRI Acquisition and Processing Pipeline for Radiation Treatment Planning and Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jutras, Jean-David

MRI-only Radiation Treatment Planning (RTP) is becoming increasingly popular because of a simplified work-flow, and less inconvenience to the patient who avoids multiple scans. The advantages of MRI-based RTP over traditional CT-based RTP lie in its superior soft-tissue contrast, and absence of ionizing radiation dose. The lack of electron-density information in MRI can be addressed by automatic tissue classification. To distinguish bone from air, which both appear dark in MRI, an ultra-short echo time (UTE) pulse sequence may be used. Quantitative MRI parametric maps can provide improved tissue segmentation/classification and better sensitivity in monitoring disease progression and treatment outcome thanmore » standard weighted images. Superior tumor contrast can be achieved on pure T{sub 1} images compared to conventional T{sub 1}-weighted images acquired in the same scan duration and voxel resolution. In this study, we have developed a robust and fast quantitative MRI acquisition and post-processing work-flow that integrates these latest advances into the MRI-based RTP of brain lesions. Using 3D multi-echo FLASH images at two different optimized flip angles (both acquired in under 9 min, and 1mm isotropic resolution), parametric maps of T{sub 1}, proton-density (M{sub 0}), and T{sub 2}{sup *} are obtained with high contrast-to-noise ratio, and negligible geometrical distortions, water-fat shifts and susceptibility effects. An additional 3D UTE MRI dataset is acquired (in under 4 min) and post-processed to classify tissues for dose simulation. The pipeline was tested on four healthy volunteers and a clinical trial on brain cancer patients is underway.« less

A graphic user interface for efficient 3D photo-reconstruction based on free software

NASA Astrophysics Data System (ADS)

Castillo, Carlos; James, Michael; Gómez, Jose A.

2015-04-01

Recently, different studies have stressed the applicability of 3D photo-reconstruction based on Structure from Motion algorithms in a wide range of geoscience applications. For the purpose of image photo-reconstruction, a number of commercial and freely available software packages have been developed (e.g. Agisoft Photoscan, VisualSFM). The workflow involves typically different stages such as image matching, sparse and dense photo-reconstruction, point cloud filtering and georeferencing. For approaches using open and free software, each of these stages usually require different applications. In this communication, we present an easy-to-use graphic user interface (GUI) developed in Matlab® code as a tool for efficient 3D photo-reconstruction making use of powerful existing software: VisualSFM (Wu, 2015) for photo-reconstruction and CloudCompare (Girardeau-Montaut, 2015) for point cloud processing. The GUI performs as a manager of configurations and algorithms, taking advantage of the command line modes of existing software, which allows an intuitive and automated processing workflow for the geoscience user. The GUI includes several additional features: a) a routine for significantly reducing the duration of the image matching operation, normally the most time consuming stage; b) graphical outputs for understanding the overall performance of the algorithm (e.g. camera connectivity, point cloud density); c) a number of useful options typically performed before and after the photo-reconstruction stage (e.g. removal of blurry images, image renaming, vegetation filtering); d) a manager of batch processing for the automated reconstruction of different image datasets. In this study we explore the advantages of this new tool by testing its performance using imagery collected in several soil erosion applications. References Girardeau-Montaut, D. 2015. CloudCompare documentation accessed at http://cloudcompare.org/ Wu, C. 2015. VisualSFM documentation access at http://ccwu.me/vsfm/doc.html#.

Fusion of UAV photogrammetry and digital optical granulometry for detection of structural changes in floodplains

NASA Astrophysics Data System (ADS)

Langhammer, Jakub; Lendzioch, Theodora; Mirijovsky, Jakub

2016-04-01

Granulometric analysis represents a traditional, important and for the description of sedimentary material substantial method with various applications in sedimentology, hydrology and geomorphology. However, the conventional granulometric field survey methods are time consuming, laborious, costly and are invasive to the surface being sampled, which can be limiting factor for their applicability in protected areas.. The optical granulometry has recently emerged as an image analysis technique, enabling non-invasive survey, employing semi-automated identification of clasts from calibrated digital imagery, taken on site by conventional high resolution digital camera and calibrated frame. The image processing allows detection and measurement of mixed size natural grains, their sorting and quantitative analysis using standard granulometric approaches. Despite known limitations, the technique today presents reliable tool, significantly easing and speeding the field survey in fluvial geomorphology. However, the nature of such survey has still limitations in spatial coverage of the sites and applicability in research at multitemporal scale. In our study, we are presenting novel approach, based on fusion of two image analysis techniques - optical granulometry and UAV-based photogrammetry, allowing to bridge the gap between the needs of high resolution structural information for granulometric analysis and spatially accurate and data coverage. We have developed and tested a workflow that, using UAV imaging platform enabling to deliver seamless, high resolution and spatially accurate imagery of the study site from which can be derived the granulometric properties of the sedimentary material. We have set up a workflow modeling chain, providing (i) the optimum flight parameters for UAV imagery to balance the two key divergent requirements - imagery resolution and seamless spatial coverage, (ii) the workflow for the processing of UAV acquired imagery by means of the optical granulometry and (iii) the workflow for analysis of spatial distribution and temporal changes of granulometric properties across the point bar. The proposed technique was tested on a case study of an active point bar of mid-latitude mountain stream at Sumava mountains, Czech Republic, exposed to repeated flooding. The UAV photogrammetry was used to acquire very high resolution imagery to build high-precision digital terrain models and orthoimage. The orthoimage was then analyzed using the digital optical granulometric tool BaseGrain. This approach allowed us (i) to analyze the spatial distribution of the grain size in a seamless transects over an active point bar and (ii) to assess the multitemporal changes of granulometric properties of the point bar material resulting from flooding. The tested framework prove the applicability of the proposed method for granulometric analysis with accuracy comparable with field optical granulometry. The seamless nature of the data enables to study spatial distribution of granulometric properties across the study sites as well as the analysis of multitemporal changes, resulting from repeated imaging.

Digitization workflows for flat sheets and packets of plants, algae, and fungi1

PubMed Central

Nelson, Gil; Sweeney, Patrick; Wallace, Lisa E.; Rabeler, Richard K.; Allard, Dorothy; Brown, Herrick; Carter, J. Richard; Denslow, Michael W.; Ellwood, Elizabeth R.; Germain-Aubrey, Charlotte C.; Gilbert, Ed; Gillespie, Emily; Goertzen, Leslie R.; Legler, Ben; Marchant, D. Blaine; Marsico, Travis D.; Morris, Ashley B.; Murrell, Zack; Nazaire, Mare; Neefus, Chris; Oberreiter, Shanna; Paul, Deborah; Ruhfel, Brad R.; Sasek, Thomas; Shaw, Joey; Soltis, Pamela S.; Watson, Kimberly; Weeks, Andrea; Mast, Austin R.

2015-01-01

Effective workflows are essential components in the digitization of biodiversity specimen collections. To date, no comprehensive, community-vetted workflows have been published for digitizing flat sheets and packets of plants, algae, and fungi, even though latest estimates suggest that only 33% of herbarium specimens have been digitally transcribed, 54% of herbaria use a specimen database, and 24% are imaging specimens. In 2012, iDigBio, the U.S. National Science Foundation’s (NSF) coordinating center and national resource for the digitization of public, nonfederal U.S. collections, launched several working groups to address this deficiency. Here, we report the development of 14 workflow modules with 7–36 tasks each. These workflows represent the combined work of approximately 35 curators, directors, and collections managers representing more than 30 herbaria, including 15 NSF-supported plant-related Thematic Collections Networks and collaboratives. The workflows are provided for download as Portable Document Format (PDF) and Microsoft Word files. Customization of these workflows for specific institutional implementation is encouraged. PMID:26421256

Automated reconstruction of standing posture panoramas from multi-sector long limb x-ray images

NASA Astrophysics Data System (ADS)

Miller, Linzey; Trier, Caroline; Ben-Zikri, Yehuda K.; Linte, Cristian A.

2016-03-01

Due to the digital X-ray imaging system's limited field of view, several individual sector images are required to capture the posture of an individual in standing position. These images are then "stitched together" to reconstruct the standing posture. We have created an image processing application that automates the stitching, therefore minimizing user input, optimizing workflow, and reducing human error. The application begins with pre-processing the input images by removing artifacts, filtering out isolated noisy regions, and amplifying a seamless bone edge. The resulting binary images are then registered together using a rigid-body intensity based registration algorithm. The identified registration transformations are then used to map the original sector images into the panorama image. Our method focuses primarily on the use of the anatomical content of the images to generate the panoramas as opposed to using external markers employed to aid with the alignment process. Currently, results show robust edge detection prior to registration and we have tested our approach by comparing the resulting automatically-stitched panoramas to the manually stitched panoramas in terms of registration parameters, target registration error of homologous markers, and the homogeneity of the digitally subtracted automatically- and manually-stitched images using 26 patient datasets.

Workflow for high-content, individual cell quantification of fluorescent markers from universal microscope data, supported by open source software.

PubMed

Stockwell, Simon R; Mittnacht, Sibylle

2014-12-16

Advances in understanding the control mechanisms governing the behavior of cells in adherent mammalian tissue culture models are becoming increasingly dependent on modes of single-cell analysis. Methods which deliver composite data reflecting the mean values of biomarkers from cell populations risk losing subpopulation dynamics that reflect the heterogeneity of the studied biological system. In keeping with this, traditional approaches are being replaced by, or supported with, more sophisticated forms of cellular assay developed to allow assessment by high-content microscopy. These assays potentially generate large numbers of images of fluorescent biomarkers, which enabled by accompanying proprietary software packages, allows for multi-parametric measurements per cell. However, the relatively high capital costs and overspecialization of many of these devices have prevented their accessibility to many investigators. Described here is a universally applicable workflow for the quantification of multiple fluorescent marker intensities from specific subcellular regions of individual cells suitable for use with images from most fluorescent microscopes. Key to this workflow is the implementation of the freely available Cell Profiler software(1) to distinguish individual cells in these images, segment them into defined subcellular regions and deliver fluorescence marker intensity values specific to these regions. The extraction of individual cell intensity values from image data is the central purpose of this workflow and will be illustrated with the analysis of control data from a siRNA screen for G1 checkpoint regulators in adherent human cells. However, the workflow presented here can be applied to analysis of data from other means of cell perturbation (e.g., compound screens) and other forms of fluorescence based cellular markers and thus should be useful for a wide range of laboratories.

Local Surface Reconstruction from MER images using Stereo Workstation

NASA Astrophysics Data System (ADS)

Shin, Dongjoe; Muller, Jan-Peter

2010-05-01

The authors present a semi-automatic workflow that reconstructs the 3D shape of the martian surface from local stereo images delivered by PnCam or NavCam on systems such as the NASA Mars Exploration Rover (MER) Mission and in the future the ESA-NASA ExoMars rover PanCam. The process is initiated with manually selected tiepoints on a stereo workstation which is then followed by a tiepoint refinement, stereo-matching using region growing and Levenberg-Marquardt Algorithm (LMA)-based bundle adjustment processing. The stereo workstation, which is being developed by UCL in collaboration with colleagues at the Jet Propulsion Laboratory (JPL) within the EU FP7 ProVisG project, includes a set of practical GUI-based tools that enable an operator to define a visually correct tiepoint via a stereo display. To achieve platform and graphic hardware independence, the stereo application has been implemented using JPL's JADIS graphic library which is written in JAVA and the remaining processing blocks used in the reconstruction workflow have also been developed as a JAVA package to increase the code re-usability, portability and compatibility. Although initial tiepoints from the stereo workstation are reasonably acceptable as true correspondences, it is often required to employ an optional validity check and/or quality enhancing process. To meet this requirement, the workflow has been designed to include a tiepoint refinement process based on the Adaptive Least Square Correlation (ALSC) matching algorithm so that the initial tiepoints can be further enhanced to sub-pixel precision or rejected if they fail to pass the ALSC matching threshold. Apart from the accuracy of reconstruction, it is obvious that the other criterion to assess the quality of reconstruction is the density (or completeness) of reconstruction, which is not attained in the refinement process. Thus, we re-implemented a stereo region growing process, which is a core matching algorithm within the UCL-HRSC reconstruction workflow. This algorithm's performance is reasonable even for close-range imagery so long as the stereo -pair does not too large a baseline displacement. For post-processing, a Bundle Adjustment (BA) is used to optimise the initial calibration parameters, which bootstrap the reconstruction results. Amongst many options for the non-linear optimisation, the LMA has been adopted due to its stability so that the BA searches the best calibration parameters whilst iteratively minimising the re-projection errors of the initial reconstruction points. For the evaluation of the proposed method, the result of the method is compared with the reconstruction from a disparity map provided by JPL using their operational processing system. Visual and quantitative comparison will be presented as well as updated camera parameters. As part of future work, we will investigate a method expediting the processing speed of the stereo region growing process and look into the possibility of extending the use of the stereo workstation to orbital image processing. Such an interactive stereo workstation can also be used to digitize points and line features as well as assess the accuracy of stereo processed results produced from other stereo matching algorithms available from within the consortium and elsewhere. It can also provide "ground truth" when suitably refined for stereo matching algorithms as well as provide visual cues as to why these matching algorithms sometimes fail to mitigate this in the future. The research leading to these results has received funding from the European Community's Seventh Framework Programme (FP7/2007-2013) under grant agreement n° 218814 "PRoVisG".

A review of GPU-based medical image reconstruction.

PubMed

Després, Philippe; Jia, Xun

2017-10-01

Tomographic image reconstruction is a computationally demanding task, even more so when advanced models are used to describe a more complete and accurate picture of the image formation process. Such advanced modeling and reconstruction algorithms can lead to better images, often with less dose, but at the price of long calculation times that are hardly compatible with clinical workflows. Fortunately, reconstruction tasks can often be executed advantageously on Graphics Processing Units (GPUs), which are exploited as massively parallel computational engines. This review paper focuses on recent developments made in GPU-based medical image reconstruction, from a CT, PET, SPECT, MRI and US perspective. Strategies and approaches to get the most out of GPUs in image reconstruction are presented as well as innovative applications arising from an increased computing capacity. The future of GPU-based image reconstruction is also envisioned, based on current trends in high-performance computing. Copyright © 2017 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

Positional Quality Assessment of Orthophotos Obtained from Sensors Onboard Multi-Rotor UAV Platforms

PubMed Central

Mesas-Carrascosa, Francisco Javier; Rumbao, Inmaculada Clavero; Berrocal, Juan Alberto Barrera; Porras, Alfonso García-Ferrer

2014-01-01

In this study we explored the positional quality of orthophotos obtained by an unmanned aerial vehicle (UAV). A multi-rotor UAV was used to obtain images using a vertically mounted digital camera. The flight was processed taking into account the photogrammetry workflow: perform the aerial triangulation, generate a digital surface model, orthorectify individual images and finally obtain a mosaic image or final orthophoto. The UAV orthophotos were assessed with various spatial quality tests used by national mapping agencies (NMAs). Results showed that the orthophotos satisfactorily passed the spatial quality tests and are therefore a useful tool for NMAs in their production flowchart. PMID:25587877

Positional quality assessment of orthophotos obtained from sensors onboard multi-rotor UAV platforms.

PubMed

Mesas-Carrascosa, Francisco Javier; Rumbao, Inmaculada Clavero; Berrocal, Juan Alberto Barrera; Porras, Alfonso García-Ferrer

2014-11-26

In this study we explored the positional quality of orthophotos obtained by an unmanned aerial vehicle (UAV). A multi-rotor UAV was used to obtain images using a vertically mounted digital camera. The flight was processed taking into account the photogrammetry workflow: perform the aerial triangulation, generate a digital surface model, orthorectify individual images and finally obtain a mosaic image or final orthophoto. The UAV orthophotos were assessed with various spatial quality tests used by national mapping agencies (NMAs). Results showed that the orthophotos satisfactorily passed the spatial quality tests and are therefore a useful tool for NMAs in their production flowchart.

Enabling outsourcing XDS for imaging on the public cloud.

PubMed

Ribeiro, Luís S; Rodrigues, Renato P; Costa, Carlos; Oliveira, José Luís

2013-01-01

Picture Archiving and Communication System (PACS) has been the main paradigm in supporting medical imaging workflows during the last decades. Despite its consolidation, the appearance of Cross-Enterprise Document Sharing for imaging (XDS-I), within IHE initiative, constitutes a great opportunity to readapt PACS workflow for inter-institutional data exchange. XDS-I provides a centralized discovery of medical imaging and associated reports. However, the centralized XDS-I actors (document registry and repository) must be deployed in a trustworthy node in order to safeguard patient privacy, data confidentiality and integrity. This paper presents XDS for Protected Imaging (XDS-p), a new approach to XDS-I that is capable of being outsourced (e.g. Cloud Computing) while maintaining privacy, confidentiality, integrity and legal concerns about patients' medical information.

A framework for service enterprise workflow simulation with multi-agents cooperation

NASA Astrophysics Data System (ADS)

Tan, Wenan; Xu, Wei; Yang, Fujun; Xu, Lida; Jiang, Chuanqun

2013-11-01

Process dynamic modelling for service business is the key technique for Service-Oriented information systems and service business management, and the workflow model of business processes is the core part of service systems. Service business workflow simulation is the prevalent approach to be used for analysis of service business process dynamically. Generic method for service business workflow simulation is based on the discrete event queuing theory, which is lack of flexibility and scalability. In this paper, we propose a service workflow-oriented framework for the process simulation of service businesses using multi-agent cooperation to address the above issues. Social rationality of agent is introduced into the proposed framework. Adopting rationality as one social factor for decision-making strategies, a flexible scheduling for activity instances has been implemented. A system prototype has been developed to validate the proposed simulation framework through a business case study.

Advances in Global Full Waveform Inversion

NASA Astrophysics Data System (ADS)

Tromp, J.; Bozdag, E.; Lei, W.; Ruan, Y.; Lefebvre, M. P.; Modrak, R. T.; Orsvuran, R.; Smith, J. A.; Komatitsch, D.; Peter, D. B.

2017-12-01

Information about Earth's interior comes from seismograms recorded at its surface. Seismic imaging based on spectral-element and adjoint methods has enabled assimilation of this information for the construction of 3D (an)elastic Earth models. These methods account for the physics of wave excitation and propagation by numerically solving the equations of motion, and require the execution of complex computational procedures that challenge the most advanced high-performance computing systems. Current research is petascale; future research will require exascale capabilities. The inverse problem consists of reconstructing the characteristics of the medium from -often noisy- observations. A nonlinear functional is minimized, which involves both the misfit to the measurements and a Tikhonov-type regularization term to tackle inherent ill-posedness. Achieving scalability for the inversion process on tens of thousands of multicore processors is a task that offers many research challenges. We initiated global "adjoint tomography" using 253 earthquakes and produced the first-generation model named GLAD-M15, with a transversely isotropic model parameterization. We are currently running iterations for a second-generation anisotropic model based on the same 253 events. In parallel, we continue iterations for a transversely isotropic model with a larger dataset of 1,040 events to determine higher-resolution plume and slab images. A significant part of our research has focused on eliminating I/O bottlenecks in the adjoint tomography workflow. This has led to the development of a new Adaptable Seismic Data Format based on HDF5, and post-processing tools based on the ADIOS library developed by Oak Ridge National Laboratory. We use the Ensemble Toolkit for workflow stabilization & management to automate the workflow with minimal human interaction.

End-to-end workflow for finite element analysis of tumor treating fields in glioblastomas

NASA Astrophysics Data System (ADS)

Timmons, Joshua J.; Lok, Edwin; San, Pyay; Bui, Kevin; Wong, Eric T.

2017-11-01

Tumor Treating Fields (TTFields) therapy is an approved modality of treatment for glioblastoma. Patient anatomy-based finite element analysis (FEA) has the potential to reveal not only how these fields affect tumor control but also how to improve efficacy. While the automated tools for segmentation speed up the generation of FEA models, multi-step manual corrections are required, including removal of disconnected voxels, incorporation of unsegmented structures and the addition of 36 electrodes plus gel layers matching the TTFields transducers. Existing approaches are also not scalable for the high throughput analysis of large patient volumes. A semi-automated workflow was developed to prepare FEA models for TTFields mapping in the human brain. Magnetic resonance imaging (MRI) pre-processing, segmentation, electrode and gel placement, and post-processing were all automated. The material properties of each tissue were applied to their corresponding mask in silico using COMSOL Multiphysics (COMSOL, Burlington, MA, USA). The fidelity of the segmentations with and without post-processing was compared against the full semi-automated segmentation workflow approach using Dice coefficient analysis. The average relative differences for the electric fields generated by COMSOL were calculated in addition to observed differences in electric field-volume histograms. Furthermore, the mesh file formats in MPHTXT and NASTRAN were also compared using the differences in the electric field-volume histogram. The Dice coefficient was less for auto-segmentation without versus auto-segmentation with post-processing, indicating convergence on a manually corrected model. An existent but marginal relative difference of electric field maps from models with manual correction versus those without was identified, and a clear advantage of using the NASTRAN mesh file format was found. The software and workflow outlined in this article may be used to accelerate the investigation of TTFields in glioblastoma patients by facilitating the creation of FEA models derived from patient MRI datasets.

Multispectral imaging approach for simplified non-invasive in-vivo evaluation of gingival erythema

NASA Astrophysics Data System (ADS)

Eckhard, Timo; Valero, Eva M.; Nieves, Juan L.; Gallegos-Rueda, José M.; Mesa, Francisco

2012-03-01

Erythema is a common visual sign of gingivitis. In this work, a new and simple low-cost image capture and analysis method for erythema assessment is proposed. The method is based on digital still images of gingivae and applied on a pixel-by-pixel basis. Multispectral images are acquired with a conventional digital camera and multiplexed LED illumination panels at 460nm and 630nm peak wavelength. An automatic work-flow segments teeth from gingiva regions in the images and creates a map of local blood oxygenation levels, which relates to the presence of erythema. The map is computed from the ratio of the two spectral images. An advantage of the proposed approach is that the whole process is easy to manage by dental health care professionals in clinical environment.

Geometric registration of remotely sensed data with SAMIR

NASA Astrophysics Data System (ADS)

Gianinetto, Marco; Barazzetti, Luigi; Dini, Luigi; Fusiello, Andrea; Toldo, Roberto

2015-06-01

The commercial market offers several software packages for the registration of remotely sensed data through standard one-to-one image matching. Although very rapid and simple, this strategy does not take into consideration all the interconnections among the images of a multi-temporal data set. This paper presents a new scientific software, called Satellite Automatic Multi-Image Registration (SAMIR), able to extend the traditional registration approach towards multi-image global processing. Tests carried out with high-resolution optical (IKONOS) and high-resolution radar (COSMO-SkyMed) data showed that SAMIR can improve the registration phase with a more rigorous and robust workflow without initial approximations, user's interaction or limitation in spatial/spectral data size. The validation highlighted a sub-pixel accuracy in image co-registration for the considered imaging technologies, including optical and radar imagery.

Widening the adoption of workflows to include human and human-machine scientific processes

NASA Astrophysics Data System (ADS)

Salayandia, L.; Pinheiro da Silva, P.; Gates, A. Q.

2010-12-01

Scientific workflows capture knowledge in the form of technical recipes to access and manipulate data that help scientists manage and reuse established expertise to conduct their work. Libraries of scientific workflows are being created in particular fields, e.g., Bioinformatics, where combined with cyber-infrastructure environments that provide on-demand access to data and tools, result in powerful workbenches for scientists of those communities. The focus in these particular fields, however, has been more on automating rather than documenting scientific processes. As a result, technical barriers have impeded a wider adoption of scientific workflows by scientific communities that do not rely as heavily on cyber-infrastructure and computing environments. Semantic Abstract Workflows (SAWs) are introduced to widen the applicability of workflows as a tool to document scientific recipes or processes. SAWs intend to capture a scientists’ perspective about the process of how she or he would collect, filter, curate, and manipulate data to create the artifacts that are relevant to her/his work. In contrast, scientific workflows describe the process from the point of view of how technical methods and tools are used to conduct the work. By focusing on a higher level of abstraction that is closer to a scientist’s understanding, SAWs effectively capture the controlled vocabularies that reflect a particular scientific community, as well as the types of datasets and methods used in a particular domain. From there on, SAWs provide the flexibility to adapt to different environments to carry out the recipes or processes. These environments range from manual fieldwork to highly technical cyber-infrastructure environments, i.e., such as those already supported by scientific workflows. Two cases, one from Environmental Science and another from Geophysics, are presented as illustrative examples.

Multiphase flow predictions from carbonate pore space images using extracted network models

NASA Astrophysics Data System (ADS)

Al-Kharusi, Anwar S.; Blunt, Martin J.

2008-06-01

A methodology to extract networks from pore space images is used to make predictions of multiphase transport properties for subsurface carbonate samples. The extraction of the network model is based on the computation of the location and sizes of pores and throats to create a topological representation of the void space of three-dimensional (3-D) rock images, using the concept of maximal balls. In this work, we follow a multistaged workflow. We start with a 2-D thin-section image; convert it statistically into a 3-D representation of the pore space; extract a network model from this image; and finally, simulate primary drainage, waterflooding, and secondary drainage flow processes using a pore-scale simulator. We test this workflow for a reservoir carbonate rock. The network-predicted absolute permeability is similar to the core plug measured value and the value computed on the 3-D void space image using the lattice Boltzmann method. The predicted capillary pressure during primary drainage agrees well with a mercury-air experiment on a core sample, indicating that we have an adequate representation of the rock's pore structure. We adjust the contact angles in the network to match the measured waterflood and secondary drainage capillary pressures. We infer a significant degree of contact angle hysteresis. We then predict relative permeabilities for primary drainage, waterflooding, and secondary drainage that agree well with laboratory measured values. This approach can be used to predict multiphase transport properties when wettability and pore structure vary in a reservoir, where experimental data is scant or missing. There are shortfalls to this approach, however. We compare results from three networks, one of which was derived from a section of the rock containing vugs. Our method fails to predict properties reliably when an unrepresentative image is processed to construct the 3-D network model. This occurs when the image volume is not sufficient to represent the geological variations observed in a core plug sample.

Image Guided Radiation Therapy (IGRT) Practice Patterns and IGRT's Impact on Workflow and Treatment Planning: Results From a National Survey of American Society for Radiation Oncology Members

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nabavizadeh, Nima, E-mail: nabaviza@ohsu.edu; Elliott, David A.; Chen, Yiyi

Purpose: To survey image guided radiation therapy (IGRT) practice patterns, as well as IGRT's impact on clinical workflow and planning treatment volumes (PTVs). Methods and Materials: A sample of 5979 treatment site–specific surveys was e-mailed to the membership of the American Society for Radiation Oncology (ASTRO), with questions pertaining to IGRT modality/frequency, PTV expansions, method of image verification, and perceived utility/value of IGRT. On-line image verification was defined as images obtained and reviewed by the physician before treatment. Off-line image verification was defined as images obtained before treatment and then reviewed by the physician before the next treatment. Results: Of 601 evaluablemore » responses, 95% reported IGRT capabilities other than portal imaging. The majority (92%) used volumetric imaging (cone-beam CT [CBCT] or megavoltage CT), with volumetric imaging being the most commonly used modality for all sites except breast. The majority of respondents obtained daily CBCTs for head and neck intensity modulated radiation therapy (IMRT), lung 3-dimensional conformal radiation therapy or IMRT, anus or pelvis IMRT, prostate IMRT, and prostatic fossa IMRT. For all sites, on-line image verification was most frequently performed during the first few fractions only. No association was seen between IGRT frequency or CBCT utilization and clinical treatment volume to PTV expansions. Of the 208 academic radiation oncologists who reported working with residents, only 41% reported trainee involvement in IGRT verification processes. Conclusion: Consensus guidelines, further evidence-based approaches for PTV margin selection, and greater resident involvement are needed for standardized use of IGRT practices.« less

Image Guided Radiation Therapy (IGRT) Practice Patterns and IGRT's Impact on Workflow and Treatment Planning: Results From a National Survey of American Society for Radiation Oncology Members.

PubMed

Nabavizadeh, Nima; Elliott, David A; Chen, Yiyi; Kusano, Aaron S; Mitin, Timur; Thomas, Charles R; Holland, John M

2016-03-15

To survey image guided radiation therapy (IGRT) practice patterns, as well as IGRT's impact on clinical workflow and planning treatment volumes (PTVs). A sample of 5979 treatment site-specific surveys was e-mailed to the membership of the American Society for Radiation Oncology (ASTRO), with questions pertaining to IGRT modality/frequency, PTV expansions, method of image verification, and perceived utility/value of IGRT. On-line image verification was defined as images obtained and reviewed by the physician before treatment. Off-line image verification was defined as images obtained before treatment and then reviewed by the physician before the next treatment. Of 601 evaluable responses, 95% reported IGRT capabilities other than portal imaging. The majority (92%) used volumetric imaging (cone-beam CT [CBCT] or megavoltage CT), with volumetric imaging being the most commonly used modality for all sites except breast. The majority of respondents obtained daily CBCTs for head and neck intensity modulated radiation therapy (IMRT), lung 3-dimensional conformal radiation therapy or IMRT, anus or pelvis IMRT, prostate IMRT, and prostatic fossa IMRT. For all sites, on-line image verification was most frequently performed during the first few fractions only. No association was seen between IGRT frequency or CBCT utilization and clinical treatment volume to PTV expansions. Of the 208 academic radiation oncologists who reported working with residents, only 41% reported trainee involvement in IGRT verification processes. Consensus guidelines, further evidence-based approaches for PTV margin selection, and greater resident involvement are needed for standardized use of IGRT practices. Copyright © 2016 Elsevier Inc. All rights reserved.

A software tool for advanced MRgFUS prostate therapy planning and follow up

NASA Astrophysics Data System (ADS)

van Straaten, Dörte; Hoogenboom, Martijn; van Amerongen, Martinus J.; Weiler, Florian; Issawi, Jumana Al; Günther, Matthias; Fütterer, Jurgen; Jenne, Jürgen W.

2017-03-01

US guided HIFU/FUS ablation for the therapy of prostate cancer is a clinical established method, while MR guided HIFU/FUS applications for prostate recently started clinical evaluation. Even if MRI examination is an excellent diagnostic tool for prostate cancer, it is a time consuming procedure and not practicable within an MRgFUS therapy session. The aim of our ongoing work is to develop software to support therapy planning and post-therapy follow-up for MRgFUS on localized prostate cancer, based on multi-parametric MR protocols. The clinical workflow of diagnosis, therapy and follow-up of MR guided FUS on prostate cancer was deeply analyzed. Based on this, the image processing workflow was designed and all necessary components, e.g. GUI, viewer, registration tools etc. were defined and implemented. The software bases on MeVisLab with several implemented C++ modules for the image processing tasks. The developed software, called LTC (Local Therapy Control) will register and visualize automatically all images (T1w, T2w, DWI etc.) and ADC or perfusion maps gained from the diagnostic MRI session. This maximum of diagnostic information helps to segment all necessary ROIs, e.g. the tumor, for therapy planning. Final therapy planning will be performed based on these segmentation data in the following MRgFUS therapy session. In addition, the developed software should help to evaluate the therapy success, by synchronization and display of pre-therapeutic, therapy and follow-up image data including the therapy plan and thermal dose information. In this ongoing project, the first stand-alone prototype was completed and will be clinically evaluated.

Image Reconstruction is a New Frontier of Machine Learning.

PubMed

Wang, Ge; Ye, Jong Chu; Mueller, Klaus; Fessler, Jeffrey A

2018-06-01

Over past several years, machine learning, or more generally artificial intelligence, has generated overwhelming research interest and attracted unprecedented public attention. As tomographic imaging researchers, we share the excitement from our imaging perspective [item 1) in the Appendix], and organized this special issue dedicated to the theme of "Machine learning for image reconstruction." This special issue is a sister issue of the special issue published in May 2016 of this journal with the theme "Deep learning in medical imaging" [item 2) in the Appendix]. While the previous special issue targeted medical image processing/analysis, this special issue focuses on data-driven tomographic reconstruction. These two special issues are highly complementary, since image reconstruction and image analysis are two of the main pillars for medical imaging. Together we cover the whole workflow of medical imaging: from tomographic raw data/features to reconstructed images and then extracted diagnostic features/readings.

Chang'E-3 data pre-processing system based on scientific workflow

NASA Astrophysics Data System (ADS)

tan, xu; liu, jianjun; wang, yuanyuan; yan, wei; zhang, xiaoxia; li, chunlai

2016-04-01

The Chang'E-3(CE3) mission have obtained a huge amount of lunar scientific data. Data pre-processing is an important segment of CE3 ground research and application system. With a dramatic increase in the demand of data research and application, Chang'E-3 data pre-processing system(CEDPS) based on scientific workflow is proposed for the purpose of making scientists more flexible and productive by automating data-driven. The system should allow the planning, conduct and control of the data processing procedure with the following possibilities: • describe a data processing task, include:1)define input data/output data, 2)define the data relationship, 3)define the sequence of tasks,4)define the communication between tasks,5)define mathematical formula, 6)define the relationship between task and data. • automatic processing of tasks. Accordingly, Describing a task is the key point whether the system is flexible. We design a workflow designer which is a visual environment for capturing processes as workflows, the three-level model for the workflow designer is discussed:1) The data relationship is established through product tree.2)The process model is constructed based on directed acyclic graph(DAG). Especially, a set of process workflow constructs, including Sequence, Loop, Merge, Fork are compositional one with another.3)To reduce the modeling complexity of the mathematical formulas using DAG, semantic modeling based on MathML is approached. On top of that, we will present how processed the CE3 data with CEDPS.

Retrieval of land cover information under thin fog in Landsat TM image

NASA Astrophysics Data System (ADS)

Wei, Yuchun

2008-04-01

Thin fog, which often appears in remote sensing image of subtropical climate region, has resulted in the low image quantity and bad image mapping. Therefore, it is necessary to develop the image processing method to retrieve land cover information under thin fog. In this paper, the Landsat TM image near the Taihu Lake that is in the subtropical climate zone of China was used as an example, and the workflow and method used to retrieve the land cover information under thin fog have been built based on ENVI software and a single TM image. The basic step covers three parts: 1) isolating the thin fog area in image according to the spectral difference of different bands; 2) retrieving the visible band information of different land cover types under thin fog from the near-infrared bands according to the relationships between near-infrared bands and visible bands of different land cover types in the area without fog; 3) image post-process. The result showed that the method in the paper is easy and suitable, and can be used to improve the quantity of TM image mapping more effectively.

Building Digital Audio Preservation Infrastructure and Workflows

ERIC Educational Resources Information Center

Young, Anjanette; Olivieri, Blynne; Eckler, Karl; Gerontakos, Theodore

2010-01-01

In 2009 the University of Washington (UW) Libraries special collections received funding for the digital preservation of its audio indigenous language holdings. The university libraries, where the authors work in various capacities, had begun digitizing image and text collections in 1997. Because of this, at the onset of the project, workflows (a…

Medical image computing for computer-supported diagnostics and therapy. Advances and perspectives.

PubMed

Handels, H; Ehrhardt, J

2009-01-01

Medical image computing has become one of the most challenging fields in medical informatics. In image-based diagnostics of the future software assistance will become more and more important, and image analysis systems integrating advanced image computing methods are needed to extract quantitative image parameters to characterize the state and changes of image structures of interest (e.g. tumors, organs, vessels, bones etc.) in a reproducible and objective way. Furthermore, in the field of software-assisted and navigated surgery medical image computing methods play a key role and have opened up new perspectives for patient treatment. However, further developments are needed to increase the grade of automation, accuracy, reproducibility and robustness. Moreover, the systems developed have to be integrated into the clinical workflow. For the development of advanced image computing systems methods of different scientific fields have to be adapted and used in combination. The principal methodologies in medical image computing are the following: image segmentation, image registration, image analysis for quantification and computer assisted image interpretation, modeling and simulation as well as visualization and virtual reality. Especially, model-based image computing techniques open up new perspectives for prediction of organ changes and risk analysis of patients and will gain importance in diagnostic and therapy of the future. From a methodical point of view the authors identify the following future trends and perspectives in medical image computing: development of optimized application-specific systems and integration into the clinical workflow, enhanced computational models for image analysis and virtual reality training systems, integration of different image computing methods, further integration of multimodal image data and biosignals and advanced methods for 4D medical image computing. The development of image analysis systems for diagnostic support or operation planning is a complex interdisciplinary process. Image computing methods enable new insights into the patient's image data and have the future potential to improve medical diagnostics and patient treatment.

Potential of PET-MRI for imaging of non-oncologic musculoskeletal disease.

PubMed

Kogan, Feliks; Fan, Audrey P; Gold, Garry E

2016-12-01

Early detection of musculoskeletal disease leads to improved therapies and patient outcomes, and would benefit greatly from imaging at the cellular and molecular level. As it becomes clear that assessment of multiple tissues and functional processes are often necessary to study the complex pathogenesis of musculoskeletal disorders, the role of multi-modality molecular imaging becomes increasingly important. New positron emission tomography-magnetic resonance imaging (PET-MRI) systems offer to combine high-resolution MRI with simultaneous molecular information from PET to study the multifaceted processes involved in numerous musculoskeletal disorders. In this article, we aim to outline the potential clinical utility of hybrid PET-MRI to these non-oncologic musculoskeletal diseases. We summarize current applications of PET molecular imaging in osteoarthritis (OA), rheumatoid arthritis (RA), metabolic bone diseases and neuropathic peripheral pain. Advanced MRI approaches that reveal biochemical and functional information offer complementary assessment in soft tissues. Additionally, we discuss technical considerations for hybrid PET-MR imaging including MR attenuation correction, workflow, radiation dose, and quantification.

Workflows for microarray data processing in the Kepler environment.

PubMed

Stropp, Thomas; McPhillips, Timothy; Ludäscher, Bertram; Bieda, Mark

2012-05-17

Microarray data analysis has been the subject of extensive and ongoing pipeline development due to its complexity, the availability of several options at each analysis step, and the development of new analysis demands, including integration with new data sources. Bioinformatics pipelines are usually custom built for different applications, making them typically difficult to modify, extend and repurpose. Scientific workflow systems are intended to address these issues by providing general-purpose frameworks in which to develop and execute such pipelines. The Kepler workflow environment is a well-established system under continual development that is employed in several areas of scientific research. Kepler provides a flexible graphical interface, featuring clear display of parameter values, for design and modification of workflows. It has capabilities for developing novel computational components in the R, Python, and Java programming languages, all of which are widely used for bioinformatics algorithm development, along with capabilities for invoking external applications and using web services. We developed a series of fully functional bioinformatics pipelines addressing common tasks in microarray processing in the Kepler workflow environment. These pipelines consist of a set of tools for GFF file processing of NimbleGen chromatin immunoprecipitation on microarray (ChIP-chip) datasets and more comprehensive workflows for Affymetrix gene expression microarray bioinformatics and basic primer design for PCR experiments, which are often used to validate microarray results. Although functional in themselves, these workflows can be easily customized, extended, or repurposed to match the needs of specific projects and are designed to be a toolkit and starting point for specific applications. These workflows illustrate a workflow programming paradigm focusing on local resources (programs and data) and therefore are close to traditional shell scripting or R/BioConductor scripting approaches to pipeline design. Finally, we suggest that microarray data processing task workflows may provide a basis for future example-based comparison of different workflow systems. We provide a set of tools and complete workflows for microarray data analysis in the Kepler environment, which has the advantages of offering graphical, clear display of conceptual steps and parameters and the ability to easily integrate other resources such as remote data and web services.

Inselect: Automating the Digitization of Natural History Collections

PubMed Central

Hudson, Lawrence N.; Blagoderov, Vladimir; Heaton, Alice; Holtzhausen, Pieter; Livermore, Laurence; Price, Benjamin W.; van der Walt, Stéfan; Smith, Vincent S.

2015-01-01

The world’s natural history collections constitute an enormous evidence base for scientific research on the natural world. To facilitate these studies and improve access to collections, many organisations are embarking on major programmes of digitization. This requires automated approaches to mass-digitization that support rapid imaging of specimens and associated data capture, in order to process the tens of millions of specimens common to most natural history collections. In this paper we present Inselect—a modular, easy-to-use, cross-platform suite of open-source software tools that supports the semi-automated processing of specimen images generated by natural history digitization programmes. The software is made up of a Windows, Mac OS X, and Linux desktop application, together with command-line tools that are designed for unattended operation on batches of images. Blending image visualisation algorithms that automatically recognise specimens together with workflows to support post-processing tasks such as barcode reading, label transcription and metadata capture, Inselect fills a critical gap to increase the rate of specimen digitization. PMID:26599208

Inselect: Automating the Digitization of Natural History Collections.

PubMed

Hudson, Lawrence N; Blagoderov, Vladimir; Heaton, Alice; Holtzhausen, Pieter; Livermore, Laurence; Price, Benjamin W; van der Walt, Stéfan; Smith, Vincent S

2015-01-01

The world's natural history collections constitute an enormous evidence base for scientific research on the natural world. To facilitate these studies and improve access to collections, many organisations are embarking on major programmes of digitization. This requires automated approaches to mass-digitization that support rapid imaging of specimens and associated data capture, in order to process the tens of millions of specimens common to most natural history collections. In this paper we present Inselect-a modular, easy-to-use, cross-platform suite of open-source software tools that supports the semi-automated processing of specimen images generated by natural history digitization programmes. The software is made up of a Windows, Mac OS X, and Linux desktop application, together with command-line tools that are designed for unattended operation on batches of images. Blending image visualisation algorithms that automatically recognise specimens together with workflows to support post-processing tasks such as barcode reading, label transcription and metadata capture, Inselect fills a critical gap to increase the rate of specimen digitization.

Towards an intelligent hospital environment: OR of the future.

PubMed

Sutherland, Jeffrey V; van den Heuvel, Willem-Jan; Ganous, Tim; Burton, Matthew M; Kumar, Animesh

2005-01-01

Patients, providers, payers, and government demand more effective and efficient healthcare services, and the healthcare industry needs innovative ways to re-invent core processes. Business process reengineering (BPR) showed adopting new hospital information systems can leverage this transformation and workflow management technologies can automate process management. Our research indicates workflow technologies in healthcare require real time patient monitoring, detection of adverse events, and adaptive responses to breakdown in normal processes. Adaptive workflow systems are rarely implemented making current workflow implementations inappropriate for healthcare. The advent of evidence based medicine, guideline based practice, and better understanding of cognitive workflow combined with novel technologies including Radio Frequency Identification (RFID), mobile/wireless technologies, internet workflow, intelligent agents, and Service Oriented Architectures (SOA) opens up new and exciting ways of automating business processes. Total situational awareness of events, timing, and location of healthcare activities can generate self-organizing change in behaviors of humans and machines. A test bed of a novel approach towards continuous process management was designed for the new Weinburg Surgery Building at the University of Maryland Medical. Early results based on clinical process mapping and analysis of patient flow bottlenecks demonstrated 100% improvement in delivery of supplies and instruments at surgery start time. This work has been directly applied to the design of the DARPA Trauma Pod research program where robotic surgery will be performed on wounded soldiers on the battlefield.

Automated Processing Workflow for Ambient Seismic Recordings

NASA Astrophysics Data System (ADS)

Girard, A. J.; Shragge, J.

2017-12-01

Structural imaging using body-wave energy present in ambient seismic data remains a challenging task, largely because these wave modes are commonly much weaker than surface wave energy. In a number of situations body-wave energy has been extracted successfully; however, (nearly) all successful body-wave extraction and imaging approaches have focused on cross-correlation processing. While this is useful for interferometric purposes, it can also lead to the inclusion of unwanted noise events that dominate the resulting stack, leaving body-wave energy overpowered by the coherent noise. Conversely, wave-equation imaging can be applied directly on non-correlated ambient data that has been preprocessed to mitigate unwanted energy (i.e., surface waves, burst-like and electromechanical noise) to enhance body-wave arrivals. Following this approach, though, requires a significant preprocessing effort on often Terabytes of ambient seismic data, which is expensive and requires automation to be a feasible approach. In this work we outline an automated processing workflow designed to optimize body wave energy from an ambient seismic data set acquired on a large-N array at a mine site near Lalor Lake, Manitoba, Canada. We show that processing ambient seismic data in the recording domain, rather than the cross-correlation domain, allows us to mitigate energy that is inappropriate for body-wave imaging. We first develop a method for window selection that automatically identifies and removes data contaminated by coherent high-energy bursts. We then apply time- and frequency-domain debursting techniques to mitigate the effects of remaining strong amplitude and/or monochromatic energy without severely degrading the overall waveforms. After each processing step we implement a QC check to investigate improvements in the convergence rates - and the emergence of reflection events - in the cross-correlation plus stack waveforms over hour-long windows. Overall, the QC analyses suggest that automated preprocessing of ambient seismic recordings in the recording domain successfully mitigates unwanted coherent noise events in both the time and frequency domain. Accordingly, we assert that this method is beneficial for direct wave-equation imaging with ambient seismic recordings.

Imaging industry expectations for compressed sensing in MRI

NASA Astrophysics Data System (ADS)

King, Kevin F.; Kanwischer, Adriana; Peters, Rob

2015-09-01

Compressed sensing requires compressible data, incoherent acquisition and a nonlinear reconstruction algorithm to force creation of a compressible image consistent with the acquired data. MRI images are compressible using various transforms (commonly total variation or wavelets). Incoherent acquisition of MRI data by appropriate selection of pseudo-random or non-Cartesian locations in k-space is straightforward. Increasingly, commercial scanners are sold with enough computing power to enable iterative reconstruction in reasonable times. Therefore integration of compressed sensing into commercial MRI products and clinical practice is beginning. MRI frequently requires the tradeoff of spatial resolution, temporal resolution and volume of spatial coverage to obtain reasonable scan times. Compressed sensing improves scan efficiency and reduces the need for this tradeoff. Benefits to the user will include shorter scans, greater patient comfort, better image quality, more contrast types per patient slot, the enabling of previously impractical applications, and higher throughput. Challenges to vendors include deciding which applications to prioritize, guaranteeing diagnostic image quality, maintaining acceptable usability and workflow, and acquisition and reconstruction algorithm details. Application choice depends on which customer needs the vendor wants to address. The changing healthcare environment is putting cost and productivity pressure on healthcare providers. The improved scan efficiency of compressed sensing can help alleviate some of this pressure. Image quality is strongly influenced by image compressibility and acceleration factor, which must be appropriately limited. Usability and workflow concerns include reconstruction time and user interface friendliness and response. Reconstruction times are limited to about one minute for acceptable workflow. The user interface should be designed to optimize workflow and minimize additional customer training. Algorithm concerns include the decision of which algorithms to implement as well as the problem of optimal setting of adjustable parameters. It will take imaging vendors several years to work through these challenges and provide solutions for a wide range of applications.

Toward a Virtual Laboratory to Assess Biodiversity from Data Produced by an Underwater Microscope

NASA Astrophysics Data System (ADS)

Beaulieu, S.; Ball, M.; Futrelle, J.; Sosik, H. M.

2016-12-01

Real-time data from sensors deployed in the ocean are increasingly available online for broad use by scientists, educators, and the public. Such data have previously been limited to physical parameters, but data for biological parameters are becoming more prevalent with the development of new submersible instruments. Imaging FlowCytobot (IFCB), for example, automatically and rapidly acquires images of microscopic algae (phytoplankton) at the base of the food web in marine ecosystems. These images and products from image processing and automated classification are accessible via web services from an IFCB dashboard. However, until now, to process these data further into results representing the biodiversity of the phytoplankton required a complex workflow that could only be executed by scientists involved in the instrument development. Also, because these data have been collected near continuously for a decade, a number of "big data" challenges arise in attempting to implement and reproduce the workflow. Our research is geared toward the development of a virtual laboratory to enable other scientists and educators, as new users of data from this underwater microscope, to generate biodiversity data products. Our solution involves an electronic notebook (Jupyter Notebook) that can be re-purposed by users with some Python programming experience. However, when we scaled the virtual laboratory to accommodate a 2-month example time series (thousands of binned files each representing thousands of images), we needed to expand the execution environment to include batch processing outside of the notebook. We will share how we packaged these tools to share with other scientists to perform their own biodiversity assessment from data available on an IFCB dashboard. Additional outcomes of software development in this project include a prototype for time-series visualizations to be generated in near-real-time and recommendations for new products accessible via web services from the IFCB dashboard.

MO-E-BRD-01: Adapt-A-Thon - Texas Hold’em Invitational

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kessler, M; Brock, K; Pouliot, J

2014-06-15

Software tools for image-based adaptive radiotherapy such as deformable image registration, contour propagation and dose mapping have progressed beyond the research setting and are now commercial products available as part of both treatment planning systems and stand-alone applications. These software tools are used together to create clinical workflows to detect, track and evaluate changes in the patient and to accumulate dose. Deviations uncovered in this process are used to guide decisions about replanning/adaptation with the goal of keeping the delivery of prescribed dose “on target” throughout the entire course of radiotherapy. Since the output from one step of the adaptivemore » process is used as an input for another, it is essential to understand and document the uncertainty associated with each of the step and how these uncertainties are propagated. This in turn requires an understanding how the underlying tools work. Unfortunately, important details about the algorithms used to implement these tools are scarce or incomplete, too often for competitive reasons. This is in contrast to the situation involving other basic treatment planning algorithms such as dose calculations, where the medical physics community essentially requires vendors to provide physically important details about their underlying theory and clinical implementation. Vendors should adopt this same level of information sharing when it comes to the tools and techniques for image guided adaptive radiotherapy. The goal of this session is to start this process by inviting vendors and medical physicists to discuss and demonstrate the available tools and describe how they are intended to be used in clinical practice. The format of the session will involve a combination of formal presentations, interactive demonstrations, audience participation and some friendly “Texas style” competition. Learning Objectives: Understand the components of the image-based adaptive radiotherapy process. Understand the how these components are implemented in various commercial systems. Understand the different use cases and workflows currently supported these tools.« less

The whole mesh deformation model: a fast image segmentation method suitable for effective parallelization

NASA Astrophysics Data System (ADS)

Lenkiewicz, Przemyslaw; Pereira, Manuela; Freire, Mário M.; Fernandes, José

2013-12-01

In this article, we propose a novel image segmentation method called the whole mesh deformation (WMD) model, which aims at addressing the problems of modern medical imaging. Such problems have raised from the combination of several factors: (1) significant growth of medical image volumes sizes due to increasing capabilities of medical acquisition devices; (2) the will to increase the complexity of image processing algorithms in order to explore new functionality; (3) change in processor development and turn towards multi processing units instead of growing bus speeds and the number of operations per second of a single processing unit. Our solution is based on the concept of deformable models and is characterized by a very effective and precise segmentation capability. The proposed WMD model uses a volumetric mesh instead of a contour or a surface to represent the segmented shapes of interest, which allows exploiting more information in the image and obtaining results in shorter times, independently of image contents. The model also offers a good ability for topology changes and allows effective parallelization of workflow, which makes it a very good choice for large datasets. We present a precise model description, followed by experiments on artificial images and real medical data.

An Integrative Object-Based Image Analysis Workflow for Uav Images

NASA Astrophysics Data System (ADS)

Yu, Huai; Yan, Tianheng; Yang, Wen; Zheng, Hong

2016-06-01

In this work, we propose an integrative framework to process UAV images. The overall process can be viewed as a pipeline consisting of the geometric and radiometric corrections, subsequent panoramic mosaicking and hierarchical image segmentation for later Object Based Image Analysis (OBIA). More precisely, we first introduce an efficient image stitching algorithm after the geometric calibration and radiometric correction, which employs a fast feature extraction and matching by combining the local difference binary descriptor and the local sensitive hashing. We then use a Binary Partition Tree (BPT) representation for the large mosaicked panoramic image, which starts by the definition of an initial partition obtained by an over-segmentation algorithm, i.e., the simple linear iterative clustering (SLIC). Finally, we build an object-based hierarchical structure by fully considering the spectral and spatial information of the super-pixels and their topological relationships. Moreover, an optimal segmentation is obtained by filtering the complex hierarchies into simpler ones according to some criterions, such as the uniform homogeneity and semantic consistency. Experimental results on processing the post-seismic UAV images of the 2013 Ya'an earthquake demonstrate the effectiveness and efficiency of our proposed method.

Load-sensitive dynamic workflow re-orchestration and optimisation for faster patient healthcare.

PubMed

Meli, Christopher L; Khalil, Ibrahim; Tari, Zahir

2014-01-01

Hospital waiting times are considerably long, with no signs of reducing any-time soon. A number of factors including population growth, the ageing population and a lack of new infrastructure are expected to further exacerbate waiting times in the near future. In this work, we show how healthcare services can be modelled as queueing nodes, together with healthcare service workflows, such that these workflows can be optimised during execution in order to reduce patient waiting times. Services such as X-ray, computer tomography, and magnetic resonance imaging often form queues, thus, by taking into account the waiting times of each service, the workflow can be re-orchestrated and optimised. Experimental results indicate average waiting time reductions are achievable by optimising workflows using dynamic re-orchestration. Crown Copyright © 2013. Published by Elsevier Ireland Ltd. All rights reserved.

Modeling of workflow-engaged networks on radiology transfers across a metro network.

PubMed

Camorlinga, Sergio; Schofield, Bruce

2006-04-01

Radiology metro networks bear the challenging proposition of interconnecting several hospitals in a region to provide a comprehensive diagnostic imaging service. Consequences of a poorly designed and implemented metro network could cause delays or no access at all when health care providers try to retrieve medical cases across the network. This could translate into limited diagnostic services to patients, resulting in negative impacts to the patients' medical treatment. A workflow-engaged network (WEN) is a new network paradigm. A WEN appreciates radiology workflows and priorities in using the network. A WEN greatly improves the network performance by guaranteeing that critical image transfers experience minimal delay. It adjusts network settings to ensure the application's requirements are met. This means that high-priority image transfers will have guaranteed and known delay times, whereas lower-priority traffic will have increased delays. This paper introduces a modeling to understand the benefits that WEN brings to a radiology metro network. The modeling uses actual data patterns and flows found in a hospital metro region. The workflows considered are based on the Integrating the Healthcare Enterprise profiles. This modeling has been applied to metropolitan workflows of a health region. The modeling helps identify the kind of metro network that supports data patterns and flows in a metro area. The results of the modeling show that a 155-Mb/s metropolitan area network (MAN) with WEN operates virtually equal to a normal 622-Mb/s MAN without WEN, with potential cost savings for leased line services measured in the millions of dollars per year.

Common Workflow Service: Standards Based Solution for Managing Operational Processes

NASA Astrophysics Data System (ADS)

Tinio, A. W.; Hollins, G. A.

2017-06-01

The Common Workflow Service is a collaborative and standards-based solution for managing mission operations processes using techniques from the Business Process Management (BPM) discipline. This presentation describes the CWS and its benefits.

ARIES: Enabling Visual Exploration and Organization of Art Image Collections.

PubMed

Crissaff, Lhaylla; Wood Ruby, Louisa; Deutch, Samantha; DuBois, R Luke; Fekete, Jean-Daniel; Freire, Juliana; Silva, Claudio

2018-01-01

Art historians have traditionally used physical light boxes to prepare exhibits or curate collections. On a light box, they can place slides or printed images, move the images around at will, group them as desired, and visual-ly compare them. The transition to digital images has rendered this workflow obsolete. Now, art historians lack well-designed, unified interactive software tools that effectively support the operations they perform with physi-cal light boxes. To address this problem, we designed ARIES (ARt Image Exploration Space), an interactive image manipulation system that enables the exploration and organization of fine digital art. The system allows images to be compared in multiple ways, offering dynamic overlays analogous to a physical light box, and sup-porting advanced image comparisons and feature-matching functions, available through computational image processing. We demonstrate the effectiveness of our system to support art historians tasks through real use cases.

CG2Real: Improving the Realism of Computer Generated Images Using a Large Collection of Photographs.

PubMed

Johnson, Micah K; Dale, Kevin; Avidan, Shai; Pfister, Hanspeter; Freeman, William T; Matusik, Wojciech

2011-09-01

Computer-generated (CG) images have achieved high levels of realism. This realism, however, comes at the cost of long and expensive manual modeling, and often humans can still distinguish between CG and real images. We introduce a new data-driven approach for rendering realistic imagery that uses a large collection of photographs gathered from online repositories. Given a CG image, we retrieve a small number of real images with similar global structure. We identify corresponding regions between the CG and real images using a mean-shift cosegmentation algorithm. The user can then automatically transfer color, tone, and texture from matching regions to the CG image. Our system only uses image processing operations and does not require a 3D model of the scene, making it fast and easy to integrate into digital content creation workflows. Results of a user study show that our hybrid images appear more realistic than the originals.

Development of a fusion approach selection tool

NASA Astrophysics Data System (ADS)

Pohl, C.; Zeng, Y.

2015-06-01

During the last decades number and quality of available remote sensing satellite sensors for Earth observation has grown significantly. The amount of available multi-sensor images along with their increased spatial and spectral resolution provides new challenges to Earth scientists. With a Fusion Approach Selection Tool (FAST) the remote sensing community would obtain access to an optimized and improved image processing technology. Remote sensing image fusion is a mean to produce images containing information that is not inherent in the single image alone. In the meantime the user has access to sophisticated commercialized image fusion techniques plus the option to tune the parameters of each individual technique to match the anticipated application. This leaves the operator with an uncountable number of options to combine remote sensing images, not talking about the selection of the appropriate images, resolution and bands. Image fusion can be a machine and time-consuming endeavour. In addition it requires knowledge about remote sensing, image fusion, digital image processing and the application. FAST shall provide the user with a quick overview of processing flows to choose from to reach the target. FAST will ask for available images, application parameters and desired information to process this input to come out with a workflow to quickly obtain the best results. It will optimize data and image fusion techniques. It provides an overview on the possible results from which the user can choose the best. FAST will enable even inexperienced users to use advanced processing methods to maximize the benefit of multi-sensor image exploitation.

SU-E-T-419: Workflow and FMEA in a New Proton Therapy (PT) Facility

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, C; Wessels, B; Hamilton, H

2014-06-01

Purpose: Workflow is an important component in the operational planning of a new proton facility. By integrating the concept of failure mode and effect analysis (FMEA) and traditional QA requirements, a workflow for a proton therapy treatment course is set up. This workflow serves as the blue print for the planning of computer hardware/software requirements and network flow. A slight modification of the workflow generates a process map(PM) for FMEA and the planning of QA program in PT. Methods: A flowchart is first developed outlining the sequence of processes involved in a PT treatment course. Each process consists of amore » number of sub-processes to encompass a broad scope of treatment and QA procedures. For each subprocess, the personnel involved, the equipment needed and the computer hardware/software as well as network requirements are defined by a team of clinical staff, administrators and IT personnel. Results: Eleven intermediate processes with a total of 70 sub-processes involved in a PT treatment course are identified. The number of sub-processes varies, ranging from 2-12. The sub-processes within each process are used for the operational planning. For example, in the CT-Sim process, there are 12 sub-processes: three involve data entry/retrieval from a record-and-verify system, two controlled by the CT computer, two require department/hospital network, and the other five are setup procedures. IT then decides the number of computers needed and the software and network requirement. By removing the traditional QA procedures from the workflow, a PM is generated for FMEA analysis to design a QA program for PT. Conclusion: Significant efforts are involved in the development of the workflow in a PT treatment course. Our hybrid model of combining FMEA and traditional QA program serves a duo purpose of efficient operational planning and designing of a QA program in PT.« less

MITK-OpenIGTLink for combining open-source toolkits in real-time computer-assisted interventions.

PubMed

Klemm, Martin; Kirchner, Thomas; Gröhl, Janek; Cheray, Dominique; Nolden, Marco; Seitel, Alexander; Hoppe, Harald; Maier-Hein, Lena; Franz, Alfred M

2017-03-01

Due to rapid developments in the research areas of medical imaging, medical image processing and robotics, computer-assisted interventions (CAI) are becoming an integral part of modern patient care. From a software engineering point of view, these systems are highly complex and research can benefit greatly from reusing software components. This is supported by a number of open-source toolkits for medical imaging and CAI such as the medical imaging interaction toolkit (MITK), the public software library for ultrasound imaging research (PLUS) and 3D Slicer. An independent inter-toolkit communication such as the open image-guided therapy link (OpenIGTLink) can be used to combine the advantages of these toolkits and enable an easier realization of a clinical CAI workflow. MITK-OpenIGTLink is presented as a network interface within MITK that allows easy to use, asynchronous two-way messaging between MITK and clinical devices or other toolkits. Performance and interoperability tests with MITK-OpenIGTLink were carried out considering the whole CAI workflow from data acquisition over processing to visualization. We present how MITK-OpenIGTLink can be applied in different usage scenarios. In performance tests, tracking data were transmitted with a frame rate of up to 1000 Hz and a latency of 2.81 ms. Transmission of images with typical ultrasound (US) and greyscale high-definition (HD) resolutions of [Formula: see text] and [Formula: see text] is possible at up to 512 and 128 Hz, respectively. With the integration of OpenIGTLink into MITK, this protocol is now supported by all established open-source toolkits in the field. This eases interoperability between MITK and toolkits such as PLUS or 3D Slicer and facilitates cross-toolkit research collaborations. MITK and its submodule MITK-OpenIGTLink are provided open source under a BSD-style licence ( http://mitk.org ).

a Workflow for UAV's Integration Into a Geodesign Platform

NASA Astrophysics Data System (ADS)

Anca, P.; Calugaru, A.; Alixandroae, I.; Nazarie, R.

2016-06-01

This paper presents a workflow for the development of various Geodesign scenarios. The subject is important in the context of identifying patterns and designing solutions for a Smart City with optimized public transportation, efficient buildings, efficient utilities, recreational facilities a.s.o.. The workflow describes the procedures starting with acquiring data in the field, data processing, orthophoto generation, DTM generation, integration into a GIS platform and analyzing for a better support for Geodesign. Esri's City Engine is used mostly for 3D modeling capabilities that enable the user to obtain 3D realistic models. The workflow uses as inputs information extracted from images acquired using UAVs technologies, namely eBee, existing 2D GIS geodatabases, and a set of CGA rules. The method that we used further, is called procedural modeling, and uses rules in order to extrude buildings, the street network, parcel zoning and side details, based on the initial attributes from the geodatabase. The resulted products are various scenarios for redesigning, for analyzing new exploitation sites. Finally, these scenarios can be published as interactive web scenes for internal, groups or pubic consultation. In this way, problems like the impact of new constructions being build, re-arranging green spaces or changing routes for public transportation, etc. are revealed through impact and visibility analysis or shadowing analysis and are brought to the citizen's attention. This leads to better decisions.

SU-F-E-10: Student-Driven Exploration of Radiographic Material Properties, Phantom Construction, and Clinical Workflows Or: The Extraordinary Life of CANDY MAN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mahon, RN; Riblett, MJ; Hugo, GD

Purpose: To develop a hands-on learning experience that explores the radiological and structural properties of everyday items and applies this knowledge to design a simple phantom for radiotherapy exercises. Methods: Students were asked to compile a list of readily available materials thought to have radiation attenuation properties similar to tissues within the human torso. Participants scanned samples of suggested materials and regions of interest (ROIs) were used to characterize bulk attenuation properties. Properties of each material were assessed via comparison to a Gammex Tissue characterization phantom and used to construct a list of inexpensive near-tissue-equivalent materials. Critical discussions focusing onmore » samples found to differ from student expectations were used to revise and narrow the comprehensive list. From their newly acquired knowledge, students designed and constructed a simple thoracic phantom for use in a simulated clinical workflow. Students were tasked with setting up the phantom and acquiring planning CT images for use in treatment planning and dose delivery. Results: Under engineer and physicist supervision, students were trained to use a CT simulator and acquired images for approximately 60 different foodstuffs, candies, and household items. Through peer discussion, students gained valuable insights and were made to review preconceptions about radiographic material properties. From a subset of imaged materials, a simple phantom was successfully designed and constructed to represent a human thorax. Students received hands-on experience with clinical treatment workflows by learning how to perform CT simulation, create a treatment plan for an embedded tumor, align the phantom for treatment, and deliver a treatment fraction. Conclusion: In this activity, students demonstrated their ability to reason through the radiographic material selection process, construct a simple phantom to specifications, and exercise their knowledge of clinical workflows. Furthermore, the enjoyable and inexpensive nature of this project proved to attract participant interest and drive creative exploration. Mahon and Riblett have nothing to disclose; Hugo has a research agreement with Phillips Medical systems, a license agreement with Varian Medical Systems, research grants from the National Institute of Health. Authors do not have any potential conflicts of interest to disclose.« less

Whole brain myelin mapping using T1- and T2-weighted MR imaging data

PubMed Central

Ganzetti, Marco; Wenderoth, Nicole; Mantini, Dante

2014-01-01

Despite recent advancements in MR imaging, non-invasive mapping of myelin in the brain still remains an open issue. Here we attempted to provide a potential solution. Specifically, we developed a processing workflow based on T1-w and T2-w MR data to generate an optimized myelin enhanced contrast image. The workflow allows whole brain mapping using the T1-w/T2-w technique, which was originally introduced as a non-invasive method for assessing cortical myelin content. The hallmark of our approach is a retrospective calibration algorithm, applied to bias-corrected T1-w and T2-w images, that relies on image intensities outside the brain. This permits standardizing the intensity histogram of the ratio image, thereby allowing for across-subject statistical analyses. Quantitative comparisons of image histograms within and across different datasets confirmed the effectiveness of our normalization procedure. Not only did the calibrated T1-w/T2-w images exhibit a comparable intensity range, but also the shape of the intensity histograms was largely corresponding. We also assessed the reliability and specificity of the ratio image compared to other MR-based techniques, such as magnetization transfer ratio (MTR), fractional anisotropy (FA), and fluid-attenuated inversion recovery (FLAIR). With respect to these other techniques, T1-w/T2-w had consistently high values, as well as low inter-subject variability, in brain structures where myelin is most abundant. Overall, our results suggested that the T1-w/T2-w technique may be a valid tool supporting the non-invasive mapping of myelin in the brain. Therefore, it might find important applications in the study of brain development, aging and disease. PMID:25228871

Development of Neuromorphic Sift Operator with Application to High Speed Image Matching

NASA Astrophysics Data System (ADS)

Shankayi, M.; Saadatseresht, M.; Bitetto, M. A. V.

2015-12-01

There was always a speed/accuracy challenge in photogrammetric mapping process, including feature detection and matching. Most of the researches have improved algorithm's speed with simplifications or software modifications which increase the accuracy of the image matching process. This research tries to improve speed without enhancing the accuracy of the same algorithm using Neuromorphic techniques. In this research we have developed a general design of a Neuromorphic ASIC to handle algorithms such as SIFT. We also have investigated neural assignment in each step of the SIFT algorithm. With a rough estimation based on delay of the used elements including MAC and comparator, we have estimated the resulting chip's performance for 3 scenarios, Full HD movie (Videogrammetry), 24 MP (UAV photogrammetry), and 88 MP image sequence. Our estimations led to approximate 3000 fps for Full HD movie, 250 fps for 24 MP image sequence and 68 fps for 88MP Ultracam image sequence which can be a huge improvement for current photogrammetric processing systems. We also estimated the power consumption of less than10 watts which is not comparable to current workflows.

Experiences and lessons learned from creating a generalized workflow for data publication of field campaign datasets

NASA Astrophysics Data System (ADS)

Santhana Vannan, S. K.; Ramachandran, R.; Deb, D.; Beaty, T.; Wright, D.

2017-12-01

This paper summarizes the workflow challenges of curating and publishing data produced from disparate data sources and provides a generalized workflow solution to efficiently archive data generated by researchers. The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemical dynamics and the Global Hydrology Resource Center (GHRC) DAAC have been collaborating on the development of a generalized workflow solution to efficiently manage the data publication process. The generalized workflow presented here are built on lessons learned from implementations of the workflow system. Data publication consists of the following steps: Accepting the data package from the data providers, ensuring the full integrity of the data files. Identifying and addressing data quality issues Assembling standardized, detailed metadata and documentation, including file level details, processing methodology, and characteristics of data files Setting up data access mechanisms Setup of the data in data tools and services for improved data dissemination and user experience Registering the dataset in online search and discovery catalogues Preserving the data location through Digital Object Identifiers (DOI) We will describe the steps taken to automate, and realize efficiencies to the above process. The goals of the workflow system are to reduce the time taken to publish a dataset, to increase the quality of documentation and metadata, and to track individual datasets through the data curation process. Utilities developed to achieve these goal will be described. We will also share metrics driven value of the workflow system and discuss the future steps towards creation of a common software framework.

Clinical evaluation of new automatic coronary-specific best cardiac phase selection algorithm for single-beat coronary CT angiography.

PubMed

Wang, Hui; Xu, Lei; Fan, Zhanming; Liang, Junfu; Yan, Zixu; Sun, Zhonghua

2017-01-01

The aim of this study was to evaluate the workflow efficiency of a new automatic coronary-specific reconstruction technique (Smart Phase, GE Healthcare-SP) for selection of the best cardiac phase with least coronary motion when compared with expert manual selection (MS) of best phase in patients with high heart rate. A total of 46 patients with heart rates above 75 bpm who underwent single beat coronary computed tomography angiography (CCTA) were enrolled in this study. CCTA of all subjects were performed on a 256-detector row CT scanner (Revolution CT, GE Healthcare, Waukesha, Wisconsin, US). With the SP technique, the acquired phase range was automatically searched in 2% phase intervals during the reconstruction process to determine the optimal phase for coronary assessment, while for routine expert MS, reconstructions were performed at 5% intervals and a best phase was manually determined. The reconstruction and review times were recorded to measure the workflow efficiency for each method. Two reviewers subjectively assessed image quality for each coronary artery in the MS and SP reconstruction volumes using a 4-point grading scale. The average HR of the enrolled patients was 91.1±19.0bpm. A total of 204 vessels were assessed. The subjective image quality using SP was comparable to that of the MS, 1.45±0.85 vs 1.43±0.81 respectively (p = 0.88). The average time was 246 seconds for the manual best phase selection, and 98 seconds for the SP selection, resulting in average time saving of 148 seconds (60%) with use of the SP algorithm. The coronary specific automatic cardiac best phase selection technique (Smart Phase) improves clinical workflow in high heart rate patients and provides image quality comparable with manual cardiac best phase selection. Reconstruction of single-beat CCTA exams with SP can benefit the users with less experienced in CCTA image interpretation.

PACS for surgery and interventional radiology: features of a Therapy Imaging and Model Management System (TIMMS).

PubMed

Lemke, Heinz U; Berliner, Leonard

2011-05-01

Appropriate use of information and communication technology (ICT) and mechatronic (MT) systems is viewed by many experts as a means to improve workflow and quality of care in the operating room (OR). This will require a suitable information technology (IT) infrastructure, as well as communication and interface standards, such as specialized extensions of DICOM, to allow data interchange between surgical system components in the OR. A design of such an infrastructure, sometimes referred to as surgical PACS, but better defined as a Therapy Imaging and Model Management System (TIMMS), will be introduced in this article. A TIMMS should support the essential functions that enable and advance image guided therapy, and in the future, a more comprehensive form of patient-model guided therapy. Within this concept, the "image-centric world view" of the classical PACS technology is complemented by an IT "model-centric world view". Such a view is founded in the special patient modelling needs of an increasing number of modern surgical interventions as compared to the imaging intensive working mode of diagnostic radiology, for which PACS was originally conceptualised and developed. The modelling aspects refer to both patient information and workflow modelling. Standards for creating and integrating information about patients, equipment, and procedures are vitally needed when planning for an efficient OR. The DICOM Working Group 24 (WG-24) has been established to develop DICOM objects and services related to image and model guided surgery. To determine these standards, it is important to define step-by-step surgical workflow practices and create interventional workflow models per procedures or per variable cases. As the boundaries between radiation therapy, surgery and interventional radiology are becoming less well-defined, precise patient models will become the greatest common denominator for all therapeutic disciplines. In addition to imaging, the focus of WG-24 is to serve the therapeutic disciplines by enabling modelling technology to be based on standards. Copyright © 2011. Published by Elsevier Ireland Ltd.

Pervasive access to images and data--the use of computing grids and mobile/wireless devices across healthcare enterprises.

PubMed

Pohjonen, Hanna; Ross, Peeter; Blickman, Johan G; Kamman, Richard

2007-01-01

Emerging technologies are transforming the workflows in healthcare enterprises. Computing grids and handheld mobile/wireless devices are providing clinicians with enterprise-wide access to all patient data and analysis tools on a pervasive basis. In this paper, emerging technologies are presented that provide computing grids and streaming-based access to image and data management functions, and system architectures that enable pervasive computing on a cost-effective basis. Finally, the implications of such technologies are investigated regarding the positive impacts on clinical workflows.

Adaptive Texture Synthesis for Large Scale City Modeling

NASA Astrophysics Data System (ADS)

Despine, G.; Colleu, T.

2015-02-01

Large scale city models textured with aerial images are well suited for bird-eye navigation but generally the image resolution does not allow pedestrian navigation. One solution to face this problem is to use high resolution terrestrial photos but it requires huge amount of manual work to remove occlusions. Another solution is to synthesize generic textures with a set of procedural rules and elementary patterns like bricks, roof tiles, doors and windows. This solution may give realistic textures but with no correlation to the ground truth. Instead of using pure procedural modelling we present a method to extract information from aerial images and adapt the texture synthesis to each building. We describe a workflow allowing the user to drive the information extraction and to select the appropriate texture patterns. We also emphasize the importance to organize the knowledge about elementary pattern in a texture catalogue allowing attaching physical information, semantic attributes and to execute selection requests. Roofs are processed according to the detected building material. Façades are first described in terms of principal colours, then opening positions are detected and some window features are computed. These features allow selecting the most appropriate patterns from the texture catalogue. We experimented this workflow on two samples with 20 cm and 5 cm resolution images. The roof texture synthesis and opening detection were successfully conducted on hundreds of buildings. The window characterization is still sensitive to the distortions inherent to the projection of aerial images onto the facades.

Advanced 3-D analysis, client-server systems, and cloud computing-Integration of cardiovascular imaging data into clinical workflows of transcatheter aortic valve replacement.

PubMed

Schoenhagen, Paul; Zimmermann, Mathis; Falkner, Juergen

2013-06-01

Degenerative aortic stenosis is highly prevalent in the aging populations of industrialized countries and is associated with poor prognosis. Surgical valve replacement has been the only established treatment with documented improvement of long-term outcome. However, many of the older patients with aortic stenosis (AS) are high-risk or ineligible for surgery. For these patients, transcatheter aortic valve replacement (TAVR) has emerged as a treatment alternative. The TAVR procedure is characterized by a lack of visualization of the operative field. Therefore, pre- and intra-procedural imaging is critical for patient selection, pre-procedural planning, and intra-operative decision-making. Incremental to conventional angiography and 2-D echocardiography, multidetector computed tomography (CT) has assumed an important role before TAVR. The analysis of 3-D CT data requires extensive post-processing during direct interaction with the dataset, using advance analysis software. Organization and storage of the data according to complex clinical workflows and sharing of image information have become a critical part of these novel treatment approaches. Optimally, the data are integrated into a comprehensive image data file accessible to multiple groups of practitioners across the hospital. This creates new challenges for data management requiring a complex IT infrastructure, spanning across multiple locations, but is increasingly achieved with client-server solutions and private cloud technology. This article describes the challenges and opportunities created by the increased amount of patient-specific imaging data in the context of TAVR.

New hardware and workflows for semi-automated correlative cryo-fluorescence and cryo-electron microscopy/tomography.

PubMed

Schorb, Martin; Gaechter, Leander; Avinoam, Ori; Sieckmann, Frank; Clarke, Mairi; Bebeacua, Cecilia; Bykov, Yury S; Sonnen, Andreas F-P; Lihl, Reinhard; Briggs, John A G

2017-02-01

Correlative light and electron microscopy allows features of interest defined by fluorescence signals to be located in an electron micrograph of the same sample. Rare dynamic events or specific objects can be identified, targeted and imaged by electron microscopy or tomography. To combine it with structural studies using cryo-electron microscopy or tomography, fluorescence microscopy must be performed while maintaining the specimen vitrified at liquid-nitrogen temperatures and in a dry environment during imaging and transfer. Here we present instrumentation, software and an experimental workflow that improves the ease of use, throughput and performance of correlated cryo-fluorescence and cryo-electron microscopy. The new cryo-stage incorporates a specially modified high-numerical aperture objective lens and provides a stable and clean imaging environment. It is combined with a transfer shuttle for contamination-free loading of the specimen. Optimized microscope control software allows automated acquisition of the entire specimen area by cryo-fluorescence microscopy. The software also facilitates direct transfer of the fluorescence image and associated coordinates to the cryo-electron microscope for subsequent fluorescence-guided automated imaging. Here we describe these technological developments and present a detailed workflow, which we applied for automated cryo-electron microscopy and tomography of various specimens. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Using Object Storage Technology vs Vendor Neutral Archives for an Image Data Repository Infrastructure.

PubMed

Bialecki, Brian; Park, James; Tilkin, Mike

2016-08-01

The intent of this project was to use object storage and its database, which has the ability to add custom extensible metadata to an imaging object being stored within the system, to harness the power of its search capabilities, and to close the technology gap that healthcare faces. This creates a non-disruptive tool that can be used natively by both legacy systems and the healthcare systems of today which leverage more advanced storage technologies. The base infrastructure can be populated alongside current workflows without any interruption to the delivery of services. In certain use cases, this technology can be seen as a true alternative to the VNA (Vendor Neutral Archive) systems implemented by healthcare today. The scalability, security, and ability to process complex objects makes this more than just storage for image data and a commodity to be consumed by PACS (Picture Archiving and Communication System) and workstations. Object storage is a smart technology that can be leveraged to create vendor independence, standards compliance, and a data repository that can be mined for truly relevant content by adding additional context to search capabilities. This functionality can lead to efficiencies in workflow and a wealth of minable data to improve outcomes into the future.

Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials

PubMed Central

Powers, Christina M; Mills, Karmann A; Morris, Stephanie A; Klaessig, Fred; Gaheen, Sharon; Lewinski, Nastassja

2015-01-01

Summary There is a critical opportunity in the field of nanoscience to compare and integrate information across diverse fields of study through informatics (i.e., nanoinformatics). This paper is one in a series of articles on the data curation process in nanoinformatics (nanocuration). Other articles in this series discuss key aspects of nanocuration (temporal metadata, data completeness, database integration), while the focus of this article is on the nanocuration workflow, or the process of identifying, inputting, and reviewing nanomaterial data in a data repository. In particular, the article discusses: 1) the rationale and importance of a defined workflow in nanocuration, 2) the influence of organizational goals or purpose on the workflow, 3) established workflow practices in other fields, 4) current workflow practices in nanocuration, 5) key challenges for workflows in emerging fields like nanomaterials, 6) examples to make these challenges more tangible, and 7) recommendations to address the identified challenges. Throughout the article, there is an emphasis on illustrating key concepts and current practices in the field. Data on current practices in the field are from a group of stakeholders active in nanocuration. In general, the development of workflows for nanocuration is nascent, with few individuals formally trained in data curation or utilizing available nanocuration resources (e.g., ISA-TAB-Nano). Additional emphasis on the potential benefits of cultivating nanomaterial data via nanocuration processes (e.g., capability to analyze data from across research groups) and providing nanocuration resources (e.g., training) will likely prove crucial for the wider application of nanocuration workflows in the scientific community. PMID:26425437

Performance assessment of multi-frequency processing of ICU chest images for enhanced visualization of tubes and catheters

NASA Astrophysics Data System (ADS)

Wang, Xiaohui; Couwenhoven, Mary E.; Foos, David H.; Doran, James; Yankelevitz, David F.; Henschke, Claudia I.

2008-03-01

An image-processing method has been developed to improve the visibility of tube and catheter features in portable chest x-ray (CXR) images captured in the intensive care unit (ICU). The image-processing method is based on a multi-frequency approach, wherein the input image is decomposed into different spatial frequency bands, and those bands that contain the tube and catheter signals are individually enhanced by nonlinear boosting functions. Using a random sampling strategy, 50 cases were retrospectively selected for the study from a large database of portable CXR images that had been collected from multiple institutions over a two-year period. All images used in the study were captured using photo-stimulable, storage phosphor computed radiography (CR) systems. Each image was processed two ways. The images were processed with default image processing parameters such as those used in clinical settings (control). The 50 images were then separately processed using the new tube and catheter enhancement algorithm (test). Three board-certified radiologists participated in a reader study to assess differences in both detection-confidence performance and diagnostic efficiency between the control and test images. Images were evaluated on a diagnostic-quality, 3-megapixel monochrome monitor. Two scenarios were studied: the baseline scenario, representative of today's workflow (a single-control image presented with the window/level adjustments enabled) vs. the test scenario (a control/test image pair presented with a toggle enabled and the window/level settings disabled). The radiologists were asked to read the images in each scenario as they normally would for clinical diagnosis. Trend analysis indicates that the test scenario offers improved reading efficiency while providing as good or better detection capability compared to the baseline scenario.

Evaluation of DICOM viewer software for workflow integration in clinical trials

NASA Astrophysics Data System (ADS)

Haak, Daniel; Page, Charles E.; Kabino, Klaus; Deserno, Thomas M.

2015-03-01

The digital imaging and communications in medicine (DICOM) protocol is nowadays the leading standard for capture, exchange and storage of image data in medical applications. A broad range of commercial, free, and open source software tools supporting a variety of DICOM functionality exists. However, different from patient's care in hospital, DICOM has not yet arrived in electronic data capture systems (EDCS) for clinical trials. Due to missing integration, even just the visualization of patient's image data in electronic case report forms (eCRFs) is impossible. Four increasing levels for integration of DICOM components into EDCS are conceivable, raising functionality but also demands on interfaces with each level. Hence, in this paper, a comprehensive evaluation of 27 DICOM viewer software projects is performed, investigating viewing functionality as well as interfaces for integration. Concerning general, integration, and viewing requirements the survey involves the criteria (i) license, (ii) support, (iii) platform, (iv) interfaces, (v) two-dimensional (2D) and (vi) three-dimensional (3D) image viewing functionality. Optimal viewers are suggested for applications in clinical trials for 3D imaging, hospital communication, and workflow. Focusing on open source solutions, the viewers ImageJ and MicroView are superior for 3D visualization, whereas GingkoCADx is advantageous for hospital integration. Concerning workflow optimization in multi-centered clinical trials, we suggest the open source viewer Weasis. Covering most use cases, an EDCS and PACS interconnection with Weasis is suggested.

NeuronRead, an open source semi-automated tool for morphometric analysis of phase contrast and fluorescence neuronal images.

PubMed

Dias, Roberto A; Gonçalves, Bruno P; da Rocha, Joana F; da Cruz E Silva, Odete A B; da Silva, Augusto M F; Vieira, Sandra I

2017-12-01

Neurons are specialized cells of the Central Nervous System whose function is intricately related to the neuritic network they develop to transmit information. Morphological evaluation of this network and other neuronal structures is required to establish relationships between neuronal morphology and function, and may allow monitoring physiological and pathophysiologic alterations. Fluorescence-based microphotographs are the most widely used in cellular bioimaging, but phase contrast (PhC) microphotographs are easier to obtain, more affordable, and do not require invasive, complicated and disruptive techniques. Despite the various freeware tools available for fluorescence-based images analysis, few exist that can tackle the more elusive and harder-to-analyze PhC images. To surpass this, an interactive semi-automated image processing workflow was developed to easily extract relevant information (e.g. total neuritic length, average cell body area) from both PhC and fluorescence neuronal images. This workflow, named 'NeuronRead', was developed in the form of an ImageJ macro. Its robustness and adaptability were tested and validated on rat cortical primary neurons under control and differentiation inhibitory conditions. Validation included a comparison to manual determinations and to a golden standard freeware tool for fluorescence image analysis. NeuronRead was subsequently applied to PhC images of neurons at distinct differentiation days and exposed or not to DAPT, a pharmacological inhibitor of the γ-secretase enzyme, which cleaves the well-known Alzheimer's amyloid precursor protein (APP) and the Notch receptor. Data obtained confirms a neuritogenic regulatory role for γ-secretase products and validates NeuronRead as a time- and cost-effective useful monitoring tool. Copyright © 2017. Published by Elsevier Inc.

High resolution crustal image of South California Continental Borderland: Reverse time imaging including multiples

NASA Astrophysics Data System (ADS)

Bian, A.; Gantela, C.

2014-12-01

Strong multiples were observed in marine seismic data of Los Angeles Regional Seismic Experiment (LARSE).It is crucial to eliminate these multiples in conventional ray-based or one-way wave-equation based depth image methods. As long as multiples contain information of target zone along travelling path, it's possible to use them as signal, to improve the illumination coverage thus enhance the image quality of structural boundaries. Reverse time migration including multiples is a two-way wave-equation based prestack depth image method that uses both primaries and multiples to map structural boundaries. Several factors, including source wavelet, velocity model, back ground noise, data acquisition geometry and preprocessing workflow may influence the quality of image. The source wavelet is estimated from direct arrival of marine seismic data. Migration velocity model is derived from integrated model building workflow, and the sharp velocity interfaces near sea bottom needs to be preserved in order to generate multiples in the forward and backward propagation steps. The strong amplitude, low frequency marine back ground noise needs to be removed before the final imaging process. High resolution reverse time image sections of LARSE Lines 1 and Line 2 show five interfaces: depth of sea-bottom, base of sedimentary basins, top of Catalina Schist, a deep layer and a possible pluton boundary. Catalina Schist shows highs in the San Clemente ridge, Emery Knoll, Catalina Ridge, under Catalina Basin on both the lines, and a minor high under Avalon Knoll. The high of anticlinal fold in Line 1 is under the north edge of Emery Knoll and under the San Clemente fault zone. An area devoid of any reflection features are interpreted as sides of an igneous plume.

Technical Challenges of Enterprise Imaging: HIMSS-SIIM Collaborative White Paper.

PubMed

Clunie, David A; Dennison, Don K; Cram, Dawn; Persons, Kenneth R; Bronkalla, Mark D; Primo, Henri Rik

2016-10-01

This white paper explores the technical challenges and solutions for acquiring (capturing) and managing enterprise images, particularly those involving visible light applications. The types of acquisition devices used for various general-purpose photography and specialized applications including dermatology, endoscopy, and anatomic pathology are reviewed. The formats and standards used, and the associated metadata requirements and communication protocols for transfer and workflow are considered. Particular emphasis is placed on the importance of metadata capture in both order- and encounter-based workflow. The benefits of using DICOM to provide a standard means of recording and accessing both metadata and image and video data are considered, as is the role of IHE and FHIR.

Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform.

PubMed

Moutsatsos, Ioannis K; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J; Jenkins, Jeremy L; Holway, Nicholas; Tallarico, John; Parker, Christian N

2017-03-01

High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an "off-the-shelf," open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community.

Jenkins-CI, an Open-Source Continuous Integration System, as a Scientific Data and Image-Processing Platform

PubMed Central

Moutsatsos, Ioannis K.; Hossain, Imtiaz; Agarinis, Claudia; Harbinski, Fred; Abraham, Yann; Dobler, Luc; Zhang, Xian; Wilson, Christopher J.; Jenkins, Jeremy L.; Holway, Nicholas; Tallarico, John; Parker, Christian N.

2016-01-01

High-throughput screening generates large volumes of heterogeneous data that require a diverse set of computational tools for management, processing, and analysis. Building integrated, scalable, and robust computational workflows for such applications is challenging but highly valuable. Scientific data integration and pipelining facilitate standardized data processing, collaboration, and reuse of best practices. We describe how Jenkins-CI, an “off-the-shelf,” open-source, continuous integration system, is used to build pipelines for processing images and associated data from high-content screening (HCS). Jenkins-CI provides numerous plugins for standard compute tasks, and its design allows the quick integration of external scientific applications. Using Jenkins-CI, we integrated CellProfiler, an open-source image-processing platform, with various HCS utilities and a high-performance Linux cluster. The platform is web-accessible, facilitates access and sharing of high-performance compute resources, and automates previously cumbersome data and image-processing tasks. Imaging pipelines developed using the desktop CellProfiler client can be managed and shared through a centralized Jenkins-CI repository. Pipelines and managed data are annotated to facilitate collaboration and reuse. Limitations with Jenkins-CI (primarily around the user interface) were addressed through the selection of helper plugins from the Jenkins-CI community. PMID:27899692

msCompare: A Framework for Quantitative Analysis of Label-free LC-MS Data for Comparative Candidate Biomarker Studies*

PubMed Central

Hoekman, Berend; Breitling, Rainer; Suits, Frank; Bischoff, Rainer; Horvatovich, Peter

2012-01-01

Data processing forms an integral part of biomarker discovery and contributes significantly to the ultimate result. To compare and evaluate various publicly available open source label-free data processing workflows, we developed msCompare, a modular framework that allows the arbitrary combination of different feature detection/quantification and alignment/matching algorithms in conjunction with a novel scoring method to evaluate their overall performance. We used msCompare to assess the performance of workflows built from modules of publicly available data processing packages such as SuperHirn, OpenMS, and MZmine and our in-house developed modules on peptide-spiked urine and trypsin-digested cerebrospinal fluid (CSF) samples. We found that the quality of results varied greatly among workflows, and interestingly, heterogeneous combinations of algorithms often performed better than the homogenous workflows. Our scoring method showed that the union of feature matrices of different workflows outperformed the original homogenous workflows in some cases. msCompare is open source software (https://trac.nbic.nl/mscompare), and we provide a web-based data processing service for our framework by integration into the Galaxy server of the Netherlands Bioinformatics Center (http://galaxy.nbic.nl/galaxy) to allow scientists to determine which combination of modules provides the most accurate processing for their particular LC-MS data sets. PMID:22318370

Medication Management: The Macrocognitive Workflow of Older Adults With Heart Failure

PubMed Central

2016-01-01

Background Older adults with chronic disease struggle to manage complex medication regimens. Health information technology has the potential to improve medication management, but only if it is based on a thorough understanding of the complexity of medication management workflow as it occurs in natural settings. Prior research reveals that patient work related to medication management is complex, cognitive, and collaborative. Macrocognitive processes are theorized as how people individually and collaboratively think in complex, adaptive, and messy nonlaboratory settings supported by artifacts. Objective The objective of this research was to describe and analyze the work of medication management by older adults with heart failure, using a macrocognitive workflow framework. Methods We interviewed and observed 61 older patients along with 30 informal caregivers about self-care practices including medication management. Descriptive qualitative content analysis methods were used to develop categories, subcategories, and themes about macrocognitive processes used in medication management workflow. Results We identified 5 high-level macrocognitive processes affecting medication management—sensemaking, planning, coordination, monitoring, and decision making—and 15 subprocesses. Data revealed workflow as occurring in a highly collaborative, fragile system of interacting people, artifacts, time, and space. Process breakdowns were common and patients had little support for macrocognitive workflow from current tools. Conclusions Macrocognitive processes affected medication management performance. Describing and analyzing this performance produced recommendations for technology supporting collaboration and sensemaking, decision making and problem detection, and planning and implementation. PMID:27733331

Medication Management: The Macrocognitive Workflow of Older Adults With Heart Failure.

PubMed

Mickelson, Robin S; Unertl, Kim M; Holden, Richard J

2016-10-12

Older adults with chronic disease struggle to manage complex medication regimens. Health information technology has the potential to improve medication management, but only if it is based on a thorough understanding of the complexity of medication management workflow as it occurs in natural settings. Prior research reveals that patient work related to medication management is complex, cognitive, and collaborative. Macrocognitive processes are theorized as how people individually and collaboratively think in complex, adaptive, and messy nonlaboratory settings supported by artifacts. The objective of this research was to describe and analyze the work of medication management by older adults with heart failure, using a macrocognitive workflow framework. We interviewed and observed 61 older patients along with 30 informal caregivers about self-care practices including medication management. Descriptive qualitative content analysis methods were used to develop categories, subcategories, and themes about macrocognitive processes used in medication management workflow. We identified 5 high-level macrocognitive processes affecting medication management-sensemaking, planning, coordination, monitoring, and decision making-and 15 subprocesses. Data revealed workflow as occurring in a highly collaborative, fragile system of interacting people, artifacts, time, and space. Process breakdowns were common and patients had little support for macrocognitive workflow from current tools. Macrocognitive processes affected medication management performance. Describing and analyzing this performance produced recommendations for technology supporting collaboration and sensemaking, decision making and problem detection, and planning and implementation.

Effects of a cost-effective surgical workflow on cosmesis and patient's satisfaction in open thyroid surgery.

PubMed

Billmann, Franck; Bokor-Billmann, Therezia; Voigt, Joachim; Kiffner, Erhard

2013-01-01

In thyroid surgery, minimally invasive procedures are thought to improve cosmesis and patient's satisfaction. However, studies using standardized tools are scarce, and results are controversial. Moreover, minimally invasive techniques raise the question of material costs in a context of health spending cuts. The aim of the present study is to test a cost-effective surgical workflow to improve cosmesis in conventional open thyroid surgery. Our study ran between January 2009 and November 2010, and was based on a prospectively maintained thyroid surgery register. Patients operated for benign thyroid diseases were included. Since January 2010, a standardized surgical workflow was used in addition to the reference open procedure to improve the outcome. Two groups were created: (1) G1 group (patients operated with the reference technique), (2) G2 group (patients operated with our workflow in addition to reference technique). Patients were investigated for postoperative outcomes, self-evaluated body image, cosmetic and self-confidence scores. 820 patients were included in the present study. The overall body image and cosmetic scores were significantly better in the G2 group (P < 0.05). No significant difference was noted in terms of surgical outcomes, scar length, and self-confidence. Our surgical workflow in conjunction with the reference technique is safe and shows significant better results in terms of body image and cosmesis than do the reference technique alone. Thus, we recommend its implementation in order to improve outcomes in a cost-effective way. The limitations of the present study should be kept in mind in the elaboration of future studies. Copyright © 2012 Surgical Associates Ltd. Published by Elsevier Ltd. All rights reserved.

SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects

PubMed Central

2014-01-01

Background Light microscopic analysis of diatom frustules is widely used both in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. In these applications, usually large numbers of frustules need to be identified and/or measured. Although there is a need for automation in these applications, and image processing and analysis methods supporting these tasks have previously been developed, they did not become widespread in diatom analysis. While methodological reports for a wide variety of methods for image segmentation, diatom identification and feature extraction are available, no single implementation combining a subset of these into a readily applicable workflow accessible to diatomists exists. Results The newly developed tool SHERPA offers a versatile image processing workflow focused on the identification and measurement of object outlines, handling all steps from image segmentation over object identification to feature extraction, and providing interactive functions for reviewing and revising results. Special attention was given to ease of use, applicability to a broad range of data and problems, and supporting high throughput analyses with minimal manual intervention. Conclusions Tested with several diatom datasets from different sources and of various compositions, SHERPA proved its ability to successfully analyze large amounts of diatom micrographs depicting a broad range of species. SHERPA is unique in combining the following features: application of multiple segmentation methods and selection of the one giving the best result for each individual object; identification of shapes of interest based on outline matching against a template library; quality scoring and ranking of resulting outlines supporting quick quality checking; extraction of a wide range of outline shape descriptors widely used in diatom studies and elsewhere; minimizing the need for, but enabling manual quality control and corrections. Although primarily developed for analyzing images of diatom valves originating from automated microscopy, SHERPA can also be useful for other object detection, segmentation and outline-based identification problems. PMID:24964954

SHERPA: an image segmentation and outline feature extraction tool for diatoms and other objects.

PubMed

Kloster, Michael; Kauer, Gerhard; Beszteri, Bánk

2014-06-25

Light microscopic analysis of diatom frustules is widely used both in basic and applied research, notably taxonomy, morphometrics, water quality monitoring and paleo-environmental studies. In these applications, usually large numbers of frustules need to be identified and/or measured. Although there is a need for automation in these applications, and image processing and analysis methods supporting these tasks have previously been developed, they did not become widespread in diatom analysis. While methodological reports for a wide variety of methods for image segmentation, diatom identification and feature extraction are available, no single implementation combining a subset of these into a readily applicable workflow accessible to diatomists exists. The newly developed tool SHERPA offers a versatile image processing workflow focused on the identification and measurement of object outlines, handling all steps from image segmentation over object identification to feature extraction, and providing interactive functions for reviewing and revising results. Special attention was given to ease of use, applicability to a broad range of data and problems, and supporting high throughput analyses with minimal manual intervention. Tested with several diatom datasets from different sources and of various compositions, SHERPA proved its ability to successfully analyze large amounts of diatom micrographs depicting a broad range of species. SHERPA is unique in combining the following features: application of multiple segmentation methods and selection of the one giving the best result for each individual object; identification of shapes of interest based on outline matching against a template library; quality scoring and ranking of resulting outlines supporting quick quality checking; extraction of a wide range of outline shape descriptors widely used in diatom studies and elsewhere; minimizing the need for, but enabling manual quality control and corrections. Although primarily developed for analyzing images of diatom valves originating from automated microscopy, SHERPA can also be useful for other object detection, segmentation and outline-based identification problems.

MassCascade: Visual Programming for LC-MS Data Processing in Metabolomics.

PubMed

Beisken, Stephan; Earll, Mark; Portwood, David; Seymour, Mark; Steinbeck, Christoph

2014-04-01

Liquid chromatography coupled to mass spectrometry (LC-MS) is commonly applied to investigate the small molecule complement of organisms. Several software tools are typically joined in custom pipelines to semi-automatically process and analyse the resulting data. General workflow environments like the Konstanz Information Miner (KNIME) offer the potential of an all-in-one solution to process LC-MS data by allowing easy integration of different tools and scripts. We describe MassCascade and its workflow plug-in for processing LC-MS data. The Java library integrates frequently used algorithms in a modular fashion, thus enabling it to serve as back-end for graphical front-ends. The functions available in MassCascade have been encapsulated in a plug-in for the workflow environment KNIME, allowing combined use with e.g. statistical workflow nodes from other providers and making the tool intuitive to use without knowledge of programming. The design of the software guarantees a high level of modularity where processing functions can be quickly replaced or concatenated. MassCascade is an open-source library for LC-MS data processing in metabolomics. It embraces the concept of visual programming through its KNIME plug-in, simplifying the process of building complex workflows. The library was validated using open data.

A Mixed-Methods Research Framework for Healthcare Process Improvement.

PubMed

Bastian, Nathaniel D; Munoz, David; Ventura, Marta

2016-01-01

The healthcare system in the United States is spiraling out of control due to ever-increasing costs without significant improvements in quality, access to care, satisfaction, and efficiency. Efficient workflow is paramount to improving healthcare value while maintaining the utmost standards of patient care and provider satisfaction in high stress environments. This article provides healthcare managers and quality engineers with a practical healthcare process improvement framework to assess, measure and improve clinical workflow processes. The proposed mixed-methods research framework integrates qualitative and quantitative tools to foster the improvement of processes and workflow in a systematic way. The framework consists of three distinct phases: 1) stakeholder analysis, 2a) survey design, 2b) time-motion study, and 3) process improvement. The proposed framework is applied to the pediatric intensive care unit of the Penn State Hershey Children's Hospital. The implementation of this methodology led to identification and categorization of different workflow tasks and activities into both value-added and non-value added in an effort to provide more valuable and higher quality patient care. Based upon the lessons learned from the case study, the three-phase methodology provides a better, broader, leaner, and holistic assessment of clinical workflow. The proposed framework can be implemented in various healthcare settings to support continuous improvement efforts in which complexity is a daily element that impacts workflow. We proffer a general methodology for process improvement in a healthcare setting, providing decision makers and stakeholders with a useful framework to help their organizations improve efficiency. Published by Elsevier Inc.

Inferring Clinical Workflow Efficiency via Electronic Medical Record Utilization

PubMed Central

Chen, You; Xie, Wei; Gunter, Carl A; Liebovitz, David; Mehrotra, Sanjay; Zhang, He; Malin, Bradley

2015-01-01

Complexity in clinical workflows can lead to inefficiency in making diagnoses, ineffectiveness of treatment plans and uninformed management of healthcare organizations (HCOs). Traditional strategies to manage workflow complexity are based on measuring the gaps between workflows defined by HCO administrators and the actual processes followed by staff in the clinic. However, existing methods tend to neglect the influences of EMR systems on the utilization of workflows, which could be leveraged to optimize workflows facilitated through the EMR. In this paper, we introduce a framework to infer clinical workflows through the utilization of an EMR and show how such workflows roughly partition into four types according to their efficiency. Our framework infers workflows at several levels of granularity through data mining technologies. We study four months of EMR event logs from a large medical center, including 16,569 inpatient stays, and illustrate that over approximately 95% of workflows are efficient and that 80% of patients are on such workflows. At the same time, we show that the remaining 5% of workflows may be inefficient due to a variety of factors, such as complex patients. PMID:26958173

A simple tool for stereological assessment of digital images: the STEPanizer.

PubMed

Tschanz, S A; Burri, P H; Weibel, E R

2011-07-01

STEPanizer is an easy-to-use computer-based software tool for the stereological assessment of digitally captured images from all kinds of microscopical (LM, TEM, LSM) and macroscopical (radiology, tomography) imaging modalities. The program design focuses on providing the user a defined workflow adapted to most basic stereological tasks. The software is compact, that is user friendly without being bulky. STEPanizer comprises the creation of test systems, the appropriate display of digital images with superimposed test systems, a scaling facility, a counting module and an export function for the transfer of results to spreadsheet programs. Here we describe the major workflow of the tool illustrating the application on two examples from transmission electron microscopy and light microscopy, respectively. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

An Integrated Framework for Parameter-based Optimization of Scientific Workflows.

PubMed

Kumar, Vijay S; Sadayappan, P; Mehta, Gaurang; Vahi, Karan; Deelman, Ewa; Ratnakar, Varun; Kim, Jihie; Gil, Yolanda; Hall, Mary; Kurc, Tahsin; Saltz, Joel

2009-01-01

Data analysis processes in scientific applications can be expressed as coarse-grain workflows of complex data processing operations with data flow dependencies between them. Performance optimization of these workflows can be viewed as a search for a set of optimal values in a multi-dimensional parameter space. While some performance parameters such as grouping of workflow components and their mapping to machines do not a ect the accuracy of the output, others may dictate trading the output quality of individual components (and of the whole workflow) for performance. This paper describes an integrated framework which is capable of supporting performance optimizations along multiple dimensions of the parameter space. Using two real-world applications in the spatial data analysis domain, we present an experimental evaluation of the proposed framework.

Abstracted Workow Framework with a Structure from Motion Application

NASA Astrophysics Data System (ADS)

Rossi, Adam J.

In scientific and engineering disciplines, from academia to industry, there is an increasing need for the development of custom software to perform experiments, construct systems, and develop products. The natural mindset initially is to shortcut and bypass all overhead and process rigor in order to obtain an immediate result for the problem at hand, with the misconception that the software will simply be thrown away at the end. In a majority of the cases, it turns out the software persists for many years, and likely ends up in production systems for which it was not initially intended. In the current study, a framework that can be used in both industry and academic applications mitigates underlying problems associated with developing scientific and engineering software. This results in software that is much more maintainable, documented, and usable by others, specifically allowing new users to extend capabilities of components already implemented in the framework. There is a multi-disciplinary need in the fields of imaging science, computer science, and software engineering for a unified implementation model, which motivates the development of an abstracted software framework. Structure from motion (SfM) has been identified as one use case where the abstracted workflow framework can improve research efficiencies and eliminate implementation redundancies in scientific fields. The SfM process begins by obtaining 2D images of a scene from different perspectives. Features from the images are extracted and correspondences are established. This provides a sufficient amount of information to initialize the problem for fully automated processing. Transformations are established between views, and 3D points are established via triangulation algorithms. The parameters for the camera models for all views / images are solved through bundle adjustment, establishing a highly consistent point cloud. The initial sparse point cloud and camera matrices are used to generate a dense point cloud through patch based techniques or densification algorithms such as Semi-Global Matching (SGM). The point cloud can be visualized or exploited by both humans and automated techniques. In some cases the point cloud is "draped" with original imagery in order to enhance the 3D model for a human viewer. The SfM workflow can be implemented in the abstracted framework, making it easily leverageable and extensible by multiple users. Like many processes in scientific and engineering domains, the workflow described for SfM is complex and requires many disparate components to form a functional system, often utilizing algorithms implemented by many users in different languages / environments and without knowledge of how the component fits into the larger system. In practice, this generally leads to issues interfacing the components, building the software for desired platforms, understanding its concept of operations, and how it can be manipulated in order to fit the desired function for a particular application. In addition, other scientists and engineers instinctively wish to analyze the performance of the system, establish new algorithms, optimize existing processes, and establish new functionality based on current research. This requires a framework whereby new components can be easily plugged in without affecting the current implemented functionality. The need for a universal programming environment establishes the motivation for the development of the abstracted workflow framework. This software implementation, named Catena, provides base classes from which new components must derive in order to operate within the framework. The derivation mandates requirements be satisfied in order to provide a complete implementation. Additionally, the developer must provide documentation of the component in terms of its overall function and inputs. The interface input and output values corresponding to the component must be defined in terms of their respective data types, and the implementation uses mechanisms within the framework to retrieve and send the values. This process requires the developer to componentize their algorithm rather than implement it monolithically. Although the requirements of the developer are slightly greater, the benefits realized from using Catena far outweigh the overhead, and results in extensible software. This thesis provides a basis for the abstracted workflow framework concept and the Catena software implementation. The benefits are also illustrated using a detailed examination of the SfM process as an example application.

Alchemist multimodal workflows for diabetic retinopathy research, disease prevention and investigational drug discovery.

PubMed

Riposan, Adina; Taylor, Ian; Owens, David R; Rana, Omer; Conley, Edward C

2007-01-01

In this paper we present mechanisms for imaging and spectral data discovery, as applied to the early detection of pathologic mechanisms underlying diabetic retinopathy in research and clinical trial scenarios. We discuss the Alchemist framework, built using a generic peer-to-peer architecture, supporting distributed database queries and complex search algorithms based on workflow. The Alchemist is a domain-independent search mechanism that can be applied to search and data discovery scenarios in many areas. We illustrate Alchemist's ability to perform complex searches composed as a collection of peer-to-peer overlays, Grid-based services and workflows, e.g. applied to image and spectral data discovery, as applied to the early detection and prevention of retinal disease and investigational drug discovery. The Alchemist framework is built on top of decentralised technologies and uses industry standards such as Web services and SOAP for messaging.

FAST: A fully asynchronous and status-tracking pattern for geoprocessing services orchestration

NASA Astrophysics Data System (ADS)

Wu, Huayi; You, Lan; Gui, Zhipeng; Gao, Shuang; Li, Zhenqiang; Yu, Jingmin

2014-09-01

Geoprocessing service orchestration (GSO) provides a unified and flexible way to implement cross-application, long-lived, and multi-step geoprocessing service workflows by coordinating geoprocessing services collaboratively. Usually, geoprocessing services and geoprocessing service workflows are data and/or computing intensive. The intensity feature may make the execution process of a workflow time-consuming. Since it initials an execution request without blocking other interactions on the client side, an asynchronous mechanism is especially appropriate for GSO workflows. Many critical problems remain to be solved in existing asynchronous patterns for GSO including difficulties in improving performance, status tracking, and clarifying the workflow structure. These problems are a challenge when orchestrating performance efficiency, making statuses instantly available, and constructing clearly structured GSO workflows. A Fully Asynchronous and Status-Tracking (FAST) pattern that adopts asynchronous interactions throughout the whole communication tier of a workflow is proposed for GSO. The proposed FAST pattern includes a mechanism that actively pushes the latest status to clients instantly and economically. An independent proxy was designed to isolate the status tracking logic from the geoprocessing business logic, which assists the formation of a clear GSO workflow structure. A workflow was implemented in the FAST pattern to simulate the flooding process in the Poyang Lake region. Experimental results show that the proposed FAST pattern can efficiently tackle data/computing intensive geoprocessing tasks. The performance of all collaborative partners was improved due to the asynchronous mechanism throughout communication tier. A status-tracking mechanism helps users retrieve the latest running status of a GSO workflow in an efficient and instant way. The clear structure of the GSO workflow lowers the barriers for geospatial domain experts and model designers to compose asynchronous GSO workflows. Most importantly, it provides better support for locating and diagnosing potential exceptions.

Seismic depth imaging of sequence boundaries beneath the New Jersey shelf

NASA Astrophysics Data System (ADS)

Riedel, M.; Reiche, S.; Aßhoff, K.; Buske, S.

2018-06-01

Numerical modelling of fluid flow and transport processes relies on a well-constrained geological model, which is usually provided by seismic reflection surveys. In the New Jersey shelf area a large number of 2D seismic profiles provide an extensive database for constructing a reliable geological model. However, for the purpose of modelling groundwater flow, the seismic data need to be depth-converted which is usually accomplished using complementary data from borehole logs. Due to the limited availability of such data in the New Jersey shelf, we propose a two-stage processing strategy with particular emphasis on reflection tomography and pre-stack depth imaging. We apply this workflow to a seismic section crossing the entire New Jersey shelf. Due to the tomography-based velocity modelling, the processing flow does not depend on the availability of borehole logging data. Nonetheless, we validate our results by comparing the migrated depths of selected geological horizons to borehole core data from the IODP expedition 313 drill sites, located at three positions along our seismic line. The comparison yields that in the top 450 m of the migrated section, most of the selected reflectors were positioned with an accuracy close to the seismic resolution limit (≈ 4 m) for that data. For deeper layers the accuracy still remains within one seismic wavelength for the majority of the tested horizons. These results demonstrate that the processed seismic data provide a reliable basis for constructing a hydrogeological model. Furthermore, the proposed workflow can be applied to other seismic profiles in the New Jersey shelf, which will lead to an even better constrained model.

Preservation of protein fluorescence in embedded human dendritic cells for targeted 3D light and electron microscopy

PubMed Central

HÖHN, K.; FUCHS, J.; FRÖBER, A.; KIRMSE, R.; GLASS, B.; ANDERS‐ÖSSWEIN, M.; WALTHER, P.; KRÄUSSLICH, H.‐G.

2015-01-01

Summary In this study, we present a correlative microscopy workflow to combine detailed 3D fluorescence light microscopy data with ultrastructural information gained by 3D focused ion beam assisted scanning electron microscopy. The workflow is based on an optimized high pressure freezing/freeze substitution protocol that preserves good ultrastructural detail along with retaining the fluorescence signal in the resin embedded specimens. Consequently, cellular structures of interest can readily be identified and imaged by state of the art 3D confocal fluorescence microscopy and are precisely referenced with respect to an imprinted coordinate system on the surface of the resin block. This allows precise guidance of the focused ion beam assisted scanning electron microscopy and limits the volume to be imaged to the structure of interest. This, in turn, minimizes the total acquisition time necessary to conduct the time consuming ultrastructural scanning electron microscope imaging while eliminating the risk to miss parts of the target structure. We illustrate the value of this workflow for targeting virus compartments, which are formed in HIV‐pulsed mature human dendritic cells. PMID:25786567

North by Northwestern: initial experience with PACS at Northwestern Memorial Hospital

NASA Astrophysics Data System (ADS)

Channin, David S.; Hawkins, Rodney C.; Enzmann, Dieter R.

2000-05-01

This paper describes the initial phases and configuration of the Picture Archive and Communication System (PACS) deployed at Northwestern Memorial Hospital. The primary goals of the project were to improve service to patients, improve service to referring physicians, and improve the process of radiology. Secondary goals were to enhance the academic mission, and modernize institutional information systems. The system consists of a large number of heterogeneous imaging modalities sending imaging studies via DICOM to a GE medical Systems PathSpeed PACS. The radiology department workflow is briefly described. The system is currently storing approximately 140,000 studies and over 5 million images, growing by approximately 600 studies and 25,000 images per day. Data reflecting use of the short term and long term storage is provided.

Flexible Workflow Software enables the Management of an Increased Volume and Heterogeneity of Sensors, and evolves with the Expansion of Complex Ocean Observatory Infrastructures.

NASA Astrophysics Data System (ADS)

Tomlin, M. C.; Jenkyns, R.

2015-12-01

Ocean Networks Canada (ONC) collects data from observatories in the northeast Pacific, Salish Sea, Arctic Ocean, Atlantic Ocean, and land-based sites in British Columbia. Data are streamed, collected autonomously, or transmitted via satellite from a variety of instruments. The Software Engineering group at ONC develops and maintains Oceans 2.0, an in-house software system that acquires and archives data from sensors, and makes data available to scientists, the public, government and non-government agencies. The Oceans 2.0 workflow tool was developed by ONC to manage a large volume of tasks and processes required for instrument installation, recovery and maintenance activities. Since 2013, the workflow tool has supported 70 expeditions and grown to include 30 different workflow processes for the increasing complexity of infrastructures at ONC. The workflow tool strives to keep pace with an increasing heterogeneity of sensors, connections and environments by supporting versioning of existing workflows, and allowing the creation of new processes and tasks. Despite challenges in training and gaining mutual support from multidisciplinary teams, the workflow tool has become invaluable in project management in an innovative setting. It provides a collective place to contribute to ONC's diverse projects and expeditions and encourages more repeatable processes, while promoting interactions between the multidisciplinary teams who manage various aspects of instrument development and the data they produce. The workflow tool inspires documentation of terminologies and procedures, and effectively links to other tools at ONC such as JIRA, Alfresco and Wiki. Motivated by growing sensor schemes, modes of collecting data, archiving, and data distribution at ONC, the workflow tool ensures that infrastructure is managed completely from instrument purchase to data distribution. It integrates all areas of expertise and helps fulfill ONC's mandate to offer quality data to users.

MBAT: a scalable informatics system for unifying digital atlasing workflows.

PubMed

Lee, Daren; Ruffins, Seth; Ng, Queenie; Sane, Nikhil; Anderson, Steve; Toga, Arthur

2010-12-22

Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data. The MouseBIRN Atlasing Toolkit (MBAT) project was developed as a cross-platform, free open-source application that unifies and accelerates the digital atlas workflow. A tiered, plug-in architecture was designed for the neuroinformatics and genomics goals of the project to provide a modular and extensible design. MBAT provides the ability to use a single query to search and retrieve data from multiple data sources, align image data using the user's preferred registration method, composite data from multiple sources in a common space, and link relevant informatics information to the current view of the data or atlas. The workspaces leverage tool plug-ins to extend and allow future extensions of the basic workspace functionality. A wide variety of tool plug-ins were developed that integrate pre-existing as well as newly created technology into each workspace. Novel atlasing features were also developed, such as supporting multiple label sets, dynamic selection and grouping of labels, and synchronized, context-driven display of ontological data. MBAT empowers researchers to discover correlations among disparate data by providing a unified environment for bringing together distributed reference resources, a user's image data, and biological atlases into the same spatial or semantic context. Through its extensible tiered plug-in architecture, MBAT allows researchers to customize all platform components to quickly achieve personalized workflows.

Fast segmentation and high-quality three-dimensional volume mesh creation from medical images for diffuse optical tomography

NASA Astrophysics Data System (ADS)

Jermyn, Michael; Ghadyani, Hamid; Mastanduno, Michael A.; Turner, Wes; Davis, Scott C.; Dehghani, Hamid; Pogue, Brian W.

2013-08-01

Multimodal approaches that combine near-infrared (NIR) and conventional imaging modalities have been shown to improve optical parameter estimation dramatically and thus represent a prevailing trend in NIR imaging. These approaches typically involve applying anatomical templates from magnetic resonance imaging/computed tomography/ultrasound images to guide the recovery of optical parameters. However, merging these data sets using current technology requires multiple software packages, substantial expertise, significant time-commitment, and often results in unacceptably poor mesh quality for optical image reconstruction, a reality that represents a significant roadblock for translational research of multimodal NIR imaging. This work addresses these challenges directly by introducing automated digital imaging and communications in medicine image stack segmentation and a new one-click three-dimensional mesh generator optimized for multimodal NIR imaging, and combining these capabilities into a single software package (available for free download) with a streamlined workflow. Image processing time and mesh quality benchmarks were examined for four common multimodal NIR use-cases (breast, brain, pancreas, and small animal) and were compared to a commercial image processing package. Applying these tools resulted in a fivefold decrease in image processing time and 62% improvement in minimum mesh quality, in the absence of extra mesh postprocessing. These capabilities represent a significant step toward enabling translational multimodal NIR research for both expert and nonexpert users in an open-source platform.

Using Resin-Based 3D Printing to Build Geometrically Accurate Proxies of Porous Sedimentary Rocks.

PubMed

Ishutov, Sergey; Hasiuk, Franciszek J; Jobe, Dawn; Agar, Susan

2018-05-01

Three-dimensional (3D) printing is capable of transforming intricate digital models into tangible objects, allowing geoscientists to replicate the geometry of 3D pore networks of sedimentary rocks. We provide a refined method for building scalable pore-network models ("proxies") using stereolithography 3D printing that can be used in repeated flow experiments (e.g., core flooding, permeametry, porosimetry). Typically, this workflow involves two steps, model design and 3D printing. In this study, we explore how the addition of post-processing and validation can reduce uncertainty in the 3D-printed proxy accuracy (difference of proxy geometry from the digital model). Post-processing is a multi-step cleaning of porous proxies involving pressurized ethanol flushing and oven drying. Proxies are validated by: (1) helium porosimetry and (2) digital measurements of porosity from thin-section images of 3D-printed proxies. 3D printer resolution was determined by measuring the smallest open channel in 3D-printed "gap test" wafers. This resolution (400 µm) was insufficient to build porosity of Fontainebleau sandstone (∼13%) from computed tomography data at the sample's natural scale, so proxies were printed at 15-, 23-, and 30-fold magnifications to validate the workflow. Helium porosities of the 3D-printed proxies differed from digital calculations by up to 7% points. Results improved after pressurized flushing with ethanol (e.g., porosity difference reduced to ∼1% point), though uncertainties remain regarding the nature of sub-micron "artifact" pores imparted by the 3D printing process. This study shows the benefits of including post-processing and validation in any workflow to produce porous rock proxies. © 2017, National Ground Water Association.

Workflow computing. Improving management and efficiency of pathology diagnostic services.

PubMed

Buffone, G J; Moreau, D; Beck, J R

1996-04-01

Traditionally, information technology in health care has helped practitioners to collect, store, and present information and also to add a degree of automation to simple tasks (instrument interfaces supporting result entry, for example). Thus commercially available information systems do little to support the need to model, execute, monitor, coordinate, and revise the various complex clinical processes required to support health-care delivery. Workflow computing, which is already implemented and improving the efficiency of operations in several nonmedical industries, can address the need to manage complex clinical processes. Workflow computing not only provides a means to define and manage the events, roles, and information integral to health-care delivery but also supports the explicit implementation of policy or rules appropriate to the process. This article explains how workflow computing may be applied to health-care and the inherent advantages of the technology, and it defines workflow system requirements for use in health-care delivery with special reference to diagnostic pathology.

Modelling and analysis of workflow for lean supply chains

NASA Astrophysics Data System (ADS)

Ma, Jinping; Wang, Kanliang; Xu, Lida

2011-11-01

Cross-organisational workflow systems are a component of enterprise information systems which support collaborative business process among organisations in supply chain. Currently, the majority of workflow systems is developed in perspectives of information modelling without considering actual requirements of supply chain management. In this article, we focus on the modelling and analysis of the cross-organisational workflow systems in the context of lean supply chain (LSC) using Petri nets. First, the article describes the assumed conditions of cross-organisation workflow net according to the idea of LSC and then discusses the standardisation of collaborating business process between organisations in the context of LSC. Second, the concept of labelled time Petri nets (LTPNs) is defined through combining labelled Petri nets with time Petri nets, and the concept of labelled time workflow nets (LTWNs) is also defined based on LTPNs. Cross-organisational labelled time workflow nets (CLTWNs) is then defined based on LTWNs. Third, the article proposes the notion of OR-silent CLTWNS and a verifying approach to the soundness of LTWNs and CLTWNs. Finally, this article illustrates how to use the proposed method by a simple example. The purpose of this research is to establish a formal method of modelling and analysis of workflow systems for LSC. This study initiates a new perspective of research on cross-organisational workflow management and promotes operation management of LSC in real world settings.

Agile parallel bioinformatics workflow management using Pwrake.

PubMed

Mishima, Hiroyuki; Sasaki, Kensaku; Tanaka, Masahiro; Tatebe, Osamu; Yoshiura, Koh-Ichiro

2011-09-08

In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error.Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability and maintainability of rakefiles may facilitate sharing workflows among the scientific community. Workflows for GATK and Dindel are available at http://github.com/misshie/Workflows.

Agile parallel bioinformatics workflow management using Pwrake

PubMed Central

2011-01-01

Background In bioinformatics projects, scientific workflow systems are widely used to manage computational procedures. Full-featured workflow systems have been proposed to fulfil the demand for workflow management. However, such systems tend to be over-weighted for actual bioinformatics practices. We realize that quick deployment of cutting-edge software implementing advanced algorithms and data formats, and continuous adaptation to changes in computational resources and the environment are often prioritized in scientific workflow management. These features have a greater affinity with the agile software development method through iterative development phases after trial and error. Here, we show the application of a scientific workflow system Pwrake to bioinformatics workflows. Pwrake is a parallel workflow extension of Ruby's standard build tool Rake, the flexibility of which has been demonstrated in the astronomy domain. Therefore, we hypothesize that Pwrake also has advantages in actual bioinformatics workflows. Findings We implemented the Pwrake workflows to process next generation sequencing data using the Genomic Analysis Toolkit (GATK) and Dindel. GATK and Dindel workflows are typical examples of sequential and parallel workflows, respectively. We found that in practice, actual scientific workflow development iterates over two phases, the workflow definition phase and the parameter adjustment phase. We introduced separate workflow definitions to help focus on each of the two developmental phases, as well as helper methods to simplify the descriptions. This approach increased iterative development efficiency. Moreover, we implemented combined workflows to demonstrate modularity of the GATK and Dindel workflows. Conclusions Pwrake enables agile management of scientific workflows in the bioinformatics domain. The internal domain specific language design built on Ruby gives the flexibility of rakefiles for writing scientific workflows. Furthermore, readability and maintainability of rakefiles may facilitate sharing workflows among the scientific community. Workflows for GATK and Dindel are available at http://github.com/misshie/Workflows. PMID:21899774

Bacterial cell identification in differential interference contrast microscopy images.

PubMed

Obara, Boguslaw; Roberts, Mark A J; Armitage, Judith P; Grau, Vicente

2013-04-23

Microscopy image segmentation lays the foundation for shape analysis, motion tracking, and classification of biological objects. Despite its importance, automated segmentation remains challenging for several widely used non-fluorescence, interference-based microscopy imaging modalities. For example in differential interference contrast microscopy which plays an important role in modern bacterial cell biology. Therefore, new revolutions in the field require the development of tools, technologies and work-flows to extract and exploit information from interference-based imaging data so as to achieve new fundamental biological insights and understanding. We have developed and evaluated a high-throughput image analysis and processing approach to detect and characterize bacterial cells and chemotaxis proteins. Its performance was evaluated using differential interference contrast and fluorescence microscopy images of Rhodobacter sphaeroides. Results demonstrate that the proposed approach provides a fast and robust method for detection and analysis of spatial relationship between bacterial cells and their chemotaxis proteins.

Generic worklist handler for workflow-enabled products

NASA Astrophysics Data System (ADS)

Schmidt, Joachim; Meetz, Kirsten; Wendler, Thomas

1999-07-01

Workflow management (WfM) is an emerging field of medical information technology. It appears as a promising key technology to model, optimize and automate processes, for the sake of improved efficiency, reduced costs and improved patient care. The Application of WfM concepts requires the standardization of architectures and interfaces. A component of central interest proposed in this report is a generic work list handler: A standardized interface between a workflow enactment service and application system. Application systems with embedded work list handlers will be called 'Workflow Enabled Application Systems'. In this paper we discus functional requirements of work list handlers, as well as their integration into workflow architectures and interfaces. To lay the foundation for this specification, basic workflow terminology, the fundamentals of workflow management and - later in the paper - the available standards as defined by the Workflow Management Coalition are briefly reviewed.

A fully actuated robotic assistant for MRI-guided prostate biopsy and brachytherapy

NASA Astrophysics Data System (ADS)

Li, Gang; Su, Hao; Shang, Weijian; Tokuda, Junichi; Hata, Nobuhiko; Tempany, Clare M.; Fischer, Gregory S.

2013-03-01

Intra-operative medical imaging enables incorporation of human experience and intelligence in a controlled, closed-loop fashion. Magnetic resonance imaging (MRI) is an ideal modality for surgical guidance of diagnostic and therapeutic procedures, with its ability to perform high resolution, real-time, high soft tissue contrast imaging without ionizing radiation. However, for most current image-guided approaches only static pre-operative images are accessible for guidance, which are unable to provide updated information during a surgical procedure. The high magnetic field, electrical interference, and limited access of closed-bore MRI render great challenges to developing robotic systems that can perform inside a diagnostic high-field MRI while obtaining interactively updated MR images. To overcome these limitations, we are developing a piezoelectrically actuated robotic assistant for actuated percutaneous prostate interventions under real-time MRI guidance. Utilizing a modular design, the system enables coherent and straight forward workflow for various percutaneous interventions, including prostate biopsy sampling and brachytherapy seed placement, using various needle driver configurations. The unified workflow compromises: 1) system hardware and software initialization, 2) fiducial frame registration, 3) target selection and motion planning, 4) moving to the target and performing the intervention (e.g. taking a biopsy sample) under live imaging, and 5) visualization and verification. Phantom experiments of prostate biopsy and brachytherapy were executed under MRI-guidance to evaluate the feasibility of the workflow. The robot successfully performed fully actuated biopsy sampling and delivery of simulated brachytherapy seeds under live MR imaging, as well as precise delivery of a prostate brachytherapy seed distribution with an RMS accuracy of 0.98mm.

CamBAfx: Workflow Design, Implementation and Application for Neuroimaging

PubMed Central

Ooi, Cinly; Bullmore, Edward T.; Wink, Alle-Meije; Sendur, Levent; Barnes, Anna; Achard, Sophie; Aspden, John; Abbott, Sanja; Yue, Shigang; Kitzbichler, Manfred; Meunier, David; Maxim, Voichita; Salvador, Raymond; Henty, Julian; Tait, Roger; Subramaniam, Naresh; Suckling, John

2009-01-01

CamBAfx is a workflow application designed for both researchers who use workflows to process data (consumers) and those who design them (designers). It provides a front-end (user interface) optimized for data processing designed in a way familiar to consumers. The back-end uses a pipeline model to represent workflows since this is a common and useful metaphor used by designers and is easy to manipulate compared to other representations like programming scripts. As an Eclipse Rich Client Platform application, CamBAfx's pipelines and functions can be bundled with the software or downloaded post-installation. The user interface contains all the workflow facilities expected by consumers. Using the Eclipse Extension Mechanism designers are encouraged to customize CamBAfx for their own pipelines. CamBAfx wraps a workflow facility around neuroinformatics software without modification. CamBAfx's design, licensing and Eclipse Branding Mechanism allow it to be used as the user interface for other software, facilitating exchange of innovative computational tools between originating labs. PMID:19826470

Automated Topographic Change Detection via Dem Differencing at Large Scales Using The Arcticdem Database

NASA Astrophysics Data System (ADS)

Candela, S. G.; Howat, I.; Noh, M. J.; Porter, C. C.; Morin, P. J.

2016-12-01

In the last decade, high resolution satellite imagery has become an increasingly accessible tool for geoscientists to quantify changes in the Arctic land surface due to geophysical, ecological and anthropomorphic processes. However, the trade off between spatial coverage and spatial-temporal resolution has limited detailed, process-level change detection over large (i.e. continental) scales. The ArcticDEM project utilized over 300,000 Worldview image pairs to produce a nearly 100% coverage elevation model (above 60°N) offering the first polar, high spatial - high resolution (2-8m by region) dataset, often with multiple repeats in areas of particular interest to geo-scientists. A dataset of this size (nearly 250 TB) offers endless new avenues of scientific inquiry, but quickly becomes unmanageable computationally and logistically for the computing resources available to the average scientist. Here we present TopoDiff, a framework for a generalized. automated workflow that requires minimal input from the end user about a study site, and utilizes cloud computing resources to provide a temporally sorted and differenced dataset, ready for geostatistical analysis. This hands-off approach allows the end user to focus on the science, without having to manage thousands of files, or petabytes of data. At the same time, TopoDiff provides a consistent and accurate workflow for image sorting, selection, and co-registration enabling cross-comparisons between research projects.

Automating radiologist workflow, part 3: education and training.

PubMed

Reiner, Bruce

2008-12-01

The current model for radiologist education consists largely of mentorship during residency, followed by peer-to-peer training thereafter. The traditional focus of this radiologist education has historically been restricted to anatomy, pathology, and imaging modality. This "human" mentoring model becomes a limiting factor in the current practice environment because of rapid and dramatic changes in imaging and information technologies, along with the increased time demands placed on practicing radiologists. One novel way to address these burgeoning education and training challenges is to leverage technology, with the creation of user-specific and context-specific automated workflow templates. These automated templates would provide a low-stress, time-efficient, and easy-to-use equivalent of "computerized" mentoring. A radiologist could identify the workflow template of interest on the basis of the specific computer application, pathology, anatomy, or modality of interest. While the corresponding workflow template is activated, the radiologist "student" could effectively start and stop at areas of interest and use the functionality of an electronic wizard to identify additional educational resource of interest. An additional training feature of the technology is the ability to review "proven" cases for the purposes of establishing competence and credentialing.

Histostitcher™: An informatics software platform for reconstructing whole-mount prostate histology using the extensible imaging platform framework

PubMed Central

Toth, Robert J.; Shih, Natalie; Tomaszewski, John E.; Feldman, Michael D.; Kutter, Oliver; Yu, Daphne N.; Paulus, John C.; Paladini, Ginaluca; Madabhushi, Anant

2014-01-01

Context: Co-registration of ex-vivo histologic images with pre-operative imaging (e.g., magnetic resonance imaging [MRI]) can be used to align and map disease extent, and to identify quantitative imaging signatures. However, ex-vivo histology images are frequently sectioned into quarters prior to imaging. Aims: This work presents Histostitcher™, a software system designed to create a pseudo whole mount histology section (WMHS) from a stitching of four individual histology quadrant images. Materials and Methods: Histostitcher™ uses user-identified fiducials on the boundary of two quadrants to stitch such quadrants. An original prototype of Histostitcher™ was designed using the Matlab programming languages. However, clinical use was limited due to slow performance, computer memory constraints and an inefficient workflow. The latest version was created using the extensible imaging platform (XIP™) architecture in the C++ programming language. A fast, graphics processor unit renderer was designed to intelligently cache the visible parts of the histology quadrants and the workflow was significantly improved to allow modifying existing fiducials, fast transformations of the quadrants and saving/loading sessions. Results: The new stitching platform yielded significantly more efficient workflow and reconstruction than the previous prototype. It was tested on a traditional desktop computer, a Windows 8 Surface Pro table device and a 27 inch multi-touch display, with little performance difference between the different devices. Conclusions: Histostitcher™ is a fast, efficient framework for reconstructing pseudo WMHS from individually imaged quadrants. The highly modular XIP™ framework was used to develop an intuitive interface and future work will entail mapping the disease extent from the pseudo WMHS onto pre-operative MRI. PMID:24843820

The continual innovation of commercial PET/CT solutions in nuclear cardiology: Siemens Healthineers.

PubMed

Bendriem, Bernard; Reed, Jessie; McCullough, Kathryn; Khan, Mohammad Raza; Smith, Anne M; Thomas, Damita; Long, Misty

2018-04-10

Cardiac PET/CT is an evolving, non-invasive imaging modality that impacts patient management in many clinical scenarios. Beyond offering the capability to assess myocardial perfusion, inflammatory cardiac pathologies, and myocardial viability, cardiac PET/CT also allows for the non-invasive quantitative assessment of myocardial blood flow (MBF) and myocardial flow reserve (MFR). Recognizing the need for an enhanced comprehension of coronary physiology, Siemens Healthineers implemented a sophisticated solution for the calculation of MBF and MFR in 2009. As a result, each aspect of their innovative scanner and image-processing technology seamlessly integrates into an efficient, easy-to-use workflow for everyday clinical use that maximizes the number of patients who potentially benefit from this imaging modality.

Flexible Early Warning Systems with Workflows and Decision Tables

NASA Astrophysics Data System (ADS)

Riedel, F.; Chaves, F.; Zeiner, H.

2012-04-01

An essential part of early warning systems and systems for crisis management are decision support systems that facilitate communication and collaboration. Often official policies specify how different organizations collaborate and what information is communicated to whom. For early warning systems it is crucial that information is exchanged dynamically in a timely manner and all participants get exactly the information they need to fulfil their role in the crisis management process. Information technology obviously lends itself to automate parts of the process. We have experienced however that in current operational systems the information logistics processes are hard-coded, even though they are subject to change. In addition, systems are tailored to the policies and requirements of a certain organization and changes can require major software refactoring. We seek to develop a system that can be deployed and adapted to multiple organizations with different dynamic runtime policies. A major requirement for such a system is that changes can be applied locally without affecting larger parts of the system. In addition to the flexibility regarding changes in policies and processes, the system needs to be able to evolve; when new information sources become available, it should be possible to integrate and use these in the decision process. In general, this kind of flexibility comes with a significant increase in complexity. This implies that only IT professionals can maintain a system that can be reconfigured and adapted; end-users are unable to utilise the provided flexibility. In the business world similar problems arise and previous work suggested using business process management systems (BPMS) or workflow management systems (WfMS) to guide and automate early warning processes or crisis management plans. However, the usability and flexibility of current WfMS are limited, because current notations and user interfaces are still not suitable for end-users, and workflows are usually only suited for rigid processes. We show how improvements can be achieved by using decision tables and rule-based adaptive workflows. Decision tables have been shown to be an intuitive tool that can be used by domain experts to express rule sets that can be interpreted automatically at runtime. Adaptive workflows use a rule-based approach to increase the flexibility of workflows by providing mechanisms to adapt workflows based on context changes, human intervention and availability of services. The combination of workflows, decision tables and rule-based adaption creates a framework that opens up new possibilities for flexible and adaptable workflows, especially, for use in early warning and crisis management systems.

A Model of Workflow Composition for Emergency Management

NASA Astrophysics Data System (ADS)

Xin, Chen; Bin-ge, Cui; Feng, Zhang; Xue-hui, Xu; Shan-shan, Fu

The common-used workflow technology is not flexible enough in dealing with concurrent emergency situations. The paper proposes a novel model for defining emergency plans, in which workflow segments appear as a constituent part. A formal abstraction, which contains four operations, is defined to compose workflow segments under constraint rule. The software system of the business process resources construction and composition is implemented and integrated into Emergency Plan Management Application System.

OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid.

PubMed

Poehlman, William L; Rynge, Mats; Branton, Chris; Balamurugan, D; Feltus, Frank A

2016-01-01

High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG). We describe the usage of the workflow (OSG-GEM), discuss workflow design, inspect performance data, and assess accuracy in mapping paired-end sequencing reads to a reference genome. A target OSG-GEM user is proficient with the Linux command line and possesses basic bioinformatics experience. The user may run this workflow directly on the OSG or adapt it to novel computing environments.

OSG-GEM: Gene Expression Matrix Construction Using the Open Science Grid

PubMed Central

Poehlman, William L.; Rynge, Mats; Branton, Chris; Balamurugan, D.; Feltus, Frank A.

2016-01-01

High-throughput DNA sequencing technology has revolutionized the study of gene expression while introducing significant computational challenges for biologists. These computational challenges include access to sufficient computer hardware and functional data processing workflows. Both these challenges are addressed with our scalable, open-source Pegasus workflow for processing high-throughput DNA sequence datasets into a gene expression matrix (GEM) using computational resources available to U.S.-based researchers on the Open Science Grid (OSG). We describe the usage of the workflow (OSG-GEM), discuss workflow design, inspect performance data, and assess accuracy in mapping paired-end sequencing reads to a reference genome. A target OSG-GEM user is proficient with the Linux command line and possesses basic bioinformatics experience. The user may run this workflow directly on the OSG or adapt it to novel computing environments. PMID:27499617

Multi-modality molecular imaging: pre-clinical laboratory configuration

NASA Astrophysics Data System (ADS)

Wu, Yanjun; Wellen, Jeremy W.; Sarkar, Susanta K.

2006-02-01

In recent years, the prevalence of in vivo molecular imaging applications has rapidly increased. Here we report on the construction of a multi-modality imaging facility in a pharmaceutical setting that is expected to further advance existing capabilities for in vivo imaging of drug distribution and the interaction with their target. The imaging instrumentation in our facility includes a microPET scanner, a four wavelength time-domain optical imaging scanner, a 9.4T/30cm MRI scanner and a SPECT/X-ray CT scanner. An electronics shop and a computer room dedicated to image analysis are additional features of the facility. The layout of the facility was designed with a central animal preparation room surrounded by separate laboratory rooms for each of the major imaging modalities to accommodate the work-flow of simultaneous in vivo imaging experiments. This report will focus on the design of and anticipated applications for our microPET and optical imaging laboratory spaces. Additionally, we will discuss efforts to maximize the daily throughput of animal scans through development of efficient experimental work-flows and the use of multiple animals in a single scanning session.

Using lean methodology to improve productivity in a hospital oncology pharmacy.

PubMed

Sullivan, Peter; Soefje, Scott; Reinhart, David; McGeary, Catherine; Cabie, Eric D

2014-09-01

Quality improvements achieved by a hospital pharmacy through the use of lean methodology to guide i.v. compounding workflow changes are described. The outpatient oncology pharmacy of Yale-New Haven Hospital conducted a quality-improvement initiative to identify and implement workflow changes to support a major expansion of chemotherapy services. Applying concepts of lean methodology (i.e., elimination of non-value-added steps and waste in the production process), the pharmacy team performed a failure mode and effects analysis, workflow mapping, and impact analysis; staff pharmacists and pharmacy technicians identified 38 opportunities to decrease waste and increase efficiency. Three workflow processes (order verification, compounding, and delivery) accounted for 24 of 38 recommendations and were targeted for lean process improvements. The workflow was decreased to 14 steps, eliminating 6 non-value-added steps, and pharmacy staff resources and schedules were realigned with the streamlined workflow. The time required for pharmacist verification of patient-specific oncology orders was decreased by 33%; the time required for product verification was decreased by 52%. The average medication delivery time was decreased by 47%. The results of baseline and postimplementation time trials indicated a decrease in overall turnaround time to about 70 minutes, compared with a baseline time of about 90 minutes. The use of lean methodology to identify non-value-added steps in oncology order processing and the implementation of staff-recommended workflow changes resulted in an overall reduction in the turnaround time per dose. Copyright © 2014 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

Processing MALDI mass spectra to improve mass spectral direct tissue analysis

NASA Astrophysics Data System (ADS)

Norris, Jeremy L.; Cornett, Dale S.; Mobley, James A.; Andersson, Malin; Seeley, Erin H.; Chaurand, Pierre; Caprioli, Richard M.

2007-02-01

Profiling and imaging biological specimens using MALDI mass spectrometry has significant potential to contribute to our understanding and diagnosis of disease. The technique is efficient and high-throughput providing a wealth of data about the biological state of the sample from a very simple and direct experiment. However, in order for these techniques to be put to use for clinical purposes, the approaches used to process and analyze the data must improve. This study examines some of the existing tools to baseline subtract, normalize, align, and remove spectral noise for MALDI data, comparing the advantages of each. A preferred workflow is presented that can be easily implemented for data in ASCII format. The advantages of using such an approach are discussed for both molecular profiling and imaging mass spectrometry.

Using location tracking data to assess efficiency in established clinical workflows.

PubMed

Meyer, Mark; Fairbrother, Pamela; Egan, Marie; Chueh, Henry; Sandberg, Warren S

2006-01-01

Location tracking systems are becoming more prevalent in clinical settings yet applications still are not common. We have designed a system to aid in the assessment of clinical workflow efficiency. Location data is captured from active RFID tags and processed into usable data. These data are stored and presented visually with trending capability over time. The system allows quick assessments of the impact of process changes on workflow, and isolates areas for improvement.

How to Take HRMS Process Management to the Next Level with Workflow Business Event System

NASA Technical Reports Server (NTRS)

Rajeshuni, Sarala; Yagubian, Aram; Kunamaneni, Krishna

2006-01-01

Oracle Workflow with the Business Event System offers a complete process management solution for enterprises to manage business processes cost-effectively. Using Workflow event messaging, event subscriptions, AQ Servlet and advanced queuing technologies, this presentation will demonstrate the step-by-step design and implementation of system solutions in order to integrate two dissimilar systems and establish communication remotely. As a case study, the presentation walks you through the process of propagating organization name changes in other applications that originated from the HRMS module without changing applications code. The solution can be applied to your particular business cases for streamlining or modifying business processes across Oracle and non-Oracle applications.

Toward the Design of Personalized Continuum Surgical Robots.

PubMed

Morimoto, Tania K; Greer, Joseph D; Hawkes, Elliot W; Hsieh, Michael H; Okamura, Allison M

2018-05-31

Robot-assisted minimally invasive surgical systems enable procedures with reduced pain, recovery time, and scarring compared to traditional surgery. While these improvements benefit a large number of patients, safe access to diseased sites is not always possible for specialized patient groups, including pediatric patients, due to their anatomical differences. We propose a patient-specific design paradigm that leverages the surgeon's expertise to design and fabricate robots based on preoperative medical images. The components of the patient-specific robot design process are a virtual reality design interface enabling the surgeon to design patient-specific tools, 3-D printing of these tools with a biodegradable polyester, and an actuation and control system for deployment. The designed robot is a concentric tube robot, a type of continuum robot constructed from precurved, elastic, nesting tubes. We demonstrate the overall patient-specific design workflow, from preoperative images to physical implementation, for an example clinical scenario: nonlinear renal access to a pediatric kidney. We also measure the system's behavior as it is deployed through real and artificial tissue. System integration and successful benchtop experiments in ex vivo liver and in a phantom patient model demonstrate the feasibility of using a patient-specific design workflow to plan, fabricate, and deploy personalized, flexible continuum robots.

Interfaces and Integration of Medical Image Analysis Frameworks: Challenges and Opportunities.

PubMed

Covington, Kelsie; McCreedy, Evan S; Chen, Min; Carass, Aaron; Aucoin, Nicole; Landman, Bennett A

2010-05-25

Clinical research with medical imaging typically involves large-scale data analysis with interdependent software toolsets tied together in a processing workflow. Numerous, complementary platforms are available, but these are not readily compatible in terms of workflows or data formats. Both image scientists and clinical investigators could benefit from using the framework which is a most natural fit to the specific problem at hand, but pragmatic choices often dictate that a compromise platform is used for collaboration. Manual merging of platforms through carefully tuned scripts has been effective, but exceptionally time consuming and is not feasible for large-scale integration efforts. Hence, the benefits of innovation are constrained by platform dependence. Removing this constraint via integration of algorithms from one framework into another is the focus of this work. We propose and demonstrate a light-weight interface system to expose parameters across platforms and provide seamless integration. In this initial effort, we focus on four platforms Medical Image Analysis and Visualization (MIPAV), Java Image Science Toolkit (JIST), command line tools, and 3D Slicer. We explore three case studies: (1) providing a system for MIPAV to expose internal algorithms and utilize these algorithms within JIST, (2) exposing JIST modules through self-documenting command line interface for inclusion in scripting environments, and (3) detecting and using JIST modules in 3D Slicer. We review the challenges and opportunities for light-weight software integration both within development language (e.g., Java in MIPAV and JIST) and across languages (e.g., C/C++ in 3D Slicer and shell in command line tools).

Design of low noise imaging system

NASA Astrophysics Data System (ADS)

Hu, Bo; Chen, Xiaolai

2017-10-01

In order to meet the needs of engineering applications for low noise imaging system under the mode of global shutter, a complete imaging system is designed based on the SCMOS (Scientific CMOS) image sensor CIS2521F. The paper introduces hardware circuit and software system design. Based on the analysis of key indexes and technologies about the imaging system, the paper makes chips selection and decides SCMOS + FPGA+ DDRII+ Camera Link as processing architecture. Then it introduces the entire system workflow and power supply and distribution unit design. As for the software system, which consists of the SCMOS control module, image acquisition module, data cache control module and transmission control module, the paper designs in Verilog language and drives it to work properly based on Xilinx FPGA. The imaging experimental results show that the imaging system exhibits a 2560*2160 pixel resolution, has a maximum frame frequency of 50 fps. The imaging quality of the system satisfies the requirement of the index.

Preclinical Feasibility of a Technology Framework for MRI-guided Iliac Angioplasty

PubMed Central

Rube, Martin A.; Fernandez-Gutierrez, Fabiola; Cox, Benjamin F.; Holbrook, Andrew B.; Houston, J. Graeme; White, Richard D.; McLeod, Helen; Fatahi, Mahsa; Melzer, Andreas

2015-01-01

Purpose Interventional MRI has significant potential for image guidance of iliac angioplasty and related vascular procedures. A technology framework with in-room image display, control, communication and MRI-guided intervention techniques was designed and tested for its potential to provide safe, fast and efficient MRI-guided angioplasty of the iliac arteries. Methods A 1.5T MRI scanner was adapted for interactive imaging during endovascular procedures using new or modified interventional devices such as guidewires and catheters. A perfused vascular phantom was used for testing. Pre-, intra- and post-procedural visualization and measurement of vascular morphology and flow was implemented. A detailed analysis of X-Ray fluoroscopic angiography workflow was conducted and applied. Two interventional radiologists and one physician in training performed 39 procedures. All procedures were timed and analyzed. Results MRI-guided iliac angioplasty procedures were successfully performed with progressive adaptation of techniques and workflow. The workflow, setup and protocol enabled a reduction in table time for a dedicated MRI-guided procedure to 6 min 33 s with a mean procedure time of 9 min 2 s, comparable to the mean procedure time of 8 min 42 s for the standard X-Ray guided procedure. Conclusions MRI-guided iliac vascular interventions were found to be feasible and practical using this framework and optimized workflow. In particular the real-time flow analysis was found to be helpful for pre- and post-interventional assessments. Design optimization of the catheters and in vivo experiments are required before clinical evaluation. PMID:25102933

Quantitative workflow based on NN for weighting criteria in landfill suitability mapping

NASA Astrophysics Data System (ADS)

Abujayyab, Sohaib K. M.; Ahamad, Mohd Sanusi S.; Yahya, Ahmad Shukri; Ahmad, Siti Zubaidah; Alkhasawneh, Mutasem Sh.; Aziz, Hamidi Abdul

2017-10-01

Our study aims to introduce a new quantitative workflow that integrates neural networks (NNs) and multi criteria decision analysis (MCDA). Existing MCDA workflows reveal a number of drawbacks, because of the reliance on human knowledge in the weighting stage. Thus, new workflow presented to form suitability maps at the regional scale for solid waste planning based on NNs. A feed-forward neural network employed in the workflow. A total of 34 criteria were pre-processed to establish the input dataset for NN modelling. The final learned network used to acquire the weights of the criteria. Accuracies of 95.2% and 93.2% achieved for the training dataset and testing dataset, respectively. The workflow was found to be capable of reducing human interference to generate highly reliable maps. The proposed workflow reveals the applicability of NN in generating landfill suitability maps and the feasibility of integrating them with existing MCDA workflows.

Cloud-based opportunities in scientific computing: insights from processing Suomi National Polar-Orbiting Partnership (S-NPP) Direct Broadcast data

NASA Astrophysics Data System (ADS)

Evans, J. D.; Hao, W.; Chettri, S.

2013-12-01

The cloud is proving to be a uniquely promising platform for scientific computing. Our experience with processing satellite data using Amazon Web Services highlights several opportunities for enhanced performance, flexibility, and cost effectiveness in the cloud relative to traditional computing -- for example: - Direct readout from a polar-orbiting satellite such as the Suomi National Polar-Orbiting Partnership (S-NPP) requires bursts of processing a few times a day, separated by quiet periods when the satellite is out of receiving range. In the cloud, by starting and stopping virtual machines in minutes, we can marshal significant computing resources quickly when needed, but not pay for them when not needed. To take advantage of this capability, we are automating a data-driven approach to the management of cloud computing resources, in which new data availability triggers the creation of new virtual machines (of variable size and processing power) which last only until the processing workflow is complete. - 'Spot instances' are virtual machines that run as long as one's asking price is higher than the provider's variable spot price. Spot instances can greatly reduce the cost of computing -- for software systems that are engineered to withstand unpredictable interruptions in service (as occurs when a spot price exceeds the asking price). We are implementing an approach to workflow management that allows data processing workflows to resume with minimal delays after temporary spot price spikes. This will allow systems to take full advantage of variably-priced 'utility computing.' - Thanks to virtual machine images, we can easily launch multiple, identical machines differentiated only by 'user data' containing individualized instructions (e.g., to fetch particular datasets or to perform certain workflows or algorithms) This is particularly useful when (as is the case with S-NPP data) we need to launch many very similar machines to process an unpredictable number of data files concurrently. Our experience shows the viability and flexibility of this approach to workflow management for scientific data processing. - Finally, cloud computing is a promising platform for distributed volunteer ('interstitial') computing, via mechanisms such as the Berkeley Open Infrastructure for Network Computing (BOINC) popularized with the SETI@Home project and others such as ClimatePrediction.net and NASA's Climate@Home. Interstitial computing faces significant challenges as commodity computing shifts from (always on) desktop computers towards smartphones and tablets (untethered and running on scarce battery power); but cloud computing offers significant slack capacity. This capacity includes virtual machines with unused RAM or underused CPUs; virtual storage volumes allocated (& paid for) but not full; and virtual machines that are paid up for the current hour but whose work is complete. We are devising ways to facilitate the reuse of these resources (i.e., cloud-based interstitial computing) for satellite data processing and related analyses. We will present our findings and research directions on these and related topics.

Addressing the coming radiology crisis-the Society for Computer Applications in Radiology transforming the radiological interpretation process (TRIP) initiative.

PubMed

Andriole, Katherine P; Morin, Richard L; Arenson, Ronald L; Carrino, John A; Erickson, Bradley J; Horii, Steven C; Piraino, David W; Reiner, Bruce I; Seibert, J Anthony; Siegel, Eliot

2004-12-01

The Society for Computer Applications in Radiology (SCAR) Transforming the Radiological Interpretation Process (TRIP) Initiative aims to spearhead research, education, and discovery of innovative solutions to address the problem of information and image data overload. The initiative will foster interdisciplinary research on technological, environmental and human factors to better manage and exploit the massive amounts of data. TRIP will focus on the following basic objectives: improving the efficiency of interpretation of large data sets, improving the timeliness and effectiveness of communication, and decreasing medical errors. The ultimate goal of the initiative is to improve the quality and safety of patient care. Interdisciplinary research into several broad areas will be necessary to make progress in managing the ever-increasing volume of data. The six concepts involved are human perception, image processing and computer-aided detection (CAD), visualization, navigation and usability, databases and integration, and evaluation and validation of methods and performance. The result of this transformation will affect several key processes in radiology, including image interpretation; communication of imaging results; workflow and efficiency within the health care enterprise; diagnostic accuracy and a reduction in medical errors; and, ultimately, the overall quality of care.

Artificial Neural Networks as a powerful numerical tool to classify specific features of a tooth based on 3D scan data.

PubMed

Raith, Stefan; Vogel, Eric Per; Anees, Naeema; Keul, Christine; Güth, Jan-Frederik; Edelhoff, Daniel; Fischer, Horst

2017-01-01

Chairside manufacturing based on digital image acquisition is gainingincreasing importance in dentistry. For the standardized application of these methods, it is paramount to have highly automated digital workflows that can process acquired 3D image data of dental surfaces. Artificial Neural Networks (ANNs) arenumerical methods primarily used to mimic the complex networks of neural connections in the natural brain. Our hypothesis is that an ANNcan be developed that is capable of classifying dental cusps with sufficient accuracy. This bears enormous potential for an application in chairside manufacturing workflows in the dental field, as it closes the gap between digital acquisition of dental geometries and modern computer-aided manufacturing techniques.Three-dimensional surface scans of dental casts representing natural full dental arches were transformed to range image data. These data were processed using an automated algorithm to detect candidates for tooth cusps according to salient geometrical features. These candidates were classified following common dental terminology and used as training data for a tailored ANN.For the actual cusp feature description, two different approaches were developed and applied to the available data: The first uses the relative location of the detected cusps as input data and the second method directly takes the image information given in the range images. In addition, a combination of both was implemented and investigated.Both approaches showed high performance with correct classifications of 93.3% and 93.5%, respectively, with improvements by the combination shown to be minor.This article presents for the first time a fully automated method for the classification of teeththat could be confirmed to work with sufficient precision to exhibit the potential for its use in clinical practice,which is a prerequisite for automated computer-aided planning of prosthetic treatments with subsequent automated chairside manufacturing. Copyright © 2016 Elsevier Ltd. All rights reserved.

A De-Identification Pipeline for Ultrasound Medical Images in DICOM Format.

PubMed

Monteiro, Eriksson; Costa, Carlos; Oliveira, José Luís

2017-05-01

Clinical data sharing between healthcare institutions, and between practitioners is often hindered by privacy protection requirements. This problem is critical in collaborative scenarios where data sharing is fundamental for establishing a workflow among parties. The anonymization of patient information burned in DICOM images requires elaborate processes somewhat more complex than simple de-identification of textual information. Usually, before sharing, there is a need for manual removal of specific areas containing sensitive information in the images. In this paper, we present a pipeline for ultrasound medical image de-identification, provided as a free anonymization REST service for medical image applications, and a Software-as-a-Service to streamline automatic de-identification of medical images, which is freely available for end-users. The proposed approach applies image processing functions and machine-learning models to bring about an automatic system to anonymize medical images. To perform character recognition, we evaluated several machine-learning models, being Convolutional Neural Networks (CNN) selected as the best approach. For accessing the system quality, 500 processed images were manually inspected showing an anonymization rate of 89.2%. The tool can be accessed at https://bioinformatics.ua.pt/dicom/anonymizer and it is available with the most recent version of Google Chrome, Mozilla Firefox and Safari. A Docker image containing the proposed service is also publicly available for the community.

[Intelligent operating room suite : From passive medical devices to the self-thinking cognitive surgical assistant].

PubMed

Kenngott, H G; Wagner, M; Preukschas, A A; Müller-Stich, B P

2016-12-01

Modern operating room (OR) suites are mostly digitally connected but until now the primary focus was on the presentation, transfer and distribution of images. Device information and processes within the operating theaters are barely considered. Cognitive assistance systems have triggered a fundamental rethinking in the automotive industry as well as in logistics. In principle, tasks in the OR, some of which are highly repetitive, also have great potential to be supported by automated cognitive assistance via a self-thinking system. This includes the coordination of the entire workflow in the perioperative process in both the operating theater and the whole hospital. With corresponding data from hospital information systems, medical devices and appropriate models of the surgical process, intelligent systems could optimize the workflow in the operating theater in the near future and support the surgeon. Preliminary results on the use of device information and automatically controlled OR suites are already available. Such systems include, for example the guidance of laparoscopic camera systems. Nevertheless, cognitive assistance systems that make use of knowledge about patients, processes and other pieces of information to improve surgical treatment are not yet available in the clinical routine but are urgently needed in order to automatically assist the surgeon in situation-related activities and thus substantially improve patient care.

Does transitioning from computed radiography (CR) to direct radiography (DR) with portable imaging systems affect workflow efficiency?

NASA Astrophysics Data System (ADS)

Gali, Raja L.; Roth, Christopher G.; Smith, Elizabeth; Dave, Jaydev K.

2018-03-01

In digital radiography, computed radiography (CR) technology is based on latent image capture by storage phosphors whereas direct radiography (DR) technology is based either on indirect conversion using a scintillator or direct conversion using a photoconductor. DR-based portable imaging systems may enhance workflow efficiency. The purpose of this work was to investigate changes in workflow efficiency at a tertiary healthcare center after transitioning from CR to DR technology for imaging with portable x-ray units. An IRB exemption was obtained. Data for all inpatient-radiographs acquired with portable x-ray units from July-2014 till June-2015 (period 1) with CR technology (AMX4 or AMX4+ portable unit from GE Healthcare, NX workstation from Agfa Healthcare for digitization), from July-2015 till June-2016 (period 2) with DR technology (Carestream DRX-Revolution x-ray units and DRX-1C image receptors) and from July-2016 till January-2017 (period 3; same DR technology) were extracted using Centricity RIS-IC (GE Healthcare). Duration between the imaging-examination scheduled time and completed time (timesch-com) was calculated and compared using non-parametric tests (between the three time periods with corrections for multiple comparisons; three time periods were used to identify if there were any other potential temporal trends not related to transitioning from CR to DR). IBM's SPSS package was used for statistical analysis. Overall data was obtained from 33131, 32194, and 18015 cases in periods 1, 2 and 3, respectively. Independent-Samples Kruskal-Wallis test revealed a statistically significant difference in timesch-com across the three time periods (χ2(2, n= 83,340) = 2053, p < 0.001). The timesch-com was highest for period 1 i.e., radiographs acquired with CR technology (median: 64 minutes) and it decreased significantly for radiographs acquired with DR technology in periods 2 (median: 49 minutes; p < 0.001) and 3 (median∶ 44 minutes; p < 0.001). Overall, adoption of DR technology resulted in a drop in timesch-com by 27% relative to the use of CR technology. Transitioning from CR to DR was associated with improved workflow efficiency for radiographic imaging with portable x-ray units.

Transforming medical imaging applications into collaborative PACS-based telemedical systems

NASA Astrophysics Data System (ADS)

Maani, Rouzbeh; Camorlinga, Sergio; Arnason, Neil

2011-03-01

Telemedical systems are not practical for use in a clinical workflow unless they are able to communicate with the Picture Archiving and Communications System (PACS). On the other hand, there are many medical imaging applications that are not developed as telemedical systems. Some medical imaging applications do not support collaboration and some do not communicate with the PACS and therefore limit their usability in clinical workflows. This paper presents a general architecture based on a three-tier architecture model. The architecture and the components developed within it, transform medical imaging applications into collaborative PACS-based telemedical systems. As a result, current medical imaging applications that are not telemedical, not supporting collaboration, and not communicating with PACS, can be enhanced to support collaboration among a group of physicians, be accessed remotely, and be clinically useful. The main advantage of the proposed architecture is that it does not impose any modification to the current medical imaging applications and does not make any assumptions about the underlying architecture or operating system.

Coupling of a continuum ice sheet model and a discrete element calving model using a scientific workflow system

NASA Astrophysics Data System (ADS)

Memon, Shahbaz; Vallot, Dorothée; Zwinger, Thomas; Neukirchen, Helmut

2017-04-01

Scientific communities generate complex simulations through orchestration of semi-structured analysis pipelines which involves execution of large workflows on multiple, distributed and heterogeneous computing and data resources. Modeling ice dynamics of glaciers requires workflows consisting of many non-trivial, computationally expensive processing tasks which are coupled to each other. From this domain, we present an e-Science use case, a workflow, which requires the execution of a continuum ice flow model and a discrete element based calving model in an iterative manner. Apart from the execution, this workflow also contains data format conversion tasks that support the execution of ice flow and calving by means of transition through sequential, nested and iterative steps. Thus, the management and monitoring of all the processing tasks including data management and transfer of the workflow model becomes more complex. From the implementation perspective, this workflow model was initially developed on a set of scripts using static data input and output references. In the course of application usage when more scripts or modifications introduced as per user requirements, the debugging and validation of results were more cumbersome to achieve. To address these problems, we identified a need to have a high-level scientific workflow tool through which all the above mentioned processes can be achieved in an efficient and usable manner. We decided to make use of the e-Science middleware UNICORE (Uniform Interface to Computing Resources) that allows seamless and automated access to different heterogenous and distributed resources which is supported by a scientific workflow engine. Based on this, we developed a high-level scientific workflow model for coupling of massively parallel High-Performance Computing (HPC) jobs: a continuum ice sheet model (Elmer/Ice) and a discrete element calving and crevassing model (HiDEM). In our talk we present how the use of a high-level scientific workflow middleware enables reproducibility of results more convenient and also provides a reusable and portable workflow template that can be deployed across different computing infrastructures. Acknowledgements This work was kindly supported by NordForsk as part of the Nordic Center of Excellence (NCoE) eSTICC (eScience Tools for Investigating Climate Change at High Northern Latitudes) and the Top-level Research Initiative NCoE SVALI (Stability and Variation of Arctic Land Ice).

Scientific Data Management (SDM) Center for Enabling Technologies. 2007-2012

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ludascher, Bertram; Altintas, Ilkay

Over the past five years, our activities have both established Kepler as a viable scientific workflow environment and demonstrated its value across multiple science applications. We have published numerous peer-reviewed papers on the technologies highlighted in this short paper and have given Kepler tutorials at SC06,SC07,SC08,and SciDAC 2007. Our outreach activities have allowed scientists to learn best practices and better utilize Kepler to address their individual workflow problems. Our contributions to advancing the state-of-the-art in scientific workflows have focused on the following areas. Progress in each of these areas is described in subsequent sections. Workflow development. The development of amore » deeper understanding of scientific workflows "in the wild" and of the requirements for support tools that allow easy construction of complex scientific workflows; Generic workflow components and templates. The development of generic actors (i.e.workflow components and processes) which can be broadly applied to scientific problems; Provenance collection and analysis. The design of a flexible provenance collection and analysis infrastructure within the workflow environment; and, Workflow reliability and fault tolerance. The improvement of the reliability and fault-tolerance of workflow environments.« less

Understanding the dispensary workflow at the Birmingham Free Clinic: a proposed framework for an informatics intervention.

PubMed

Fisher, Arielle M; Herbert, Mary I; Douglas, Gerald P

2016-02-19

The Birmingham Free Clinic (BFC) in Pittsburgh, Pennsylvania, USA is a free, walk-in clinic that serves medically uninsured populations through the use of volunteer health care providers and an on-site medication dispensary. The introduction of an electronic medical record (EMR) has improved several aspects of clinic workflow. However, pharmacists' tasks involving medication management and dispensing have become more challenging since EMR implementation due to its inability to support workflows between the medical and pharmaceutical services. To inform the design of a systematic intervention, we conducted a needs assessment study to identify workflow challenges and process inefficiencies in the dispensary. We used contextual inquiry to document the dispensary workflow and facilitate identification of critical aspects of intervention design specific to the user. Pharmacists were observed according to contextual inquiry guidelines. Graphical models were produced to aid data and process visualization. We created a list of themes describing workflow challenges and asked the pharmacists to rank them in order of significance to narrow the scope of intervention design. Three pharmacists were observed at the BFC. Observer notes were documented and analyzed to produce 13 themes outlining the primary challenges pharmacists encounter during dispensation at the BFC. The dispensary workflow is labor intensive, redundant, and inefficient when integrated with the clinical service. Observations identified inefficiencies that may benefit from the introduction of informatics interventions including: medication labeling, insufficient process notification, triple documentation, and inventory control. We propose a system for Prescription Management and General Inventory Control (RxMAGIC). RxMAGIC is a framework designed to mitigate workflow challenges and improve the processes of medication management and inventory control. While RxMAGIC is described in the context of the BFC dispensary, we believe it will be generalizable to pharmacies in other low-resource settings, both domestically and internationally.

Improved compliance by BPM-driven workflow automation.

PubMed

Holzmüller-Laue, Silke; Göde, Bernd; Fleischer, Heidi; Thurow, Kerstin

2014-12-01

Using methods and technologies of business process management (BPM) for the laboratory automation has important benefits (i.e., the agility of high-level automation processes, rapid interdisciplinary prototyping and implementation of laboratory tasks and procedures, and efficient real-time process documentation). A principal goal of the model-driven development is the improved transparency of processes and the alignment of process diagrams and technical code. First experiences of using the business process model and notation (BPMN) show that easy-to-read graphical process models can achieve and provide standardization of laboratory workflows. The model-based development allows one to change processes quickly and an easy adaption to changing requirements. The process models are able to host work procedures and their scheduling in compliance with predefined guidelines and policies. Finally, the process-controlled documentation of complex workflow results addresses modern laboratory needs of quality assurance. BPMN 2.0 as an automation language to control every kind of activity or subprocess is directed to complete workflows in end-to-end relationships. BPMN is applicable as a system-independent and cross-disciplinary graphical language to document all methods in laboratories (i.e., screening procedures or analytical processes). That means, with the BPM standard, a communication method of sharing process knowledge of laboratories is also available. © 2014 Society for Laboratory Automation and Screening.

Preservation of protein fluorescence in embedded human dendritic cells for targeted 3D light and electron microscopy.

PubMed

Höhn, K; Fuchs, J; Fröber, A; Kirmse, R; Glass, B; Anders-Össwein, M; Walther, P; Kräusslich, H-G; Dietrich, C

2015-08-01

In this study, we present a correlative microscopy workflow to combine detailed 3D fluorescence light microscopy data with ultrastructural information gained by 3D focused ion beam assisted scanning electron microscopy. The workflow is based on an optimized high pressure freezing/freeze substitution protocol that preserves good ultrastructural detail along with retaining the fluorescence signal in the resin embedded specimens. Consequently, cellular structures of interest can readily be identified and imaged by state of the art 3D confocal fluorescence microscopy and are precisely referenced with respect to an imprinted coordinate system on the surface of the resin block. This allows precise guidance of the focused ion beam assisted scanning electron microscopy and limits the volume to be imaged to the structure of interest. This, in turn, minimizes the total acquisition time necessary to conduct the time consuming ultrastructural scanning electron microscope imaging while eliminating the risk to miss parts of the target structure. We illustrate the value of this workflow for targeting virus compartments, which are formed in HIV-pulsed mature human dendritic cells. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Case-based lung image categorization and retrieval for interstitial lung diseases: clinical workflows.

PubMed

Depeursinge, Adrien; Vargas, Alejandro; Gaillard, Frédéric; Platon, Alexandra; Geissbuhler, Antoine; Poletti, Pierre-Alexandre; Müller, Henning

2012-01-01

Clinical workflows and user interfaces of image-based computer-aided diagnosis (CAD) for interstitial lung diseases in high-resolution computed tomography are introduced and discussed. Three use cases are implemented to assist students, radiologists, and physicians in the diagnosis workup of interstitial lung diseases. In a first step, the proposed system shows a three-dimensional map of categorized lung tissue patterns with quantification of the diseases based on texture analysis of the lung parenchyma. Then, based on the proportions of abnormal and normal lung tissue as well as clinical data of the patients, retrieval of similar cases is enabled using a multimodal distance aggregating content-based image retrieval (CBIR) and text-based information search. The global system leads to a hybrid detection-CBIR-based CAD, where detection-based and CBIR-based CAD show to be complementary both on the user's side and on the algorithmic side. The proposed approach is in accordance with the classical workflow of clinicians searching for similar cases in textbooks and personal collections. The developed system enables objective and customizable inter-case similarity assessment, and the performance measures obtained with a leave-one-patient-out cross-validation (LOPO CV) are representative of a clinical usage of the system.

Heterogeneous Optimization Framework: Reproducible Preprocessing of Multi-Spectral Clinical MRI for Neuro-Oncology Imaging Research.

PubMed

Milchenko, Mikhail; Snyder, Abraham Z; LaMontagne, Pamela; Shimony, Joshua S; Benzinger, Tammie L; Fouke, Sarah Jost; Marcus, Daniel S

2016-07-01

Neuroimaging research often relies on clinically acquired magnetic resonance imaging (MRI) datasets that can originate from multiple institutions. Such datasets are characterized by high heterogeneity of modalities and variability of sequence parameters. This heterogeneity complicates the automation of image processing tasks such as spatial co-registration and physiological or functional image analysis. Given this heterogeneity, conventional processing workflows developed for research purposes are not optimal for clinical data. In this work, we describe an approach called Heterogeneous Optimization Framework (HOF) for developing image analysis pipelines that can handle the high degree of clinical data non-uniformity. HOF provides a set of guidelines for configuration, algorithm development, deployment, interpretation of results and quality control for such pipelines. At each step, we illustrate the HOF approach using the implementation of an automated pipeline for Multimodal Glioma Analysis (MGA) as an example. The MGA pipeline computes tissue diffusion characteristics of diffusion tensor imaging (DTI) acquisitions, hemodynamic characteristics using a perfusion model of susceptibility contrast (DSC) MRI, and spatial cross-modal co-registration of available anatomical, physiological and derived patient images. Developing MGA within HOF enabled the processing of neuro-oncology MR imaging studies to be fully automated. MGA has been successfully used to analyze over 160 clinical tumor studies to date within several research projects. Introduction of the MGA pipeline improved image processing throughput and, most importantly, effectively produced co-registered datasets that were suitable for advanced analysis despite high heterogeneity in acquisition protocols.

Development of the workflow kine systems for support on KAIZEN.

PubMed

Mizuno, Yuki; Ito, Toshihiko; Yoshikawa, Toru; Yomogida, Satoshi; Morio, Koji; Sakai, Kazuhiro

2012-01-01

In this paper, we introduce the new workflow line system consisted of the location and image recording, which led to the acquisition of workflow information and the analysis display. From the results of workflow line investigation, we considered the anticipated effects and the problems on KAIZEN. Workflow line information included the location information and action contents information. These technologies suggest the viewpoints to help improvement, for example, exclusion of useless movement, the redesign of layout and the review of work procedure. Manufacturing factory, it was clear that there was much movement from the standard operation place and accumulation residence time. The following was shown as a result of this investigation, to be concrete, the efficient layout was suggested by this system. In the case of the hospital, similarly, it is pointed out that the workflow has the problem of layout and setup operations based on the effective movement pattern of the experts. This system could adapt to routine work, including as well as non-routine work. By the development of this system which can fit and adapt to industrial diversification, more effective "visual management" (visualization of work) is expected in the future.

Fast and objective detection and analysis of structures in downhole images

NASA Astrophysics Data System (ADS)

Wedge, Daniel; Holden, Eun-Jung; Dentith, Mike; Spadaccini, Nick

2017-09-01

Downhole acoustic and optical televiewer images, and formation microimager (FMI) logs are important datasets for structural and geotechnical analyses for the mineral and petroleum industries. Within these data, dipping planar structures appear as sinusoids, often in incomplete form and in abundance. Their detection is a labour intensive and hence expensive task and as such is a significant bottleneck in data processing as companies may have hundreds of kilometres of logs to process each year. We present an image analysis system that harnesses the power of automated image analysis and provides an interactive user interface to support the analysis of televiewer images by users with different objectives. Our algorithm rapidly produces repeatable, objective results. We have embedded it in an interactive workflow to complement geologists' intuition and experience in interpreting data to improve efficiency and assist, rather than replace the geologist. The main contributions include a new image quality assessment technique for highlighting image areas most suited to automated structure detection and for detecting boundaries of geological zones, and a novel sinusoid detection algorithm for detecting and selecting sinusoids with given confidence levels. Further tools are provided to perform rapid analysis of and further detection of structures e.g. as limited to specific orientations.

Support for Taverna workflows in the VPH-Share cloud platform.

PubMed

Kasztelnik, Marek; Coto, Ernesto; Bubak, Marian; Malawski, Maciej; Nowakowski, Piotr; Arenas, Juan; Saglimbeni, Alfredo; Testi, Debora; Frangi, Alejandro F

2017-07-01

To address the increasing need for collaborative endeavours within the Virtual Physiological Human (VPH) community, the VPH-Share collaborative cloud platform allows researchers to expose and share sequences of complex biomedical processing tasks in the form of computational workflows. The Taverna Workflow System is a very popular tool for orchestrating complex biomedical & bioinformatics processing tasks in the VPH community. This paper describes the VPH-Share components that support the building and execution of Taverna workflows, and explains how they interact with other VPH-Share components to improve the capabilities of the VPH-Share platform. Taverna workflow support is delivered by the Atmosphere cloud management platform and the VPH-Share Taverna plugin. These components are explained in detail, along with the two main procedures that were developed to enable this seamless integration: workflow composition and execution. 1) Seamless integration of VPH-Share with other components and systems. 2) Extended range of different tools for workflows. 3) Successful integration of scientific workflows from other VPH projects. 4) Execution speed improvement for medical applications. The presented workflow integration provides VPH-Share users with a wide range of different possibilities to compose and execute workflows, such as desktop or online composition, online batch execution, multithreading, remote execution, etc. The specific advantages of each supported tool are presented, as are the roles of Atmosphere and the VPH-Share plugin within the VPH-Share project. The combination of the VPH-Share plugin and Atmosphere engenders the VPH-Share infrastructure with far more flexible, powerful and usable capabilities for the VPH-Share community. As both components can continue to evolve and improve independently, we acknowledge that further improvements are still to be developed and will be described. Copyright © 2017 Elsevier B.V. All rights reserved.

Semantic orchestration of image processing services for environmental analysis

NASA Astrophysics Data System (ADS)

Ranisavljević, Élisabeth; Devin, Florent; Laffly, Dominique; Le Nir, Yannick

2013-09-01

In order to analyze environmental dynamics, a major process is the classification of the different phenomena of the site (e.g. ice and snow for a glacier). When using in situ pictures, this classification requires data pre-processing. Not all the pictures need the same sequence of processes depending on the disturbances. Until now, these sequences have been done manually, which restricts the processing of large amount of data. In this paper, we present how to realize a semantic orchestration to automate the sequencing for the analysis. It combines two advantages: solving the problem of the amount of processing, and diversifying the possibilities in the data processing. We define a BPEL description to express the sequences. This BPEL uses some web services to run the data processing. Each web service is semantically annotated using an ontology of image processing. The dynamic modification of the BPEL is done using SPARQL queries on these annotated web services. The results obtained by a prototype implementing this method validate the construction of the different workflows that can be applied to a large number of pictures.

AutoDrug: fully automated macromolecular crystallography workflows for fragment-based drug discovery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsai, Yingssu; Stanford University, 333 Campus Drive, Mudd Building, Stanford, CA 94305-5080; McPhillips, Scott E.

New software has been developed for automating the experimental and data-processing stages of fragment-based drug discovery at a macromolecular crystallography beamline. A new workflow-automation framework orchestrates beamline-control and data-analysis software while organizing results from multiple samples. AutoDrug is software based upon the scientific workflow paradigm that integrates the Stanford Synchrotron Radiation Lightsource macromolecular crystallography beamlines and third-party processing software to automate the crystallography steps of the fragment-based drug-discovery process. AutoDrug screens a cassette of fragment-soaked crystals, selects crystals for data collection based on screening results and user-specified criteria and determines optimal data-collection strategies. It then collects and processes diffraction data,more » performs molecular replacement using provided models and detects electron density that is likely to arise from bound fragments. All processes are fully automated, i.e. are performed without user interaction or supervision. Samples can be screened in groups corresponding to particular proteins, crystal forms and/or soaking conditions. A single AutoDrug run is only limited by the capacity of the sample-storage dewar at the beamline: currently 288 samples. AutoDrug was developed in conjunction with RestFlow, a new scientific workflow-automation framework. RestFlow simplifies the design of AutoDrug by managing the flow of data and the organization of results and by orchestrating the execution of computational pipeline steps. It also simplifies the execution and interaction of third-party programs and the beamline-control system. Modeling AutoDrug as a scientific workflow enables multiple variants that meet the requirements of different user groups to be developed and supported. A workflow tailored to mimic the crystallography stages comprising the drug-discovery pipeline of CoCrystal Discovery Inc. has been deployed and successfully demonstrated. This workflow was run once on the same 96 samples that the group had examined manually and the workflow cycled successfully through all of the samples, collected data from the same samples that were selected manually and located the same peaks of unmodeled density in the resulting difference Fourier maps.« less

A hybrid image fusion system for endovascular interventions of peripheral artery disease.

PubMed

Lalys, Florent; Favre, Ketty; Villena, Alexandre; Durrmann, Vincent; Colleaux, Mathieu; Lucas, Antoine; Kaladji, Adrien

2018-07-01

Interventional endovascular treatment has become the first line of management in the treatment of peripheral artery disease (PAD). However, contrast and radiation exposure continue to limit the feasibility of these procedures. This paper presents a novel hybrid image fusion system for endovascular intervention of PAD. We present two different roadmapping methods from intra- and pre-interventional imaging that can be used either simultaneously or independently, constituting the navigation system. The navigation system is decomposed into several steps that can be entirely integrated within the procedure workflow without modifying it to benefit from the roadmapping. First, a 2D panorama of the entire peripheral artery system is automatically created based on a sequence of stepping fluoroscopic images acquired during the intra-interventional diagnosis phase. During the interventional phase, the live image can be synchronized on the panorama to form the basis of the image fusion system. Two types of augmented information are then integrated. First, an angiography panorama is proposed to avoid contrast media re-injection. Information exploiting the pre-interventional computed tomography angiography (CTA) is also brought to the surgeon by means of semiautomatic 3D/2D registration on the 2D panorama. Each step of the workflow was independently validated. Experiments for both the 2D panorama creation and the synchronization processes showed very accurate results (errors of 1.24 and [Formula: see text] mm, respectively), similarly to the registration on the 3D CTA (errors of [Formula: see text] mm), with minimal user interaction and very low computation time. First results of an on-going clinical study highlighted its major clinical added value on intraoperative parameters. No image fusion system has been proposed yet for endovascular procedures of PAD in lower extremities. More globally, such a navigation system, combining image fusion from different 2D and 3D image sources, is novel in the field of endovascular procedures.

Hierarchical storage of large volume of multidector CT data using distributed servers

NASA Astrophysics Data System (ADS)

Ratib, Osman; Rosset, Antoine; Heuberger, Joris; Bandon, David

2006-03-01

Multidector scanners and hybrid multimodality scanners have the ability to generate large number of high-resolution images resulting in very large data sets. In most cases, these datasets are generated for the sole purpose of generating secondary processed images and 3D rendered images as well as oblique and curved multiplanar reformatted images. It is therefore not essential to archive the original images after they have been processed. We have developed an architecture of distributed archive servers for temporary storage of large image datasets for 3D rendering and image processing without the need for long term storage in PACS archive. With the relatively low cost of storage devices it is possible to configure these servers to hold several months or even years of data, long enough for allowing subsequent re-processing if required by specific clinical situations. We tested the latest generation of RAID servers provided by Apple computers with a capacity of 5 TBytes. We implemented a peer-to-peer data access software based on our Open-Source image management software called OsiriX, allowing remote workstations to directly access DICOM image files located on the server through a new technology called "bonjour". This architecture offers a seamless integration of multiple servers and workstations without the need for central database or complex workflow management tools. It allows efficient access to image data from multiple workstation for image analysis and visualization without the need for image data transfer. It provides a convenient alternative to centralized PACS architecture while avoiding complex and time-consuming data transfer and storage.

SynTrack: DNA Assembly Workflow Management (SynTrack) v2.0.1

DOE Office of Scientific and Technical Information (OSTI.GOV)

MENG, XIANWEI; SIMIRENKO, LISA

2016-12-01

SynTrack is a dynamic, workflow-driven data management system that tracks the DNA build process: Management of the hierarchical relationships of the DNA fragments; Monitoring of process tasks for the assembly of multiple DNA fragments into final constructs; Creations of vendor order forms with selectable building blocks. Organizing plate layouts barcodes for vendor/pcr/fusion/chewback/bioassay/glycerol/master plate maps (default/condensed); Creating or updating Pre-Assembly/Assembly process workflows with selected building blocks; Generating Echo pooling instructions based on plate maps; Tracking of building block orders, received and final assembled for delivering; Bulk updating of colony or PCR amplification information, fusion PCR and chewback results; Updating with QA/QCmore » outcome with .csv & .xlsx template files; Re-work assembly workflow enabled before and after sequencing validation; and Tracking of plate/well data changes and status updates and reporting of master plate status with QC outcomes.« less

Haralick texture features from apparent diffusion coefficient (ADC) MRI images depend on imaging and pre-processing parameters.

PubMed

Brynolfsson, Patrik; Nilsson, David; Torheim, Turid; Asklund, Thomas; Karlsson, Camilla Thellenberg; Trygg, Johan; Nyholm, Tufve; Garpebring, Anders

2017-06-22

In recent years, texture analysis of medical images has become increasingly popular in studies investigating diagnosis, classification and treatment response assessment of cancerous disease. Despite numerous applications in oncology and medical imaging in general, there is no consensus regarding texture analysis workflow, or reporting of parameter settings crucial for replication of results. The aim of this study was to assess how sensitive Haralick texture features of apparent diffusion coefficient (ADC) MR images are to changes in five parameters related to image acquisition and pre-processing: noise, resolution, how the ADC map is constructed, the choice of quantization method, and the number of gray levels in the quantized image. We found that noise, resolution, choice of quantization method and the number of gray levels in the quantized images had a significant influence on most texture features, and that the effect size varied between different features. Different methods for constructing the ADC maps did not have an impact on any texture feature. Based on our results, we recommend using images with similar resolutions and noise levels, using one quantization method, and the same number of gray levels in all quantized images, to make meaningful comparisons of texture feature results between different subjects.

Design and development of an ethnically-diverse imaging informatics-based eFolder system for multiple sclerosis patients.

PubMed

Ma, Kevin C; Fernandez, James R; Amezcua, Lilyana; Lerner, Alex; Shiroishi, Mark S; Liu, Brent J

2015-12-01

MRI has been used to identify multiple sclerosis (MS) lesions in brain and spinal cord visually. Integrating patient information into an electronic patient record system has become key for modern patient care in medicine in recent years. Clinically, it is also necessary to track patients' progress in longitudinal studies, in order to provide comprehensive understanding of disease progression and response to treatment. As the amount of required data increases, there exists a need for an efficient systematic solution to store and analyze MS patient data, disease profiles, and disease tracking for both clinical and research purposes. An imaging informatics based system, called MS eFolder, has been developed as an integrated patient record system for data storage and analysis of MS patients. The eFolder system, with a DICOM-based database, includes a module for lesion contouring by radiologists, a MS lesion quantification tool to quantify MS lesion volume in 3D, brain parenchyma fraction analysis, and provide quantitative analysis and tracking of volume changes in longitudinal studies. Patient data, including MR images, have been collected retrospectively at University of Southern California Medical Center (USC) and Los Angeles County Hospital (LAC). The MS eFolder utilizes web-based components, such as browser-based graphical user interface (GUI) and web-based database. The eFolder database stores patient clinical data (demographics, MS disease history, family history, etc.), MR imaging-related data found in DICOM headers, and lesion quantification results. Lesion quantification results are derived from radiologists' contours on brain MRI studies and quantified into 3-dimensional volumes and locations. Quantified results of white matter lesions are integrated into a structured report based on DICOM-SR protocol and templates. The user interface displays patient clinical information, original MR images, and viewing structured reports of quantified results. The GUI also includes a data mining tool to handle unique search queries for MS. System workflow and dataflow steps has been designed based on the IHE post-processing workflow profile, including workflow process tracking, MS lesion contouring and quantification of MR images at a post-processing workstation, and storage of quantitative results as DICOM-SR in DICOM-based storage system. The web-based GUI is designed to display zero-footprint DICOM web-accessible data objects (WADO) and the SR objects. The MS eFolder system has been designed and developed as an integrated data storage and mining solution in both clinical and research environments, while providing unique features, such as quantitative lesion analysis and disease tracking over a longitudinal study. A comprehensive image and clinical data integrated database provided by MS eFolder provides a platform for treatment assessment, outcomes analysis and decision-support. The proposed system serves as a platform for future quantitative analysis derived automatically from CAD algorithms that can also be integrated within the system for individual disease tracking and future MS-related research. Ultimately the eFolder provides a decision-support infrastructure that can eventually be used as add-on value to the overall electronic medical record. Copyright © 2015 Elsevier Ltd. All rights reserved.

Design and development of an ethnically-diverse imaging informatics-based eFolder system for multiple sclerosis patients

PubMed Central

Ma, Kevin C.; Fernandez, James R.; Amezcua, Lilyana; Lerner, Alex; Shiroishi, Mark S.; Liu, Brent J.

2016-01-01

Purpose MRI has been used to identify multiple sclerosis (MS) lesions in brain and spinal cord visually. Integrating patient information into an electronic patient record system has become key for modern patient care in medicine in recent years. Clinically, it is also necessary to track patients' progress in longitudinal studies, in order to provide comprehensive understanding of disease progression and response to treatment. As the amount of required data increases, there exists a need for an efficient systematic solution to store and analyze MS patient data, disease profiles, and disease tracking for both clinical and research purposes. Method An imaging informatics based system, called MS eFolder, has been developed as an integrated patient record system for data storage and analysis of MS patients. The eFolder system, with a DICOM-based database, includes a module for lesion contouring by radiologists, a MS lesion quantification tool to quantify MS lesion volume in 3D, brain parenchyma fraction analysis, and provide quantitative analysis and tracking of volume changes in longitudinal studies. Patient data, including MR images, have been collected retrospectively at University of Southern California Medical Center (USC) and Los Angeles County Hospital (LAC). The MS eFolder utilizes web-based components, such as browser-based graphical user interface (GUI) and web-based database. The eFolder database stores patient clinical data (demographics, MS disease history, family history, etc.), MR imaging-related data found in DICOM headers, and lesion quantification results. Lesion quantification results are derived from radiologists' contours on brain MRI studies and quantified into 3-dimensional volumes and locations. Quantified results of white matter lesions are integrated into a structured report based on DICOM-SR protocol and templates. The user interface displays patient clinical information, original MR images, and viewing structured reports of quantified results. The GUI also includes a data mining tool to handle unique search queries for MS. System workflow and dataflow steps has been designed based on the IHE post-processing workflow profile, including workflow process tracking, MS lesion contouring and quantification of MR images at a post-processing workstation, and storage of quantitative results as DICOM-SR in DICOM-based storage system. The web-based GUI is designed to display zero-footprint DICOM web-accessible data objects (WADO) and the SR objects. Summary The MS eFolder system has been designed and developed as an integrated data storage and mining solution in both clinical and research environments, while providing unique features, such as quantitative lesion analysis and disease tracking over a longitudinal study. A comprehensive image and clinical data integrated database provided by MS eFolder provides a platform for treatment assessment, outcomes analysis and decision-support. The proposed system serves as a platform for future quantitative analysis derived automatically from CAD algorithms that can also be integrated within the system for individual disease tracking and future MS-related research. Ultimately the eFolder provides a decision-support infrastructure that can eventually be used as add-on value to the overall electronic medical record. PMID:26564667

Using Ready-To Drone Images in Forestry Activities: Case Study of ÇINARPINAR in Kahramanmaras, Turkey

NASA Astrophysics Data System (ADS)

Gülci, S.; Akgül, M.; Akay, A. E.; Taş, İ.

2017-11-01

This short paper aims to present pros and cons of current usage of ready-to-use drone images in the field of forestry also considering flight planning and photogrammetric processes. The capabilities of DJI Phantom 4, which is the low cost drone producing by Dji company, was evaluated through sample flights in Cinarpinar Forest Enterprise Chief in Kahramanmaras in Turkey. In addition, the photogrammetric workflow of obtained images and automated flight were presented with respect to capabilities of available software. The flight plans were created by using Pix4DCapture software with android based cell phone. The results indicated that high-resolution imagery obtained by drone can provide significant data for assessment of forest resources, forest roads, and stream channels.

The use of workflows in the design and implementation of complex experiments in macromolecular crystallography.

PubMed

Brockhauser, Sandor; Svensson, Olof; Bowler, Matthew W; Nanao, Max; Gordon, Elspeth; Leal, Ricardo M F; Popov, Alexander; Gerring, Matthew; McCarthy, Andrew A; Gotz, Andy

2012-08-01

The automation of beam delivery, sample handling and data analysis, together with increasing photon flux, diminishing focal spot size and the appearance of fast-readout detectors on synchrotron beamlines, have changed the way that many macromolecular crystallography experiments are planned and executed. Screening for the best diffracting crystal, or even the best diffracting part of a selected crystal, has been enabled by the development of microfocus beams, precise goniometers and fast-readout detectors that all require rapid feedback from the initial processing of images in order to be effective. All of these advances require the coupling of data feedback to the experimental control system and depend on immediate online data-analysis results during the experiment. To facilitate this, a Data Analysis WorkBench (DAWB) for the flexible creation of complex automated protocols has been developed. Here, example workflows designed and implemented using DAWB are presented for enhanced multi-step crystal characterizations, experiments involving crystal reorientation with kappa goniometers, crystal-burning experiments for empirically determining the radiation sensitivity of a crystal system and the application of mesh scans to find the best location of a crystal to obtain the highest diffraction quality. Beamline users interact with the prepared workflows through a specific brick within the beamline-control GUI MXCuBE.

Enterprise-wide PACS: beyond radiology, an architecture to manage all medical images.

PubMed

Bandon, David; Lovis, Christian; Geissbühler, Antoine; Vallée, Jean-Paul

2005-08-01

Picture archiving and communication systems (PACS) have the vocation to manage all medical images acquired within the hospital. To address the various situations encountered in the imaging specialties, the traditional architecture used for the radiology department has to evolve. We present our preliminarily results toward an enterprise-wide PACS intended to support all kind of image production in medicine, from biomolecular images to whole-body pictures. Our solution is based on an existing radiologic PACS system from which images are distributed through an electronic patient record to all care facilities. This platform is enriched with a flexible integration framework supporting digital image communication in medicine (DICOM) and DICOM-XML formats. In addition, a generic workflow engine highly customizable is used to drive work processes. Echocardiology; hematology; ear, nose, and throat; and dermatology, including wounds, follow-up is the first implemented extensions outside of radiology. We also propose a global strategy for further developments based on three possible architectures for an enterprise-wide PACS.

LACO-Wiki: A land cover validation tool and a new, innovative teaching resource for remote sensing and the geosciences

NASA Astrophysics Data System (ADS)

See, Linda; Perger, Christoph; Dresel, Christopher; Hofer, Martin; Weichselbaum, Juergen; Mondel, Thomas; Steffen, Fritz

2016-04-01

The validation of land cover products is an important step in the workflow of generating a land cover map from remotely-sensed imagery. Many students of remote sensing will be given exercises on classifying a land cover map followed by the validation process. Many algorithms exist for classification, embedded within proprietary image processing software or increasingly as open source tools. However, there is little standardization for land cover validation, nor a set of open tools available for implementing this process. The LACO-Wiki tool was developed as a way of filling this gap, bringing together standardized land cover validation methods and workflows into a single portal. This includes the storage and management of land cover maps and validation data; step-by-step instructions to guide users through the validation process; sound sampling designs; an easy-to-use environment for validation sample interpretation; and the generation of accuracy reports based on the validation process. The tool was developed for a range of users including producers of land cover maps, researchers, teachers and students. The use of such a tool could be embedded within the curriculum of remote sensing courses at a university level but is simple enough for use by students aged 13-18. A beta version of the tool is available for testing at: http://www.laco-wiki.net.

Wireless remote control of clinical image workflow: using a PDA for off-site distribution and disaster recovery.

PubMed

Documet, Jorge; Liu, Brent J; Documet, Luis; Huang, H K

2006-07-01

This paper describes a picture archiving and communication system (PACS) tool based on Web technology that remotely manages medical images between a PACS archive and remote destinations. Successfully implemented in a clinical environment and also demonstrated for the past 3 years at the conferences of various organizations, including the Radiological Society of North America, this tool provides a very practical and simple way to manage a PACS, including off-site image distribution and disaster recovery. The application is robust and flexible and can be used on a standard PC workstation or a Tablet PC, but more important, it can be used with a personal digital assistant (PDA). With a PDA, the Web application becomes a powerful wireless and mobile image management tool. The application's quick and easy-to-use features allow users to perform Digital Imaging and Communications in Medicine (DICOM) queries and retrievals with a single interface, without having to worry about the underlying configuration of DICOM nodes. In addition, this frees up dedicated PACS workstations to perform their specialized roles within the PACS workflow. This tool has been used at Saint John's Health Center in Santa Monica, California, for 2 years. The average number of queries per month is 2,021, with 816 C-MOVE retrieve requests. Clinical staff members can use PDAs to manage image workflow and PACS examination distribution conveniently for off-site consultations by referring physicians and radiologists and for disaster recovery. This solution also improves radiologists' effectiveness and efficiency in health care delivery both within radiology departments and for off-site clinical coverage.

A DICOM Based Collaborative Platform for Real-Time Medical Teleconsultation on Medical Images.

PubMed

Maglogiannis, Ilias; Andrikos, Christos; Rassias, Georgios; Tsanakas, Panayiotis

2017-01-01

The paper deals with the design of a Web-based platform for real-time medical teleconsultation on medical images. The proposed platform combines the principles of heterogeneous Workflow Management Systems (WfMSs), the peer-to-peer networking architecture and the SPA (Single-Page Application) concept, to facilitate medical collaboration among healthcare professionals geographically distributed. The presented work leverages state-of-the-art features of the web to support peer-to-peer communication using the WebRTC (Web Real Time Communication) protocol and client-side data processing for creating an integrated collaboration environment. The paper discusses the technical details of implementation and presents the operation of the platform in practice along with some initial results.

Tigres Workflow Library: Supporting Scientific Pipelines on HPC Systems

DOE PAGES

Hendrix, Valerie; Fox, James; Ghoshal, Devarshi; ...

2016-07-21

The growth in scientific data volumes has resulted in the need for new tools that enable users to operate on and analyze data on large-scale resources. In the last decade, a number of scientific workflow tools have emerged. These tools often target distributed environments, and often need expert help to compose and execute the workflows. Data-intensive workflows are often ad-hoc, they involve an iterative development process that includes users composing and testing their workflows on desktops, and scaling up to larger systems. In this paper, we present the design and implementation of Tigres, a workflow library that supports the iterativemore » workflow development cycle of data-intensive workflows. Tigres provides an application programming interface to a set of programming templates i.e., sequence, parallel, split, merge, that can be used to compose and execute computational and data pipelines. We discuss the results of our evaluation of scientific and synthetic workflows showing Tigres performs with minimal template overheads (mean of 13 seconds over all experiments). We also discuss various factors (e.g., I/O performance, execution mechanisms) that affect the performance of scientific workflows on HPC systems.« less

Tigres Workflow Library: Supporting Scientific Pipelines on HPC Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hendrix, Valerie; Fox, James; Ghoshal, Devarshi

The growth in scientific data volumes has resulted in the need for new tools that enable users to operate on and analyze data on large-scale resources. In the last decade, a number of scientific workflow tools have emerged. These tools often target distributed environments, and often need expert help to compose and execute the workflows. Data-intensive workflows are often ad-hoc, they involve an iterative development process that includes users composing and testing their workflows on desktops, and scaling up to larger systems. In this paper, we present the design and implementation of Tigres, a workflow library that supports the iterativemore » workflow development cycle of data-intensive workflows. Tigres provides an application programming interface to a set of programming templates i.e., sequence, parallel, split, merge, that can be used to compose and execute computational and data pipelines. We discuss the results of our evaluation of scientific and synthetic workflows showing Tigres performs with minimal template overheads (mean of 13 seconds over all experiments). We also discuss various factors (e.g., I/O performance, execution mechanisms) that affect the performance of scientific workflows on HPC systems.« less

Metaworkflows and Workflow Interoperability for Heliophysics

NASA Astrophysics Data System (ADS)

Pierantoni, Gabriele; Carley, Eoin P.

2014-06-01

Heliophysics is a relatively new branch of physics that investigates the relationship between the Sun and the other bodies of the solar system. To investigate such relationships, heliophysicists can rely on various tools developed by the community. Some of these tools are on-line catalogues that list events (such as Coronal Mass Ejections, CMEs) and their characteristics as they were observed on the surface of the Sun or on the other bodies of the Solar System. Other tools offer on-line data analysis and access to images and data catalogues. During their research, heliophysicists often perform investigations that need to coordinate several of these services and to repeat these complex operations until the phenomena under investigation are fully analyzed. Heliophysicists combine the results of these services; this service orchestration is best suited for workflows. This approach has been investigated in the HELIO project. The HELIO project developed an infrastructure for a Virtual Observatory for Heliophysics and implemented service orchestration using TAVERNA workflows. HELIO developed a set of workflows that proved to be useful but lacked flexibility and re-usability. The TAVERNA workflows also needed to be executed directly in TAVERNA workbench, and this forced all users to learn how to use the workbench. Within the SCI-BUS and ER-FLOW projects, we have started an effort to re-think and re-design the heliophysics workflows with the aim of fostering re-usability and ease of use. We base our approach on two key concepts, that of meta-workflows and that of workflow interoperability. We have divided the produced workflows in three different layers. The first layer is Basic Workflows, developed both in the TAVERNA and WS-PGRADE languages. They are building blocks that users compose to address their scientific challenges. They implement well-defined Use Cases that usually involve only one service. The second layer is Science Workflows usually developed in TAVERNA. They- implement Science Cases (the definition of a scientific challenge) by composing different Basic Workflows. The third and last layer,Iterative Science Workflows, is developed in WSPGRADE. It executes sub-workflows (either Basic or Science Workflows) as parameter sweep jobs to investigate Science Cases on large multiple data sets. So far, this approach has proven fruitful for three Science Cases of which one has been completed and two are still being tested.

Domain-Adapted Convolutional Networks for Satellite Image Classification: A Large-Scale Interactive Learning Workflow

DOE PAGES

Lunga, Dalton D.; Yang, Hsiuhan Lexie; Reith, Andrew E.; ...

2018-02-06

Satellite imagery often exhibits large spatial extent areas that encompass object classes with considerable variability. This often limits large-scale model generalization with machine learning algorithms. Notably, acquisition conditions, including dates, sensor position, lighting condition, and sensor types, often translate into class distribution shifts introducing complex nonlinear factors and hamper the potential impact of machine learning classifiers. Here, this article investigates the challenge of exploiting satellite images using convolutional neural networks (CNN) for settlement classification where the class distribution shifts are significant. We present a large-scale human settlement mapping workflow based-off multiple modules to adapt a pretrained CNN to address themore » negative impact of distribution shift on classification performance. To extend a locally trained classifier onto large spatial extents areas we introduce several submodules: First, a human-in-the-loop element for relabeling of misclassified target domain samples to generate representative examples for model adaptation; second, an efficient hashing module to minimize redundancy and noisy samples from the mass-selected examples; and third, a novel relevance ranking module to minimize the dominance of source example on the target domain. The workflow presents a novel and practical approach to achieve large-scale domain adaptation with binary classifiers that are based-off CNN features. Experimental evaluations are conducted on areas of interest that encompass various image characteristics, including multisensors, multitemporal, and multiangular conditions. Domain adaptation is assessed on source–target pairs through the transfer loss and transfer ratio metrics to illustrate the utility of the workflow.« less

Domain-Adapted Convolutional Networks for Satellite Image Classification: A Large-Scale Interactive Learning Workflow

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lunga, Dalton D.; Yang, Hsiuhan Lexie; Reith, Andrew E.

Satellite imagery often exhibits large spatial extent areas that encompass object classes with considerable variability. This often limits large-scale model generalization with machine learning algorithms. Notably, acquisition conditions, including dates, sensor position, lighting condition, and sensor types, often translate into class distribution shifts introducing complex nonlinear factors and hamper the potential impact of machine learning classifiers. Here, this article investigates the challenge of exploiting satellite images using convolutional neural networks (CNN) for settlement classification where the class distribution shifts are significant. We present a large-scale human settlement mapping workflow based-off multiple modules to adapt a pretrained CNN to address themore » negative impact of distribution shift on classification performance. To extend a locally trained classifier onto large spatial extents areas we introduce several submodules: First, a human-in-the-loop element for relabeling of misclassified target domain samples to generate representative examples for model adaptation; second, an efficient hashing module to minimize redundancy and noisy samples from the mass-selected examples; and third, a novel relevance ranking module to minimize the dominance of source example on the target domain. The workflow presents a novel and practical approach to achieve large-scale domain adaptation with binary classifiers that are based-off CNN features. Experimental evaluations are conducted on areas of interest that encompass various image characteristics, including multisensors, multitemporal, and multiangular conditions. Domain adaptation is assessed on source–target pairs through the transfer loss and transfer ratio metrics to illustrate the utility of the workflow.« less

Improving medical imaging report turnaround times: the role of technolgy.

PubMed

Marquez, Luis O; Stewart, Howard

2005-01-01

At Southern Ohio Medical Center (SOMC), the medical imaging department and the radiologists expressed a strong desire to improve workflow. The improved workflow was a major motivating factor toward implementing a new RIS and speech recognition technology. The need to monitor workflow in a real-time fashion and to evaluate productivity and resources necessitated that a new solution be found. A decision was made to roll out both the new RIS product and speech recognition to maximize the resources to interface and implement the new solution. Prior to implementation of the new RIS, the medical imaging department operated in a conventional electronic-order-entry to paper request manner. The paper request followed the study through exam completion to the radiologist. SOMC entered into a contract with its PACS vendor to participate in beta testing and clinical trials for a new RIS product for the US market. Backup plans were created in the event the product failed to function as planned--either during the beta testing period or during clinical trails. The last piece of the technology puzzle to improve report turnaround time was voice recognition technology. Speech recognition enhanced the RIS technology as soon as it was implemented. The results show that the project has been a success. The new RIS, combined with speech recognition and the PACS, makes for a very effective solution to patient, exam, and results management in the medical imaging department.

Software for MR image overlay guided needle insertions: the clinical translation process

NASA Astrophysics Data System (ADS)

Ungi, Tamas; U-Thainual, Paweena; Fritz, Jan; Iordachita, Iulian I.; Flammang, Aaron J.; Carrino, John A.; Fichtinger, Gabor

2013-03-01

PURPOSE: Needle guidance software using augmented reality image overlay was translated from the experimental phase to support preclinical and clinical studies. Major functional and structural changes were needed to meet clinical requirements. We present the process applied to fulfill these requirements, and selected features that may be applied in the translational phase of other image-guided surgical navigation systems. METHODS: We used an agile software development process for rapid adaptation to unforeseen clinical requests. The process is based on iterations of operating room test sessions, feedback discussions, and software development sprints. The open-source application framework of 3D Slicer and the NA-MIC kit provided sufficient flexibility and stable software foundations for this work. RESULTS: All requirements were addressed in a process with 19 operating room test iterations. Most features developed in this phase were related to workflow simplification and operator feedback. CONCLUSION: Efficient and affordable modifications were facilitated by an open source application framework and frequent clinical feedback sessions. Results of cadaver experiments show that software requirements were successfully solved after a limited number of operating room tests.

Global Seismic Imaging Based on Adjoint Tomography

NASA Astrophysics Data System (ADS)

Bozdag, E.; Lefebvre, M.; Lei, W.; Peter, D. B.; Smith, J. A.; Zhu, H.; Komatitsch, D.; Tromp, J.

2013-12-01

Our aim is to perform adjoint tomography at the scale of globe to image the entire planet. We have started elastic inversions with a global data set of 253 CMT earthquakes with moment magnitudes in the range 5.8 ≤ Mw ≤ 7 and used GSN stations as well as some local networks such as USArray, European stations, etc. Using an iterative pre-conditioned conjugate gradient scheme, we initially set the aim to obtain a global crustal and mantle model with confined transverse isotropy in the upper mantle. Global adjoint tomography has so far remained a challenge mainly due to computational limitations. Recent improvements in our 3D solvers (e.g., a GPU version) and access to high-performance computational centers (e.g., ORNL's Cray XK7 "Titan" system) now enable us to perform iterations with higher-resolution (T > 9 s) and longer-duration (200 min) simulations to accommodate high-frequency body waves and major-arc surface waves, respectively, which help improve data coverage. The remaining challenge is the heavy I/O traffic caused by the numerous files generated during the forward/adjoint simulations and the pre- and post-processing stages of our workflow. We improve the global adjoint tomography workflow by adopting the ADIOS file format for our seismic data as well as models, kernels, etc., to improve efficiency on high-performance clusters. Our ultimate aim is to use data from all available networks and earthquakes within the magnitude range of our interest (5.5 ≤ Mw ≤ 7) which requires a solid framework to manage big data in our global adjoint tomography workflow. We discuss the current status and future of global adjoint tomography based on our initial results as well as practical issues such as handling big data in inversions and on high-performance computing systems.

Architecture of next-generation information management systems for digital radiology enterprises

NASA Astrophysics Data System (ADS)

Wong, Stephen T. C.; Wang, Huili; Shen, Weimin; Schmidt, Joachim; Chen, George; Dolan, Tom

2000-05-01

Few information systems today offer a clear and flexible means to define and manage the automated part of radiology processes. None of them provide a coherent and scalable architecture that can easily cope with heterogeneity and inevitable local adaptation of applications. Most importantly, they often lack a model that can integrate clinical and administrative information to aid better decisions in managing resources, optimizing operations, and improving productivity. Digital radiology enterprises require cost-effective solutions to deliver information to the right person in the right place and at the right time. We propose a new architecture of image information management systems for digital radiology enterprises. Such a system is based on the emerging technologies in workflow management, distributed object computing, and Java and Web techniques, as well as Philips' domain knowledge in radiology operations. Our design adapts the approach of '4+1' architectural view. In this new architecture, PACS and RIS will become one while the user interaction can be automated by customized workflow process. Clinical service applications are implemented as active components. They can be reasonably substituted by applications of local adaptations and can be multiplied for fault tolerance and load balancing. Furthermore, it will provide powerful query and statistical functions for managing resources and improving productivity in real time. This work will lead to a new direction of image information management in the next millennium. We will illustrate the innovative design with implemented examples of a working prototype.

Task-technology fit of video telehealth for nurses in an outpatient clinic setting.

PubMed

Cady, Rhonda G; Finkelstein, Stanley M

2014-07-01

Incorporating telehealth into outpatient care delivery supports management of consumer health between clinic visits. Task-technology fit is a framework for understanding how technology helps and/or hinders a person during work processes. Evaluating the task-technology fit of video telehealth for personnel working in a pediatric outpatient clinic and providing care between clinic visits ensures the information provided matches the information needed to support work processes. The workflow of advanced practice registered nurse (APRN) care coordination provided via telephone and video telehealth was described and measured using a mixed-methods workflow analysis protocol that incorporated cognitive ethnography and time-motion study. Qualitative and quantitative results were merged and analyzed within the task-technology fit framework to determine the workflow fit of video telehealth for APRN care coordination. Incorporating video telehealth into APRN care coordination workflow provided visual information unavailable during telephone interactions. Despite additional tasks and interactions needed to obtain the visual information, APRN workflow efficiency, as measured by time, was not significantly changed. Analyzed within the task-technology fit framework, the increased visual information afforded by video telehealth supported the assessment and diagnostic information needs of the APRN. Telehealth must provide the right information to the right clinician at the right time. Evaluating task-technology fit using a mixed-methods protocol ensured rigorous analysis of fit within work processes and identified workflows that benefit most from the technology.

GUEST EDITOR'S INTRODUCTION: Guest Editor's introduction

NASA Astrophysics Data System (ADS)

Chrysanthis, Panos K.

1996-12-01

Computer Science Department, University of Pittsburgh, Pittsburgh, PA 15260, USA This special issue focuses on current efforts to represent and support workflows that integrate information systems and human resources within a business or manufacturing enterprise. Workflows may also be viewed as an emerging computational paradigm for effective structuring of cooperative applications involving human users and access to diverse data types not necessarily maintained by traditional database management systems. A workflow is an automated organizational process (also called business process) which consists of a set of activities or tasks that need to be executed in a particular controlled order over a combination of heterogeneous database systems and legacy systems. Within workflows, tasks are performed cooperatively by either human or computational agents in accordance with their roles in the organizational hierarchy. The challenge in facilitating the implementation of workflows lies in developing efficient workflow management systems. A workflow management system (also called workflow server, workflow engine or workflow enactment system) provides the necessary interfaces for coordination and communication among human and computational agents to execute the tasks involved in a workflow and controls the execution orderings of tasks as well as the flow of data that these tasks manipulate. That is, the workflow management system is responsible for correctly and reliably supporting the specification, execution, and monitoring of workflows. The six papers selected (out of the twenty-seven submitted for this special issue of Distributed Systems Engineering) address different aspects of these three functional components of a workflow management system. In the first paper, `Correctness issues in workflow management', Kamath and Ramamritham discuss the important issue of correctness in workflow management that constitutes a prerequisite for the use of workflows in the automation of the critical organizational/business processes. In particular, this paper examines the issues of execution atomicity and failure atomicity, differentiating between correctness requirements of system failures and logical failures, and surveys techniques that can be used to ensure data consistency in workflow management systems. While the first paper is concerned with correctness assuming transactional workflows in which selective transactional properties are associated with individual tasks or the entire workflow, the second paper, `Scheduling workflows by enforcing intertask dependencies' by Attie et al, assumes that the tasks can be either transactions or other activities involving legacy systems. This second paper describes the modelling and specification of conditions involving events and dependencies among tasks within a workflow using temporal logic and finite state automata. It also presents a scheduling algorithm that enforces all stated dependencies by executing at any given time only those events that are allowed by all the dependency automata and in an order as specified by the dependencies. In any system with decentralized control, there is a need to effectively cope with the tension that exists between autonomy and consistency requirements. In `A three-level atomicity model for decentralized workflow management systems', Ben-Shaul and Heineman focus on the specific requirement of enforcing failure atomicity in decentralized, autonomous and interacting workflow management systems. Their paper describes a model in which each workflow manager must be able to specify the sequence of tasks that comprise an atomic unit for the purposes of correctness, and the degrees of local and global atomicity for the purpose of cooperation with other workflow managers. The paper also discusses a realization of this model in which treaties and summits provide an agreement mechanism, while underlying transaction managers are responsible for maintaining failure atomicity. The fourth and fifth papers are experience papers describing a workflow management system and a large scale workflow application, respectively. Schill and Mittasch, in `Workflow management systems on top of OSF DCE and OMG CORBA', describe a decentralized workflow management system and discuss its implementation using two standardized middleware platforms, namely, OSF DCE and OMG CORBA. The system supports a new approach to workflow management, introducing several new concepts such as data type management for integrating various types of data and quality of service for various services provided by servers. A problem common to both database applications and workflows is the handling of missing and incomplete information. This is particularly pervasive in an `electronic market' with a huge number of retail outlets producing and exchanging volumes of data, the application discussed in `Information flow in the DAMA project beyond database managers: information flow managers'. Motivated by the need for a method that allows a task to proceed in a timely manner if not all data produced by other tasks are available by its deadline, Russell et al propose an architectural framework and a language that can be used to detect, approximate and, later on, to adjust missing data if necessary. The final paper, `The evolution towards flexible workflow systems' by Nutt, is complementary to the other papers and is a survey of issues and of work related to both workflow and computer supported collaborative work (CSCW) areas. In particular, the paper provides a model and a categorization of the dimensions which workflow management and CSCW systems share. Besides summarizing the recent advancements towards efficient workflow management, the papers in this special issue suggest areas open to investigation and it is our hope that they will also provide the stimulus for further research and development in the area of workflow management systems.

Experimental application of simulation tools for evaluating UAV video change detection

NASA Astrophysics Data System (ADS)

Saur, Günter; Bartelsen, Jan

2015-10-01

Change detection is one of the most important tasks when unmanned aerial vehicles (UAV) are used for video reconnaissance and surveillance. In this paper, we address changes on short time scale, i.e. the observations are taken within time distances of a few hours. Each observation is a short video sequence corresponding to the near-nadir overflight of the UAV above the interesting area and the relevant changes are e.g. recently added or removed objects. The change detection algorithm has to distinguish between relevant and non-relevant changes. Examples for non-relevant changes are versatile objects like trees and compression or transmission artifacts. To enable the usage of an automatic change detection within an interactive workflow of an UAV video exploitation system, an evaluation and assessment procedure has to be performed. Large video data sets which contain many relevant objects with varying scene background and altering influence parameters (e.g. image quality, sensor and flight parameters) including image metadata and ground truth data are necessary for a comprehensive evaluation. Since the acquisition of real video data is limited by cost and time constraints, from our point of view, the generation of synthetic data by simulation tools has to be considered. In this paper the processing chain of Saur et al. (2014) [1] and the interactive workflow for video change detection is described. We have selected the commercial simulation environment Virtual Battle Space 3 (VBS3) to generate synthetic data. For an experimental setup, an example scenario "road monitoring" has been defined and several video clips have been produced with varying flight and sensor parameters and varying objects in the scene. Image registration and change mask extraction, both components of the processing chain, are applied to corresponding frames of different video clips. For the selected examples, the images could be registered, the modelled changes could be extracted and the artifacts of the image rendering considered as noise (slight differences of heading angles, disparity of vegetation, 3D parallax) could be suppressed. We conclude that these image data could be considered to be realistic enough to serve as evaluation data for the selected processing components. Future work will extend the evaluation to other influence parameters and may include the human operator for mission planning and sensor control.

Geometric Calibration and Validation of Ultracam Aerial Sensors

NASA Astrophysics Data System (ADS)

Gruber, Michael; Schachinger, Bernhard; Muick, Marc; Neuner, Christian; Tschemmernegg, Helfried

2016-03-01

We present details of the calibration and validation procedure of UltraCam Aerial Camera systems. Results from the laboratory calibration and from validation flights are presented for both, the large format nadir cameras and the oblique cameras as well. Thus in this contribution we show results from the UltraCam Eagle and the UltraCam Falcon, both nadir mapping cameras, and the UltraCam Osprey, our oblique camera system. This sensor offers a mapping grade nadir component together with the four oblique camera heads. The geometric processing after the flight mission is being covered by the UltraMap software product. Thus we present details about the workflow as well. The first part consists of the initial post-processing which combines image information as well as camera parameters derived from the laboratory calibration. The second part, the traditional automated aerial triangulation (AAT) is the step from single images to blocks and enables an additional optimization process. We also present some special features of our software, which are designed to better support the operator to analyze large blocks of aerial images and to judge the quality of the photogrammetric set-up.

Data and Workflow Management Challenges in Global Adjoint Tomography

NASA Astrophysics Data System (ADS)

Lei, W.; Ruan, Y.; Smith, J. A.; Modrak, R. T.; Orsvuran, R.; Krischer, L.; Chen, Y.; Balasubramanian, V.; Hill, J.; Turilli, M.; Bozdag, E.; Lefebvre, M. P.; Jha, S.; Tromp, J.

2017-12-01

It is crucial to take the complete physics of wave propagation into account in seismic tomography to further improve the resolution of tomographic images. The adjoint method is an efficient way of incorporating 3D wave simulations in seismic tomography. However, global adjoint tomography is computationally expensive, requiring thousands of wavefield simulations and massive data processing. Through our collaboration with the Oak Ridge National Laboratory (ORNL) computing group and an allocation on Titan, ORNL's GPU-accelerated supercomputer, we are now performing our global inversions by assimilating waveform data from over 1,000 earthquakes. The first challenge we encountered is dealing with the sheer amount of seismic data. Data processing based on conventional data formats and processing tools (such as SAC), which are not designed for parallel systems, becomes our major bottleneck. To facilitate the data processing procedures, we designed the Adaptive Seismic Data Format (ASDF) and developed a set of Python-based processing tools to replace legacy FORTRAN-based software. These tools greatly enhance reproducibility and accountability while taking full advantage of highly parallel system and showing superior scaling on modern computational platforms. The second challenge is that the data processing workflow contains more than 10 sub-procedures, making it delicate to handle and prone to human mistakes. To reduce human intervention as much as possible, we are developing a framework specifically designed for seismic inversion based on the state-of-the art workflow management research, specifically the Ensemble Toolkit (EnTK), in collaboration with the RADICAL team from Rutgers University. Using the initial developments of the EnTK, we are able to utilize the full computing power of the data processing cluster RHEA at ORNL while keeping human interaction to a minimum and greatly reducing the data processing time. Thanks to all the improvements, we are now able to perform iterations fast enough on more than a 1,000 earthquakes dataset. Starting from model GLAD-M15 (Bozdag et al., 2016), an elastic 3D model with a transversely isotropic upper mantle, we have successfully performed 5 iterations. Our goal is to finish 10 iterations, i.e., generating GLAD M25* by the end of this year.

Considering Time in Orthophotography Production: from a General Workflow to a Shortened Workflow for a Faster Disaster Response

NASA Astrophysics Data System (ADS)

Lucas, G.

2015-08-01

This article overall deals with production time with orthophoto imagery with medium size digital frame camera. The workflow examination follows two main parts: data acquisition and post-processing. The objectives of the research are fourfold: 1/ gathering time references for the most important steps of orthophoto production (it turned out that literature is missing on this topic); these figures are used later for total production time estimation; 2/ identifying levers for reducing orthophoto production time; 3/ building a simplified production workflow for emergency response: less exigent with accuracy and faster; and compare it to a classical workflow; 4/ providing methodical elements for the estimation of production time with a custom project. In the data acquisition part a comprehensive review lists and describes all the factors that may affect the acquisition efficiency. Using a simulation with different variables (average line length, time of the turns, flight speed) their effect on acquisition efficiency is quantitatively examined. Regarding post-processing, the time references figures were collected from the processing of a 1000 frames case study with 15 cm GSD covering a rectangular area of 447 km2; the time required to achieve each step during the production is written down. When several technical options are possible, each one is tested and time documented so as all alternatives are available. Based on a technical choice with the workflow and using the compiled time reference of the elementary steps, a total time is calculated for the post-processing of the 1000 frames. Two scenarios are compared as regards to time and accuracy. The first one follows the "normal" practices, comprising triangulation, orthorectification and advanced mosaicking methods (feature detection, seam line editing and seam applicator); the second is simplified and make compromise over positional accuracy (using direct geo-referencing) and seamlines preparation in order to achieve orthophoto production faster. The shortened workflow reduces the production time by more than three whereas the positional error increases from 1 GSD to 1.5 GSD. The examination of time allocation through the production process shows that it is worth sparing time in the post-processing phase.

Bridging the integration gap between imaging and information systems: a uniform data concept for content-based image retrieval in computer-aided diagnosis.

PubMed

Welter, Petra; Riesmeier, Jörg; Fischer, Benedikt; Grouls, Christoph; Kuhl, Christiane; Deserno, Thomas M

2011-01-01

It is widely accepted that content-based image retrieval (CBIR) can be extremely useful for computer-aided diagnosis (CAD). However, CBIR has not been established in clinical practice yet. As a widely unattended gap of integration, a unified data concept for CBIR-based CAD results and reporting is lacking. Picture archiving and communication systems and the workflow of radiologists must be considered for successful data integration to be achieved. We suggest that CBIR systems applied to CAD should integrate their results in a picture archiving and communication systems environment such as Digital Imaging and Communications in Medicine (DICOM) structured reporting documents. A sample DICOM structured reporting template adaptable to CBIR and an appropriate integration scheme is presented. The proposed CBIR data concept may foster the promulgation of CBIR systems in clinical environments and, thereby, improve the diagnostic process.

Bridging the integration gap between imaging and information systems: a uniform data concept for content-based image retrieval in computer-aided diagnosis

PubMed Central

Riesmeier, Jörg; Fischer, Benedikt; Grouls, Christoph; Kuhl, Christiane; Deserno (né Lehmann), Thomas M

2011-01-01

It is widely accepted that content-based image retrieval (CBIR) can be extremely useful for computer-aided diagnosis (CAD). However, CBIR has not been established in clinical practice yet. As a widely unattended gap of integration, a unified data concept for CBIR-based CAD results and reporting is lacking. Picture archiving and communication systems and the workflow of radiologists must be considered for successful data integration to be achieved. We suggest that CBIR systems applied to CAD should integrate their results in a picture archiving and communication systems environment such as Digital Imaging and Communications in Medicine (DICOM) structured reporting documents. A sample DICOM structured reporting template adaptable to CBIR and an appropriate integration scheme is presented. The proposed CBIR data concept may foster the promulgation of CBIR systems in clinical environments and, thereby, improve the diagnostic process. PMID:21672913

Enterprise-wide implementation of digital radiography in oral and maxillofacial imaging: the University of Florida Dentistry System.

PubMed

Nair, Madhu K; Pettigrew, James C; Loomis, Jeffrey S; Bates, Robert E; Kostewicz, Stephen; Robinson, Boyd; Sweitzer, Jean; Dolan, Teresa A

2009-06-01

The implementation of digital radiography in dentistry in a large healthcare enterprise setting is discussed. A distinct need for a dedicated dental picture archiving and communication systems (PACS) exists for seamless integration of different vendor products across the system. Complex issues are contended with as each clinical department migrated to a digital environment with unique needs and workflow patterns. The University of Florida has had a dental PACS installed over 2 years ago. This paper describes the process of conversion from film-based imaging from the planning stages through clinical implementation. Dentistry poses many unique challenges as it strives to achieve better integration with systems primarily designed for imaging; however, the technical requirements for high-resolution image capture in dentistry far exceed those in medicine, as most routine dental diagnostic tasks are challenging. The significance of specification, evaluation, vendor selection, installation, trial runs, training, and phased clinical implementation is emphasized.

Radiology Architecture Project Primer.

PubMed

Sze, Raymond W; Hogan, Laurie; Teshima, Satoshi; Davidson, Scott

2017-12-19

The rapid pace of technologic advancement and increasing expectations for patient- and family-friendly environments make it common for radiology leaders to be involved in imaging remodel and construction projects. Most radiologists and business directors lack formal training in architectural and construction processes but are expected to play significant and often leading roles in all phases of an imaging construction project. Avoidable mistakes can result in significant increased costs and scheduling delays; knowledgeable participation and communication can result in a final product that enhances staff workflow and morale and improves patient care and experience. This article presents practical guidelines for preparing for and leading a new imaging architectural and construction project. We share principles derived from the radiology and nonradiology literature and our own experience over the past decade completely remodeling a large pediatric radiology department and building a full-service outpatient imaging center. Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.

MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.

PubMed

Caetano, Fabiana A; Dirk, Brennan S; Tam, Joshua H K; Cavanagh, P Craig; Goiko, Maria; Ferguson, Stephen S G; Pasternak, Stephen H; Dikeakos, Jimmy D; de Bruyn, John R; Heit, Bryan

2015-12-01

Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR) software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell.

D Imaging for Museum Artefacts: a Portable Test Object for Heritage and Museum Documentation of Small Objects

NASA Astrophysics Data System (ADS)

Hess, M.; Robson, S.

2012-07-01

3D colour image data generated for the recording of small museum objects and archaeological finds are highly variable in quality and fitness for purpose. Whilst current technology is capable of extremely high quality outputs, there are currently no common standards or applicable guidelines in either the museum or engineering domain suited to scientific evaluation, understanding and tendering for 3D colour digital data. This paper firstly explains the rationale towards and requirements for 3D digital documentation in museums. Secondly it describes the design process, development and use of a new portable test object suited to sensor evaluation and the provision of user acceptance metrics. The test object is specifically designed for museums and heritage institutions and includes known surface and geometric properties which support quantitative and comparative imaging on different systems. The development for a supporting protocol will allow object reference data to be included in the data processing workflow with specific reference to conservation and curation.

Quantitative multiplex immunohistochemistry reveals myeloid-inflamed tumor-immune complexity associated with poor prognosis

PubMed Central

Tsujikawa, Takahiro; Kumar, Sushil; Borkar, Rohan N.; Azimi, Vahid; Thibault, Guillaume; Chang, Young Hwan; Balter, Ariel; Kawashima, Rie; Choe, Gina; Sauer, David; El Rassi, Edward; Clayburgh, Daniel R.; Kulesz-Martin, Molly F.; Lutz, Eric R.; Zheng, Lei; Jaffee, Elizabeth M.; Leyshock, Patrick; Margolin, Adam A.; Mori, Motomi; Gray, Joe W.; Flint, Paul W.; Coussens, Lisa M.

2017-01-01

SUMMARY Here we describe a multiplexed immunohistochemical platform, with computational image processing workflows including image cytometry, enabling simultaneous evaluation of 12 biomarkers in one formalin-fixed paraffin-embedded tissue section. To validate this platform, we used tissue microarrays containing 38 archival head and neck squamous cell carcinomas, and revealed differential immune profiles based on lymphoid and myeloid cell densities, correlating with human papilloma virus status and prognosis. Based on these results, we investigated 24 pancreatic ductal adenocarcinomas from patients who received neoadjuvant GVAX vaccination, and revealed that response to therapy correlated with degree of mono-myelocytic cell density, and percentages of CD8+ T cells expressing T cell exhaustion markers. These data highlight the utility of in situ immune monitoring for patient stratification, and provide digital image processing pipelines (https://github.com/multiplexIHC/cppipe) to the community for examining immune complexity in precious tissue sections, where phenotype and tissue architecture are preserved to thus improve biomarker discovery and assessment. PMID:28380359

Business process re-engineering a cardiology department.

PubMed

Bakshi, Syed Murtuza Hussain

2014-01-01

The health care sector is the world's third largest industry and is facing several problems such as excessive waiting times for patients, lack of access to information, high costs of delivery and medical errors. Health care managers seek the help of process re-engineering methods to discover the best processes and to re-engineer existing processes to optimize productivity without compromising on quality. Business process re-engineering refers to the fundamental rethinking and radical redesign of business processes to achieve dramatic improvements in critical, contemporary measures of performance, such as cost, quality and speed. The present study is carried out at a tertiary care corporate hospital with 1000-plus-bed facility. A descriptive study and case study method is used with intensive, careful and complete observation of patient flow, delays, short comings in patient movement and workflow. Data is collected through observations, informal interviews and analyzed by matrix analysis. Flowcharts were drawn for the various work activities of the cardiology department including workflow of the admission process, workflow in the ward and ICCU, workflow of the patient for catheterization laboratory procedure, and in the billing and discharge process. The problems of the existing system were studied and necessary suggestions were recommended to cardiology department module with an illustrated flowchart.

DOMstudio: an integrated workflow for Digital Outcrop Model reconstruction and interpretation

NASA Astrophysics Data System (ADS)

Bistacchi, Andrea

2015-04-01

Different Remote Sensing technologies, including photogrammetry and LIDAR, allow collecting 3D dataset that can be used to create 3D digital representations of outcrop surfaces, called Digital Outcrop Models (DOM), or sometimes Virtual Outcrop Models (VOM). Irrespective of the Remote Sensing technique used, DOMs can be represented either by photorealistic point clouds (PC-DOM) or textured surfaces (TS-DOM). The first are datasets composed of millions of points with XYZ coordinates and RGB colour, whilst the latter are triangulated surfaces onto which images of the outcrop have been mapped or "textured" (applying a tech-nology originally developed for movies and videogames). Here we present a workflow that allows exploiting in an integrated and efficient, yet flexible way, both kinds of dataset: PC-DOMs and TS-DOMs. The workflow is composed of three main steps: (1) data collection and processing, (2) interpretation, and (3) modelling. Data collection can be performed with photogrammetry, LIDAR, or other techniques. The quality of photogrammetric datasets obtained with Structure From Motion (SFM) techniques has shown a tremendous improvement over the past few years, and this is becoming the more effective way to collect DOM datasets. The main advantages of photogrammetry over LIDAR are represented by the very simple and lightweight field equipment (a digital camera), and by the arbitrary spatial resolution, that can be increased simply getting closer to the out-crop or by using a different lens. It must be noted that concerns about the precision of close-range photogrammetric surveys, that were justified in the past, are no more a problem if modern software and acquisition schemas are applied. In any case, LIDAR is a well-tested technology and it is still very common. Irrespective of the data collection technology, the output will be a photorealistic point cloud and a collection of oriented photos, plus additional imagery in special projects (e.g. infrared images). This dataset can be used as-is (PC-DOM), or a 3D triangulated surface can be interpolated from the point cloud, and images can be used to associate a texture to this surface (TS-DOM). In the DOMstudio workflow we use both PC-DOMs and TS-DOMs. Particularly, the latter are obtained projecting the original images onto the triangulated surface, without any downsampling, thus retaining the original resolution and quality of images collected in the field. In the DOMstudio interpretation step, PC-DOM is considered the best option for fracture analysis in outcrops where facets corresponding to fractures are present. This allows obtaining orientation statistics (e.g. stereoplots, Fisher statistics, etc.) directly from a point cloud where, for each point, the unit vector normal to the outcrop surface has been calculated. A recent development in this kind of processing is represented by the possibility to automatically select (segment) subset point clouds representing single fracture surfaces, which can be used for studies on fracture length, spacing, etc., allowing to obtain parameters like the frequency-length distribution, P21, etc. PC-DOM interpretation can be combined or complemented, depending on the outcrop morphology, with an interpretation carried out on a TS-DOM in terms of traces, which are the linear intersection of "geological" surfaces (fractures, faults, bedding, etc.) with the outcrop surface. This kind of interpretation is very well suited for outcrops with smooth surfaces, and can be performed either by manual picking, or by applying image analysis techniques on the images associated with the DOM. In this case, a huge mass of data, with very high resolution, can be collected very effectively. If we consider applications like lithological or mineral map-ping, TS-DOM datasets are the only suitable support. Finally, the DOMstudio workflow produces output in formats that are compatible with all common geomodelling packages (e.g. Gocad/Skua, Petrel, Move), allowing to directly use the quantitative data collected on DOMs to generate and calibrate geological, structural, or geostatistical models. I will present examples of applications including hydrocarbon reservoir analogue studies, studies on fault zone architecture, lithological mapping on sedimentary and metamorphic rocks, and studies on the surface of planets and small bodies in the Solar System.

Big Data and High-Performance Computing in Global Seismology

NASA Astrophysics Data System (ADS)

Bozdag, Ebru; Lefebvre, Matthieu; Lei, Wenjie; Peter, Daniel; Smith, James; Komatitsch, Dimitri; Tromp, Jeroen

2014-05-01

Much of our knowledge of Earth's interior is based on seismic observations and measurements. Adjoint methods provide an efficient way of incorporating 3D full wave propagation in iterative seismic inversions to enhance tomographic images and thus our understanding of processes taking place inside the Earth. Our aim is to take adjoint tomography, which has been successfully applied to regional and continental scale problems, further to image the entire planet. This is one of the extreme imaging challenges in seismology, mainly due to the intense computational requirements and vast amount of high-quality seismic data that can potentially be assimilated. We have started low-resolution inversions (T > 30 s and T > 60 s for body and surface waves, respectively) with a limited data set (253 carefully selected earthquakes and seismic data from permanent and temporary networks) on Oak Ridge National Laboratory's Cray XK7 "Titan" system. Recent improvements in our 3D global wave propagation solvers, such as a GPU version of the SPECFEM3D_GLOBE package, will enable us perform higher-resolution (T > 9 s) and longer duration (~180 m) simulations to take the advantage of high-frequency body waves and major-arc surface waves, thereby improving imbalanced ray coverage as a result of the uneven global distribution of sources and receivers. Our ultimate goal is to use all earthquakes in the global CMT catalogue within the magnitude range of our interest and data from all available seismic networks. To take the full advantage of computational resources, we need a solid framework to manage big data sets during numerical simulations, pre-processing (i.e., data requests and quality checks, processing data, window selection, etc.) and post-processing (i.e., pre-conditioning and smoothing kernels, etc.). We address the bottlenecks in our global seismic workflow, which are mainly coming from heavy I/O traffic during simulations and the pre- and post-processing stages, by defining new data formats for seismograms and outputs of our 3D solvers (i.e., meshes, kernels, seismic models, etc.) based on ORNL's ADIOS libraries. We will discuss our global adjoint tomography workflow on HPC systems as well as the current status of our global inversions.

SU-F-T-617: Remotely Pre-Planned Stereotactic Ablative Radiation Therapy: Validation of Treatment Plan Quality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Juang, T; Bush, K; Loo, B

Purpose: We propose a workflow to improve access to stereotactic ablative radiation therapy (SABR) for rural patients. When implemented, a separate trip to the central facility for simulation can be eliminated. Two elements are required: (1) Fabrication of custom immobilization devices to match positioning on prior diagnostic CT (dxCT). (2) Remote radiation pre-planning on dxCT, with transfer of contours/plan to simulation CT (simCT) and initiation of treatment same-day or next day. In this retrospective study, we validated part 2 of the workflow using patients already treated with SABR for upper lobe lung tumors. Methods: Target/normal structures were contoured on dxCT;more » a plan was created and approved by the physician. Structures were transferred to simCT using deformable image registration and the plan was re-optimized on simCT. Plan quality was evaluated through comparison to gold-standard structures contoured on simCT and a gold-standard plan based on these structures. Workflow-generated plan quality in this study represents a worst-case scenario as these patients were not treated using custom immobilization to match dxCT position as would be done when the workflow is implemented clinically. Results: 5/6 plans created through the pre-planning workflow were clinically acceptable. For all six plans, the gold-standard GTV received full prescription dose, along with median PTV V95%=95.2% and median PTV D95%=95.4%. Median GTV DSC=0.80, indicating high degree of similarity between the deformed and gold-standard GTV contours despite small GTV sizes (mean=3.0cc). One outlier (DSC=0.49) resulted in inadequate PTV coverage (V95%=62.9%) in the workflow plan; in clinical practice, this mismatch between deformed/gold-standard GTV would be revised by the physician after deformable registration. For all patients, normal tissue doses were comparable to the gold-standard plan and well within constraints. Conclusion: Pre-planning SABR cases on diagnostic imaging generated clinically acceptable plans. Coupled with rapid-prototyped custom immobilization, this workflow may improve treatment access for rural patients.« less

UAV-Based Hyperspectral Remote Sensing for Precision Agriculture: Challenges and Opportunities

NASA Astrophysics Data System (ADS)

Angel, Y.; Parkes, S. D.; Turner, D.; Houborg, R.; Lucieer, A.; McCabe, M.

2017-12-01

Modern agricultural production relies on monitoring crop status by observing and measuring variables such as soil condition, plant health, fertilizer and pesticide effect, irrigation and crop yield. Managing all of these factors is a considerable challenge for crop producers. As such, providing integrated technological solutions that enable improved diagnostics of field condition to maximize profits, while minimizing environmental impacts, would be of much interest. Such challenges can be addressed by implementing remote sensing systems such as hyperspectral imaging to produce precise biophysical indicator maps across the various cycles of crop development. Recent progress in unmanned aerial vehicles (UAVs) have advanced traditional satellite-based capabilities, providing a capacity for high-spatial, spectral and temporal response. However, while some hyperspectral sensors have been developed for use onboard UAVs, significant investment is required to develop a system and data processing workflow that retrieves accurately georeferenced mosaics. Here we explore the use of a pushbroom hyperspectral camera that is integrated on-board a multi-rotor UAV system to measure the surface reflectance in 272 distinct spectral bands across a wavelengths range spanning 400-1000 nm, and outline the requirement for sensor calibration, integration onto a stable UAV platform enabling accurate positional data, flight planning, and development of data post-processing workflows for georeferenced mosaics. The provision of high-quality and geo-corrected imagery facilitates the development of metrics of vegetation health that can be used to identify potential problems such as production inefficiencies, diseases and nutrient deficiencies and other data-streams to enable improved crop management. Immense opportunities remain to be exploited in the implementation of UAV-based hyperspectral sensing (and its combination with other imaging systems) to provide a transferable and scalable integrated framework for crop growth monitoring and yield prediction. Here we explore some of the challenges and issues in translating the available technological capacity into a useful and useable image collection and processing flow-path that enables these potential applications to be better realized.

SU-C-9A-02: Structured Noise Index as An Automated Quality Control for Nuclear Medicine: A Two Year Experience

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nelson, J; Christianson, O; Samei, E

Purpose: Flood-field uniformity evaluation is an essential element in the assessment of nuclear medicine (NM) gamma cameras. It serves as the central element of the quality control (QC) program, acquired and analyzed on a daily basis prior to clinical imaging. Uniformity images are traditionally analyzed using pixel value-based metrics which often fail to capture subtle structure and patterns caused by changes in gamma camera performance requiring additional visual inspection which is subjective and time demanding. The goal of this project was to develop and implement a robust QC metrology for NM that is effective in identifying non-uniformity issues, reporting issuesmore » in a timely manner for efficient correction prior to clinical involvement, all incorporated into an automated effortless workflow, and to characterize the program over a two year period. Methods: A new quantitative uniformity analysis metric was developed based on 2D noise power spectrum metrology and confirmed based on expert observer visual analysis. The metric, termed Structured Noise Index (SNI) was then integrated into an automated program to analyze, archive, and report on daily NM QC uniformity images. The effectiveness of the program was evaluated over a period of 2 years. Results: The SNI metric successfully identified visually apparent non-uniformities overlooked by the pixel valuebased analysis methods. Implementation of the program has resulted in nonuniformity identification in about 12% of daily flood images. In addition, due to the vigilance of staff response, the percentage of days exceeding trigger value shows a decline over time. Conclusion: The SNI provides a robust quantification of the NM performance of gamma camera uniformity. It operates seamlessly across a fleet of multiple camera models. The automated process provides effective workflow within the NM spectra between physicist, technologist, and clinical engineer. The reliability of this process has made it the preferred platform for NM uniformity analysis.« less

[Application and prospect of digital technology in the field of orthodontics].

PubMed

Zhou, Y H

2016-06-01

The three-dimensional(3D)digital technology has brought a revolutionary change in diagnostic planning and treatment strategy of orthodontics. Acquisition of 3D image data of the hard and soft tissues of the patients, diagnostic analysis and treatment prediction, and ultimately the individualized orthodontic appliance, will become the development trend and workflow of the 3D orthodontics. With the development of 3D digital technology, the traditional plaster model has been gradually replacing by 3D digital models. Meanwhile, 3D facial soft tissue scan and cone-beam CT scan have been gradually applied to clinical orthodontics, making it possible to get 3D virtual anatomical structure for patients. With the help of digital technology, the diagnostic process is much easier for orthodontist. However how to command the whole digital workflow and put it into practice in the daily work is still a long way to go. The purpose of this article is to enlighten the orthodontists interested in digital technology and discuss the future of digital orthodontics in China.

Multiscale pore structure and its effect on gas transport in organic-rich shale

NASA Astrophysics Data System (ADS)

Wu, Tianhao; Li, Xiang; Zhao, Junliang; Zhang, Dongxiao

2017-07-01

A systematic investigation of multiscale pore structure in organic-rich shale by means of the combination of various imaging techniques is presented, including the state-of-the-art Helium-Ion-Microscope (HIM). The study achieves insight into the major features at each scale and suggests the affordable techniques for specific objectives from the aspects of resolution, dimension, and cost. The pores, which appear to be isolated, are connected by smaller pores resolved by higher-resolution imaging. This observation provides valuable information, from the microscopic perspective of pore structure, for understanding how gas accumulates and transports from where it is generated. A comprehensive workflow is proposed based on the characteristics acquired from the multiscale pore structure analysis to simulate the gas transport process. The simulations are completed with three levels: the microscopic mechanisms should be taken into consideration at level I; the spatial distribution features of organic matter, inorganic matter, and macropores constitute the major issue at level II; and the microfracture orientation and topological structure are dominant factors at level III. The results of apparent permeability from simulations agree well with the values acquired from experiments. By means of the workflow, the impact of various gas transport mechanisms at different scales can be investigated more individually and precisely than conventional experiments.

RFA Guardian: Comprehensive Simulation of Radiofrequency Ablation Treatment of Liver Tumors.

PubMed

Voglreiter, Philip; Mariappan, Panchatcharam; Pollari, Mika; Flanagan, Ronan; Blanco Sequeiros, Roberto; Portugaller, Rupert Horst; Fütterer, Jurgen; Schmalstieg, Dieter; Kolesnik, Marina; Moche, Michael

2018-01-15

The RFA Guardian is a comprehensive application for high-performance patient-specific simulation of radiofrequency ablation of liver tumors. We address a wide range of usage scenarios. These include pre-interventional planning, sampling of the parameter space for uncertainty estimation, treatment evaluation and, in the worst case, failure analysis. The RFA Guardian is the first of its kind that exhibits sufficient performance for simulating treatment outcomes during the intervention. We achieve this by combining a large number of high-performance image processing, biomechanical simulation and visualization techniques into a generalized technical workflow. Further, we wrap the feature set into a single, integrated application, which exploits all available resources of standard consumer hardware, including massively parallel computing on graphics processing units. This allows us to predict or reproduce treatment outcomes on a single personal computer with high computational performance and high accuracy. The resulting low demand for infrastructure enables easy and cost-efficient integration into the clinical routine. We present a number of evaluation cases from the clinical practice where users performed the whole technical workflow from patient-specific modeling to final validation and highlight the opportunities arising from our fast, accurate prediction techniques.

Improving data collection, documentation, and workflow in a dementia screening study.

PubMed

Read, Kevin B; LaPolla, Fred Willie Zametkin; Tolea, Magdalena I; Galvin, James E; Surkis, Alisa

2017-04-01

A clinical study team performing three multicultural dementia screening studies identified the need to improve data management practices and facilitate data sharing. A collaboration was initiated with librarians as part of the National Library of Medicine (NLM) informationist supplement program. The librarians identified areas for improvement in the studies' data collection, entry, and processing workflows. The librarians' role in this project was to meet needs expressed by the study team around improving data collection and processing workflows to increase study efficiency and ensure data quality. The librarians addressed the data collection, entry, and processing weaknesses through standardizing and renaming variables, creating an electronic data capture system using REDCap, and developing well-documented, reproducible data processing workflows. NLM informationist supplements provide librarians with valuable experience in collaborating with study teams to address their data needs. For this project, the librarians gained skills in project management, REDCap, and understanding of the challenges and specifics of a clinical research study. However, the time and effort required to provide targeted and intensive support for one study team was not scalable to the library's broader user community.

Data processing workflow for time of flight polarized neutrons inelastic measurements

DOE PAGES

Savici, Andrei T.; Zaliznyak, Igor A.; Ovidiu Garlea, V.; ...

2017-06-01

We discuss the data processing workflow for polarized neutron scattering measurements performed at HYSPEC spectrometer at the Spallation Neutron Source, Oak Ridge National Laboratory. The effects of the focusing Heusler crystal polarizer and the wide-angle supermirror transmission polarization analyzer are added to the data processing flow of the non-polarized case. The implementation is done using the Mantid software package.

Real-Time Field Data Acquisition and Remote Sensor Reconfiguration Using Scientific Workflows

NASA Astrophysics Data System (ADS)

Silva, F.; Mehta, G.; Vahi, K.; Deelman, E.

2010-12-01

Despite many technological advances, field data acquisition still consists of several manual and laborious steps. Once sensors and data loggers are deployed in the field, scientists often have to periodically return to their study sites in order to collect their data. Even when field deployments have a way to communicate and transmit data back to the laboratory (e.g. by using a satellite or a cellular modem), data analysis still requires several repetitive steps. Because data often needs to be processed and inspected manually, there is usually a significant time delay between data collection and analysis. As a result, sensor failures that could be detected almost in real-time are not noted for weeks or months. Finally, sensor reconfiguration as a result of interesting events in the field is still done manually, making rapid response nearly impossible and causing important data to be missed. By working closely with scientists from different application domains, we identified several tasks that, if automated, could greatly improve the way field data is collected, processed, and distributed. Our goals are to enable real-time data collection and validation, automate sensor reconfiguration in response to interest events in the field, and allow scientists to easily automate their data processing. We began our design by employing the Sensor Processing and Acquisition Network (SPAN) architecture. SPAN uses an embedded processor in the field to coordinate sensor data acquisition from analog and digital sensors by interfacing with different types of devices and data loggers. SPAN is also able to interact with various types of communication devices in order to provide real-time communication to and from field sites. We use the Pegasus Workflow Management System (Pegasus WMS) to coordinate data collection and control sensors and deployments in the field. Because scientific workflows can be used to automate multi-step, repetitive tasks, scientists can create simple workflows to download sensor data, perform basic QA/QC, and identify events of interest as well as sensor and data logger failures almost in real-time. As a result of this automation, scientists can quickly be notified (e.g. via e-mail or SMS) so that important events are not missed. In addition, Pegasus WMS has the ability to abstract the execution environment of where programs run. By placing a Pegasus WMS agent inside an embedded processor in the field, we allow scientists to ship simple computational models to the field, enabling remote data processing at the field site. As an example, scientists can send an image processing algorithm to the field so that the embedded processor can analyze images, thus reducing the bandwidth necessary for communication. In addition, when real-time communication to the laboratory is not possible, scientists can create simple computational models that can be run on sensor nodes autonomously, monitoring sensor data and making adjustments without any human intervention. We believe our system lowers the bar for the adoption of reconfigurable sensor networks by field scientists. In this poster, we will show how this technology can be used to provide not only data acquisition, but also real-time data validation and sensor reconfiguration.

Modeling workflow to design machine translation applications for public health practice

PubMed Central

Turner, Anne M.; Brownstein, Megumu K.; Cole, Kate; Karasz, Hilary; Kirchhoff, Katrin

2014-01-01

Objective Provide a detailed understanding of the information workflow processes related to translating health promotion materials for limited English proficiency individuals in order to inform the design of context-driven machine translation (MT) tools for public health (PH). Materials and Methods We applied a cognitive work analysis framework to investigate the translation information workflow processes of two large health departments in Washington State. Researchers conducted interviews, performed a task analysis, and validated results with PH professionals to model translation workflow and identify functional requirements for a translation system for PH. Results The study resulted in a detailed description of work related to translation of PH materials, an information workflow diagram, and a description of attitudes towards MT technology. We identified a number of themes that hold design implications for incorporating MT in PH translation practice. A PH translation tool prototype was designed based on these findings. Discussion This study underscores the importance of understanding the work context and information workflow for which systems will be designed. Based on themes and translation information workflow processes, we identified key design guidelines for incorporating MT into PH translation work. Primary amongst these is that MT should be followed by human review for translations to be of high quality and for the technology to be adopted into practice. Counclusion The time and costs of creating multilingual health promotion materials are barriers to translation. PH personnel were interested in MT's potential to improve access to low-cost translated PH materials, but expressed concerns about ensuring quality. We outline design considerations and a potential machine translation tool to best fit MT systems into PH practice. PMID:25445922

Structured recording of intraoperative surgical workflows

NASA Astrophysics Data System (ADS)

Neumuth, T.; Durstewitz, N.; Fischer, M.; Strauss, G.; Dietz, A.; Meixensberger, J.; Jannin, P.; Cleary, K.; Lemke, H. U.; Burgert, O.

2006-03-01

Surgical Workflows are used for the methodical and scientific analysis of surgical interventions. The approach described here is a step towards developing surgical assist systems based on Surgical Workflows and integrated control systems for the operating room of the future. This paper describes concepts and technologies for the acquisition of Surgical Workflows by monitoring surgical interventions and their presentation. Establishing systems which support the Surgical Workflow in operating rooms requires a multi-staged development process beginning with the description of these workflows. A formalized description of surgical interventions is needed to create a Surgical Workflow. This description can be used to analyze and evaluate surgical interventions in detail. We discuss the subdivision of surgical interventions into work steps regarding different levels of granularity and propose a recording scheme for the acquisition of manual surgical work steps from running interventions. To support the recording process during the intervention, we introduce a new software architecture. Core of the architecture is our Surgical Workflow editor that is intended to deal with the manifold, complex and concurrent relations during an intervention. Furthermore, a method for an automatic generation of graphs is shown which is able to display the recorded surgical work steps of the interventions. Finally we conclude with considerations about extensions of our recording scheme to close the gap to S-PACS systems. The approach was used to record 83 surgical interventions from 6 intervention types from 3 different surgical disciplines: ENT surgery, neurosurgery and interventional radiology. The interventions were recorded at the University Hospital Leipzig, Germany and at the Georgetown University Hospital, Washington, D.C., USA.

A Proof of Concept to Bridge the Gap between Mass Spectrometry Imaging, Protein Identification and Relative Quantitation: MSI~LC-MS/MS-LF.

PubMed

Théron, Laëtitia; Centeno, Delphine; Coudy-Gandilhon, Cécile; Pujos-Guillot, Estelle; Astruc, Thierry; Rémond, Didier; Barthelemy, Jean-Claude; Roche, Frédéric; Feasson, Léonard; Hébraud, Michel; Béchet, Daniel; Chambon, Christophe

2016-10-26

Mass spectrometry imaging (MSI) is a powerful tool to visualize the spatial distribution of molecules on a tissue section. The main limitation of MALDI-MSI of proteins is the lack of direct identification. Therefore, this study focuses on a MSI~LC-MS/MS-LF workflow to link the results from MALDI-MSI with potential peak identification and label-free quantitation, using only one tissue section. At first, we studied the impact of matrix deposition and laser ablation on protein extraction from the tissue section. Then, we did a back-correlation of the m / z of the proteins detected by MALDI-MSI to those identified by label-free quantitation. This allowed us to compare the label-free quantitation of proteins obtained in LC-MS/MS with the peak intensities observed in MALDI-MSI. We managed to link identification to nine peaks observed by MALDI-MSI. The results showed that the MSI~LC-MS/MS-LF workflow (i) allowed us to study a representative muscle proteome compared to a classical bottom-up workflow; and (ii) was sparsely impacted by matrix deposition and laser ablation. This workflow, performed as a proof-of-concept, suggests that a single tissue section can be used to perform MALDI-MSI and protein extraction, identification, and relative quantitation.

A Proof of Concept to Bridge the Gap between Mass Spectrometry Imaging, Protein Identification and Relative Quantitation: MSI~LC-MS/MS-LF

PubMed Central

Théron, Laëtitia; Centeno, Delphine; Coudy-Gandilhon, Cécile; Pujos-Guillot, Estelle; Astruc, Thierry; Rémond, Didier; Barthelemy, Jean-Claude; Roche, Frédéric; Feasson, Léonard; Hébraud, Michel; Béchet, Daniel; Chambon, Christophe

2016-01-01

Mass spectrometry imaging (MSI) is a powerful tool to visualize the spatial distribution of molecules on a tissue section. The main limitation of MALDI-MSI of proteins is the lack of direct identification. Therefore, this study focuses on a MSI~LC-MS/MS-LF workflow to link the results from MALDI-MSI with potential peak identification and label-free quantitation, using only one tissue section. At first, we studied the impact of matrix deposition and laser ablation on protein extraction from the tissue section. Then, we did a back-correlation of the m/z of the proteins detected by MALDI-MSI to those identified by label-free quantitation. This allowed us to compare the label-free quantitation of proteins obtained in LC-MS/MS with the peak intensities observed in MALDI-MSI. We managed to link identification to nine peaks observed by MALDI-MSI. The results showed that the MSI~LC-MS/MS-LF workflow (i) allowed us to study a representative muscle proteome compared to a classical bottom-up workflow; and (ii) was sparsely impacted by matrix deposition and laser ablation. This workflow, performed as a proof-of-concept, suggests that a single tissue section can be used to perform MALDI-MSI and protein extraction, identification, and relative quantitation. PMID:28248242

Driving CT developments the last mile: case examples of successful and somewhat less successful translations into clinical practice

NASA Astrophysics Data System (ADS)

Sodickson, Aaron D.

2017-03-01

CT technology has advanced rapidly in recent years, yet not all innovations translate readily into clinical practice. Technology advances must meet certain key requirements to make it into routine use: They must provide a well-defined clinical benefit. They must be easy to use and integrate readily into existing workflows, or better still, further streamline these workflows. These requirements heavily favor fully integrated or automated solutions that remove the human factor and provide a reproducible output independent of operator skill level. Further, to achieve these aims, collaboration with the ultimate end users is needed as early as possible in the development cycle, not just at the point of product testing. Technology innovators are encouraged to engage such collaborators even at early stages of feature or product definition. This manuscript highlights these concepts through exploration of challenging areas in CT imaging in an Emergency Department setting. Technique optimization for pulmonary embolus CT is described as an example of successful integration of multiple advances in radiation dose reduction and imaging speed. The typical workflow of a trauma "pan-scan" (incorporating scans from head through pelvis) is described to highlight workflow challenges and opportunities for improvement. Finally, Dual Energy CT is discussed to highlight the undeniable clinical value of the material characterization it provides, yet also its surprisingly slow integration into routine use beyond early adopters.

Playback system designed for X-Band SAR

NASA Astrophysics Data System (ADS)

Yuquan, Liu; Changyong, Dou

2014-03-01

SAR(Synthetic Aperture Radar) has extensive application because it is daylight and weather independent. In particular, X-Band SAR strip map, designed by Institute of Remote Sensing and Digital Earth, Chinese Academy of Sciences, provides high ground resolution images, at the same time it has a large spatial coverage and a short acquisition time, so it is promising in multi-applications. When sudden disaster comes, the emergency situation acquires radar signal data and image as soon as possible, in order to take action to reduce loss and save lives in the first time. This paper summarizes a type of X-Band SAR playback processing system designed for disaster response and scientific needs. It describes SAR data workflow includes the payload data transmission and reception process. Playback processing system completes signal analysis on the original data, providing SAR level 0 products and quick image. Gigabit network promises radar signal transmission efficiency from recorder to calculation unit. Multi-thread parallel computing and ping pong operation can ensure computation speed. Through gigabit network, multi-thread parallel computing and ping pong operation, high speed data transmission and processing meet the SAR radar data playback real time requirement.

Automated replication of cone beam CT-guided treatments in the Pinnacle(3) treatment planning system for adaptive radiotherapy.

PubMed

Hargrave, Catriona; Mason, Nicole; Guidi, Robyn; Miller, Julie-Anne; Becker, Jillian; Moores, Matthew; Mengersen, Kerrie; Poulsen, Michael; Harden, Fiona

2016-03-01

Time-consuming manual methods have been required to register cone-beam computed tomography (CBCT) images with plans in the Pinnacle(3) treatment planning system in order to replicate delivered treatments for adaptive radiotherapy. These methods rely on fiducial marker (FM) placement during CBCT acquisition or the image mid-point to localise the image isocentre. A quality assurance study was conducted to validate an automated CBCT-plan registration method utilising the Digital Imaging and Communications in Medicine (DICOM) Structure Set (RS) and Spatial Registration (RE) files created during online image-guided radiotherapy (IGRT). CBCTs of a phantom were acquired with FMs and predetermined setup errors using various online IGRT workflows. The CBCTs, DICOM RS and RE files were imported into Pinnacle(3) plans of the phantom and the resulting automated CBCT-plan registrations were compared to existing manual methods. A clinical protocol for the automated method was subsequently developed and tested retrospectively using CBCTs and plans for six bladder patients. The automated CBCT-plan registration method was successfully applied to thirty-four phantom CBCT images acquired with an online 0 mm action level workflow. Ten CBCTs acquired with other IGRT workflows required manual workarounds. This was addressed during the development and testing of the clinical protocol using twenty-eight patient CBCTs. The automated CBCT-plan registrations were instantaneous, replicating delivered treatments in Pinnacle(3) with errors of ±0.5 mm. These errors were comparable to mid-point-dependant manual registrations but superior to FM-dependant manual registrations. The automated CBCT-plan registration method quickly and reliably replicates delivered treatments in Pinnacle(3) for adaptive radiotherapy.

Towards better digital pathology workflows: programming libraries for high-speed sharpness assessment of Whole Slide Images.

PubMed

Ameisen, David; Deroulers, Christophe; Perrier, Valérie; Bouhidel, Fatiha; Battistella, Maxime; Legrès, Luc; Janin, Anne; Bertheau, Philippe; Yunès, Jean-Baptiste

2014-01-01

Since microscopic slides can now be automatically digitized and integrated in the clinical workflow, quality assessment of Whole Slide Images (WSI) has become a crucial issue. We present a no-reference quality assessment method that has been thoroughly tested since 2010 and is under implementation in multiple sites, both public university-hospitals and private entities. It is part of the FlexMIm R&D project which aims to improve the global workflow of digital pathology. For these uses, we have developed two programming libraries, in Java and Python, which can be integrated in various types of WSI acquisition systems, viewers and image analysis tools. Development and testing have been carried out on a MacBook Pro i7 and on a bi-Xeon 2.7GHz server. Libraries implementing the blur assessment method have been developed in Java, Python, PHP5 and MySQL5. For web applications, JavaScript, Ajax, JSON and Sockets were also used, as well as the Google Maps API. Aperio SVS files were converted into the Google Maps format using VIPS and Openslide libraries. We designed the Java library as a Service Provider Interface (SPI), extendable by third parties. Analysis is computed in real-time (3 billion pixels per minute). Tests were made on 5000 single images, 200 NDPI WSI, 100 Aperio SVS WSI converted to the Google Maps format. Applications based on our method and libraries can be used upstream, as calibration and quality control tool for the WSI acquisition systems, or as tools to reacquire tiles while the WSI is being scanned. They can also be used downstream to reacquire the complete slides that are below the quality threshold for surgical pathology analysis. WSI may also be displayed in a smarter way by sending and displaying the regions of highest quality before other regions. Such quality assessment scores could be integrated as WSI's metadata shared in clinical, research or teaching contexts, for a more efficient medical informatics workflow.

Rapid processing of PET list-mode data for efficient uncertainty estimation and data analysis

NASA Astrophysics Data System (ADS)

Markiewicz, P. J.; Thielemans, K.; Schott, J. M.; Atkinson, D.; Arridge, S. R.; Hutton, B. F.; Ourselin, S.

2016-07-01

In this technical note we propose a rapid and scalable software solution for the processing of PET list-mode data, which allows the efficient integration of list mode data processing into the workflow of image reconstruction and analysis. All processing is performed on the graphics processing unit (GPU), making use of streamed and concurrent kernel execution together with data transfers between disk and CPU memory as well as CPU and GPU memory. This approach leads to fast generation of multiple bootstrap realisations, and when combined with fast image reconstruction and analysis, it enables assessment of uncertainties of any image statistic and of any component of the image generation process (e.g. random correction, image processing) within reasonable time frames (e.g. within five minutes per realisation). This is of particular value when handling complex chains of image generation and processing. The software outputs the following: (1) estimate of expected random event data for noise reduction; (2) dynamic prompt and random sinograms of span-1 and span-11 and (3) variance estimates based on multiple bootstrap realisations of (1) and (2) assuming reasonable count levels for acceptable accuracy. In addition, the software produces statistics and visualisations for immediate quality control and crude motion detection, such as: (1) count rate curves; (2) centre of mass plots of the radiodistribution for motion detection; (3) video of dynamic projection views for fast visual list-mode skimming and inspection; (4) full normalisation factor sinograms. To demonstrate the software, we present an example of the above processing for fast uncertainty estimation of regional SUVR (standard uptake value ratio) calculation for a single PET scan of 18F-florbetapir using the Siemens Biograph mMR scanner.

CoSEC: Connecting Living With a Star Research

NASA Astrophysics Data System (ADS)

Hurlburt, N.; Freeland, S.; Bose, P.; Zimdars, A.; Slater, G.

2006-12-01

The Collaborative Sun-Earth Connector (CoSEC) provide the means for heliophysics researchers to compose the data sources and processing services published by their peers into processing workflows that reliably generate publication-worthy data. It includes: composition of computational and data services into easy-to- read workflows with data quality and version traceability; straightforward translation of existing services into workflow components, and advertisement of those components to other members of the CoSEC community; annotation of published services with functional attributes to enable discovery of capabilities required by particular workflows and identify peer subgroups in the CoSEC community; and annotation of published services with nonfunctional attributes to enable selection on the basis of quality of service (QoS). We present an overview and demonstration of the CoSEC system, discuss applications, the lessons learned and future developments.

A case study on the impacts of computerized provider order entry (CPOE) system on hospital clinical workflow.

PubMed

Mominah, Maher; Yunus, Faisel; Househ, Mowafa S

2013-01-01

Computerized provider order entry (CPOE) is a health informatics system that helps health care providers create and manage orders for medications and other health care services. Through the automation of the ordering process, CPOE has improved the overall efficiency of hospital processes and workflow. In Saudi Arabia, CPOE has been used for years, with only a few studies evaluating the impacts of CPOE on clinical workflow. In this paper, we discuss the experience of a local hospital with the use of CPOE and its impacts on clinical workflow. Results show that there are many issues related to the implementation and use of CPOE within Saudi Arabia that must be addressed, including design, training, medication errors, alert fatigue, and system dep Recommendations for improving CPOE use within Saudi Arabia are also discussed.

Task–Technology Fit of Video Telehealth for Nurses in an Outpatient Clinic Setting

PubMed Central

Finkelstein, Stanley M.

2014-01-01

Abstract Background: Incorporating telehealth into outpatient care delivery supports management of consumer health between clinic visits. Task–technology fit is a framework for understanding how technology helps and/or hinders a person during work processes. Evaluating the task–technology fit of video telehealth for personnel working in a pediatric outpatient clinic and providing care between clinic visits ensures the information provided matches the information needed to support work processes. Materials and Methods: The workflow of advanced practice registered nurse (APRN) care coordination provided via telephone and video telehealth was described and measured using a mixed-methods workflow analysis protocol that incorporated cognitive ethnography and time–motion study. Qualitative and quantitative results were merged and analyzed within the task–technology fit framework to determine the workflow fit of video telehealth for APRN care coordination. Results: Incorporating video telehealth into APRN care coordination workflow provided visual information unavailable during telephone interactions. Despite additional tasks and interactions needed to obtain the visual information, APRN workflow efficiency, as measured by time, was not significantly changed. Analyzed within the task–technology fit framework, the increased visual information afforded by video telehealth supported the assessment and diagnostic information needs of the APRN. Conclusions: Telehealth must provide the right information to the right clinician at the right time. Evaluating task–technology fit using a mixed-methods protocol ensured rigorous analysis of fit within work processes and identified workflows that benefit most from the technology. PMID:24841219

Molecular Imaging in the Era of Personalized Medicine

PubMed Central

Jung, Kyung-Ho; Lee, Kyung-Han

2015-01-01

Clinical imaging creates visual representations of the body interior for disease assessment. The role of clinical imaging significantly overlaps with that of pathology, and diagnostic workflows largely depend on both fields. The field of clinical imaging is presently undergoing a radical change through the emergence of a new field called molecular imaging. This new technology, which lies at the intersection between imaging and molecular biology, enables noninvasive visualization of biochemical processes at the molecular level within living bodies. Molecular imaging differs from traditional anatomical imaging in that biomarkers known as imaging probes are used to visualize target molecules-of-interest. This ability opens up exciting new possibilities for applications in oncologic, neurological and cardiovascular diseases. Molecular imaging is expected to make major contributions to personalized medicine by allowing earlier diagnosis and predicting treatment response. The technique is also making a huge impact on pharmaceutical development by optimizing preclinical and clinical tests for new drug candidates. This review will describe the basic principles of molecular imaging and will briefly touch on three examples (from an immense list of new techniques) that may contribute to personalized medicine: receptor imaging, angiogenesis imaging, and apoptosis imaging. PMID:25812652

Molecular imaging in the era of personalized medicine.

PubMed

Jung, Kyung-Ho; Lee, Kyung-Han

2015-01-01

Clinical imaging creates visual representations of the body interior for disease assessment. The role of clinical imaging significantly overlaps with that of pathology, and diagnostic workflows largely depend on both fields. The field of clinical imaging is presently undergoing a radical change through the emergence of a new field called molecular imaging. This new technology, which lies at the intersection between imaging and molecular biology, enables noninvasive visualization of biochemical processes at the molecular level within living bodies. Molecular imaging differs from traditional anatomical imaging in that biomarkers known as imaging probes are used to visualize target molecules-of-interest. This ability opens up exciting new possibilities for applications in oncologic, neurological and cardiovascular diseases. Molecular imaging is expected to make major contributions to personalized medicine by allowing earlier diagnosis and predicting treatment response. The technique is also making a huge impact on pharmaceutical development by optimizing preclinical and clinical tests for new drug candidates. This review will describe the basic principles of molecular imaging and will briefly touch on three examples (from an immense list of new techniques) that may contribute to personalized medicine: receptor imaging, angiogenesis imaging, and apoptosis imaging.

Summary of the white paper of DICOM WG24 'DICOM in Surgery'

NASA Astrophysics Data System (ADS)

Lemke, Heinz U.

2007-03-01

Standards for creating and integrating information about patients, equipment, and procedures are vitally needed when planning for an efficient Operating Room (OR). The DICOM Working Group 24 (WG24) has been established to develop DICOM objects and services related to Image Guided Surgery (IGS). To determine these standards, it is important to define day-to-day, step-by-step surgical workflow practices and create surgery workflow models per procedures or per variable cases. A well-defined workflow and a high fidelity patient model will be the base of activities for both, radiation therapy and surgery. Considering the present and future requirements for surgical planning and intervention, such a patient model must be n-dimensional, were n may include the spatial and temporal dimensions as well as a number of functional variables. As the boundaries between radiation therapy, surgery and interventional radiology are becoming less well-defined, precise patient models will become the greatest common denominator for all therapeutic disciplines. In addition to imaging, the focus of WG24 should, therefore, also be to serve the therapeutic disciplines by enabling modelling technology to be based on standards.

A navigation system for percutaneous needle interventions based on PET/CT images: design, workflow and error analysis of soft tissue and bone punctures.

PubMed

Oliveira-Santos, Thiago; Klaeser, Bernd; Weitzel, Thilo; Krause, Thomas; Nolte, Lutz-Peter; Peterhans, Matthias; Weber, Stefan

2011-01-01

Percutaneous needle intervention based on PET/CT images is effective, but exposes the patient to unnecessary radiation due to the increased number of CT scans required. Computer assisted intervention can reduce the number of scans, but requires handling, matching and visualization of two different datasets. While one dataset is used for target definition according to metabolism, the other is used for instrument guidance according to anatomical structures. No navigation systems capable of handling such data and performing PET/CT image-based procedures while following clinically approved protocols for oncologic percutaneous interventions are available. The need for such systems is emphasized in scenarios where the target can be located in different types of tissue such as bone and soft tissue. These two tissues require different clinical protocols for puncturing and may therefore give rise to different problems during the navigated intervention. Studies comparing the performance of navigated needle interventions targeting lesions located in these two types of tissue are not often found in the literature. Hence, this paper presents an optical navigation system for percutaneous needle interventions based on PET/CT images. The system provides viewers for guiding the physician to the target with real-time visualization of PET/CT datasets, and is able to handle targets located in both bone and soft tissue. The navigation system and the required clinical workflow were designed taking into consideration clinical protocols and requirements, and the system is thus operable by a single person, even during transition to the sterile phase. Both the system and the workflow were evaluated in an initial set of experiments simulating 41 lesions (23 located in bone tissue and 18 in soft tissue) in swine cadavers. We also measured and decomposed the overall system error into distinct error sources, which allowed for the identification of particularities involved in the process as well as highlighting the differences between bone and soft tissue punctures. An overall average error of 4.23 mm and 3.07 mm for bone and soft tissue punctures, respectively, demonstrated the feasibility of using this system for such interventions. The proposed system workflow was shown to be effective in separating the preparation from the sterile phase, as well as in keeping the system manageable by a single operator. Among the distinct sources of error, the user error based on the system accuracy (defined as the distance from the planned target to the actual needle tip) appeared to be the most significant. Bone punctures showed higher user error, whereas soft tissue punctures showed higher tissue deformation error.

Comparison of turbulence mitigation algorithms

NASA Astrophysics Data System (ADS)

Kozacik, Stephen T.; Paolini, Aaron; Sherman, Ariel; Bonnett, James; Kelmelis, Eric

2017-07-01

When capturing imagery over long distances, atmospheric turbulence often degrades the data, especially when observation paths are close to the ground or in hot environments. These issues manifest as time-varying scintillation and warping effects that decrease the effective resolution of the sensor and reduce actionable intelligence. In recent years, several image processing approaches to turbulence mitigation have shown promise. Each of these algorithms has different computational requirements, usability demands, and degrees of independence from camera sensors. They also produce different degrees of enhancement when applied to turbulent imagery. Additionally, some of these algorithms are applicable to real-time operational scenarios while others may only be suitable for postprocessing workflows. EM Photonics has been developing image-processing-based turbulence mitigation technology since 2005. We will compare techniques from the literature with our commercially available, real-time, GPU-accelerated turbulence mitigation software. These comparisons will be made using real (not synthetic), experimentally obtained data for a variety of conditions, including varying optical hardware, imaging range, subjects, and turbulence conditions. Comparison metrics will include image quality, video latency, computational complexity, and potential for real-time operation. Additionally, we will present a technique for quantitatively comparing turbulence mitigation algorithms using real images of radial resolution targets.

Phantom study and accuracy evaluation of an image-to-world registration approach used with electro-magnetic tracking system for neurosurgery

NASA Astrophysics Data System (ADS)

Li, Senhu; Sarment, David

2015-12-01

Minimally invasive neurosurgery needs intraoperative imaging updates and high efficient image guide system to facilitate the procedure. An automatic image guided system utilized with a compact and mobile intraoperative CT imager was introduced in this work. A tracking frame that can be easily attached onto the commercially available skull clamp was designed. With known geometry of fiducial and tracking sensor arranged on this rigid frame that was fabricated through high precision 3D printing, not only was an accurate, fully automatic registration method developed in a simple and less-costly approach, but also it helped in estimating the errors from fiducial localization in image space through image processing, and in patient space through the calibration of tracking frame. Our phantom study shows the fiducial registration error as 0.348+/-0.028mm, comparing the manual registration error as 1.976+/-0.778mm. The system in this study provided a robust and accurate image-to-patient registration without interruption of routine surgical workflow and any user interactions involved through the neurosurgery.

Biostatistical analysis of quantitative immunofluorescence microscopy images.

PubMed

Giles, C; Albrecht, M A; Lam, V; Takechi, R; Mamo, J C

2016-12-01

Semiquantitative immunofluorescence microscopy has become a key methodology in biomedical research. Typical statistical workflows are considered in the context of avoiding pseudo-replication and marginalising experimental error. However, immunofluorescence microscopy naturally generates hierarchically structured data that can be leveraged to improve statistical power and enrich biological interpretation. Herein, we describe a robust distribution fitting procedure and compare several statistical tests, outlining their potential advantages/disadvantages in the context of biological interpretation. Further, we describe tractable procedures for power analysis that incorporates the underlying distribution, sample size and number of images captured per sample. The procedures outlined have significant potential for increasing understanding of biological processes and decreasing both ethical and financial burden through experimental optimization. © 2016 The Authors Journal of Microscopy © 2016 Royal Microscopical Society.

Integration of implant planning workflows into the PACS infrastructure

NASA Astrophysics Data System (ADS)

Gessat, Michael; Strauß, Gero; Burgert, Oliver

2008-03-01

The integration of imaging devices, diagnostic workstations, and image servers into Picture Archiving and Communication Systems (PACS) has had an enormous effect on the efficiency of radiology workflows. The standardization of the information exchange between the devices with the DICOM standard has been an essential precondition for that development. For surgical procedures, no such infrastructure exists. With the increasingly important role computerized planning and assistance systems play in the surgical domain, an infrastructure that unifies the communication between devices becomes necessary. In recent publications, the need for a modularized system design has been established. A reference architecture for a Therapy Imaging and Model Management System (TIMMS) has been proposed. It was accepted by the DICOM Working Group 6 as the reference architecture for DICOM developments for surgery. In this paper we propose the inclusion of implant planning systems into the PACS infrastructure. We propose a generic information model for the patient specific selection and positioning of implants from a repository according to patient image data. The information models are based on clinical workflows from ENT, cardiac, and orthopedic surgery as well as technical requirements derived from different use cases and systems. We show an exemplary implementation of the model for application in ENT surgery: the selection and positioning of an ossicular implant in the middle ear. An implant repository is stored in the PACS. It makes use of an experimental implementation of the Surface Mesh Module that is currently being developed as extension to the DICOM standard.

Integrating DICOM structure reporting (SR) into the medical imaging informatics data grid

NASA Astrophysics Data System (ADS)

Lee, Jasper; Le, Anh; Liu, Brent

2008-03-01

The Medical Imaging Informatics (MI2) Data Grid developed at the USC Image Processing and Informatics Laboratory enables medical images to be shared securely between multiple imaging centers. Current applications include an imaging-based clinical trial setting where multiple field sites perform image acquisition and a centralized radiology core performs image analysis, often using computer-aided diagnosis tools (CAD) that generate a DICOM-SR to report their findings and measurements. As more and more CAD tools are being developed in the radiology field, the generated DICOM Structure Reports (SR) holding key radiological findings and measurements that are not part of the DICOM image need to be integrated into the existing Medical Imaging Informatics Data Grid with the corresponding imaging studies. We will discuss the significance and method involved in adapting DICOM-SR into the Medical Imaging Informatics Data Grid. The result is a MI2 Data Grid repository from which users can send and receive DICOM-SR objects based on the imaging-based clinical trial application. The services required to extract and categorize information from the structured reports will be discussed, and the workflow to store and retrieve a DICOM-SR file into the existing MI2 Data Grid will be shown.

An Innovative Method for Obtaining Consistent Images and Quantification of Histochemically Stained Specimens

PubMed Central

Sedgewick, Gerald J.; Ericson, Marna

2015-01-01

Obtaining digital images of color brightfield microscopy is an important aspect of biomedical research and the clinical practice of diagnostic pathology. Although the field of digital pathology has had tremendous advances in whole-slide imaging systems, little effort has been directed toward standardizing color brightfield digital imaging to maintain image-to-image consistency and tonal linearity. Using a single camera and microscope to obtain digital images of three stains, we show that microscope and camera systems inherently produce image-to-image variation. Moreover, we demonstrate that post-processing with a widely used raster graphics editor software program does not completely correct for session-to-session inconsistency. We introduce a reliable method for creating consistent images with a hardware/software solution (ChromaCal™; Datacolor Inc., NJ) along with its features for creating color standardization, preserving linear tonal levels, providing automated white balancing and setting automated brightness to consistent levels. The resulting image consistency using this method will also streamline mean density and morphometry measurements, as images are easily segmented and single thresholds can be used. We suggest that this is a superior method for color brightfield imaging, which can be used for quantification and can be readily incorporated into workflows. PMID:25575568

Interferometric imaging of the 2011-2013 Campi Flegrei unrest

NASA Astrophysics Data System (ADS)

De Siena, Luca; Nakahara, Hisashi; Zaccarelli, Lucia; Sammarco, Carmelo; La Rocca, Mario; Bianco, Francesca

2017-04-01

After its 1983-84 seismic and deformation crisis, seismologists have recorded very low and clustered seismicity at Campi Flegrei caldera (Italy). Hence, noise interferometry imaging has become the only option to image the present volcano logical state of the volcano. Three-component noise data recorded before, during, and after Campi Flegrei last deformation and geochemical unrest (2011-2013) have thus been processed with up-to-date interferometric imaging workflow based on MSNoise. Noise anisotropy, which strongly affects measurements throughout the caldera at all frequencies, has been accounted for by self-correlation measurements and smoothed by phase weighted stacking and phase-match filtering. The final group-velocity maps show strong low-velocity anomalies at the location of the last Campi Flegrei eruption (1538 A.D.). The main low-velocity anomalies contour Solfatara volcano and follow geomorphological cross-faulting. The comparison with geophysical imaging results obtained during the last seismic unrest at the caldera suggest strong changes in the physical properties of the volcano, particularly in the area of major hydrogeological hazard.

Integrating advanced visualization technology into the planetary Geoscience workflow

NASA Astrophysics Data System (ADS)

Huffman, John; Forsberg, Andrew; Loomis, Andrew; Head, James; Dickson, James; Fassett, Caleb

2011-09-01

Recent advances in computer visualization have allowed us to develop new tools for analyzing the data gathered during planetary missions, which is important, since these data sets have grown exponentially in recent years to tens of terabytes in size. As part of the Advanced Visualization in Solar System Exploration and Research (ADVISER) project, we utilize several advanced visualization techniques created specifically with planetary image data in mind. The Geoviewer application allows real-time active stereo display of images, which in aggregate have billions of pixels. The ADVISER desktop application platform allows fast three-dimensional visualization of planetary images overlain on digital terrain models. Both applications include tools for easy data ingest and real-time analysis in a programmatic manner. Incorporation of these tools into our everyday scientific workflow has proved important for scientific analysis, discussion, and publication, and enabled effective and exciting educational activities for students from high school through graduate school.

Improved workflow modelling using role activity diagram-based modelling with application to a radiology service case study.

PubMed

Shukla, Nagesh; Keast, John E; Ceglarek, Darek

2014-10-01

The modelling of complex workflows is an important problem-solving technique within healthcare settings. However, currently most of the workflow models use a simplified flow chart of patient flow obtained using on-site observations, group-based debates and brainstorming sessions, together with historic patient data. This paper presents a systematic and semi-automatic methodology for knowledge acquisition with detailed process representation using sequential interviews of people in the key roles involved in the service delivery process. The proposed methodology allows the modelling of roles, interactions, actions, and decisions involved in the service delivery process. This approach is based on protocol generation and analysis techniques such as: (i) initial protocol generation based on qualitative interviews of radiology staff, (ii) extraction of key features of the service delivery process, (iii) discovering the relationships among the key features extracted, and, (iv) a graphical representation of the final structured model of the service delivery process. The methodology is demonstrated through a case study of a magnetic resonance (MR) scanning service-delivery process in the radiology department of a large hospital. A set of guidelines is also presented in this paper to visually analyze the resulting process model for identifying process vulnerabilities. A comparative analysis of different workflow models is also conducted. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

funcLAB/G-service-oriented architecture for standards-based analysis of functional magnetic resonance imaging in HealthGrids.

PubMed

Erberich, Stephan G; Bhandekar, Manasee; Chervenak, Ann; Kesselman, Carl; Nelson, Marvin D

2007-01-01

Functional MRI is successfully being used in clinical and research applications including preoperative planning, language mapping, and outcome monitoring. However, clinical use of fMRI is less widespread due to its complexity of imaging, image workflow, post-processing, and lack of algorithmic standards hindering result comparability. As a consequence, wide-spread adoption of fMRI as clinical tool is low contributing to the uncertainty of community physicians how to integrate fMRI into practice. In addition, training of physicians with fMRI is in its infancy and requires clinical and technical understanding. Therefore, many institutions which perform fMRI have a team of basic researchers and physicians to perform fMRI as a routine imaging tool. In order to provide fMRI as an advanced diagnostic tool to the benefit of a larger patient population, image acquisition and image post-processing must be streamlined, standardized, and available at any institution which does not have these resources available. Here we describe a software architecture, the functional imaging laboratory (funcLAB/G), which addresses (i) standardized image processing using Statistical Parametric Mapping and (ii) its extension to secure sharing and availability for the community using standards-based Grid technology (Globus Toolkit). funcLAB/G carries the potential to overcome the limitations of fMRI in clinical use and thus makes standardized fMRI available to the broader healthcare enterprise utilizing the Internet and HealthGrid Web Services technology.

Digital transformation in home care. A case study.

PubMed

Bennis, Sandy; Costanzo, Diane; Flynn, Ann Marie; Reidy, Agatha; Tronni, Catherine

2007-01-01

Simply implementing software and technology does not assure that an organization's targeted clinical and financial goals will be realized. No longer is it possible to roll out a new system--by solely providing end user training and overlaying it on top of already inefficient workflows and outdated roles--and know with certainty that targets will be met. At Virtua Health's Home Care, based in south New Jersey, implementation of their electronic system initially followed this more traditional approach. Unable to completely attain their earlier identified return on investment, they enlisted the help of a new role within their health system, that of the nurse informaticist. Knowledgeable in complex clinical processes and not bound by the technology at hand, the informaticist analyzed physical workflow, digital workflow, roles and physical layout. Leveraging specific tools such as change acceleration, workouts and LEAN, the informaticist was able to redesign workflow and support new levels of functionality. This article provides a view from the "finish line", recounting how this role worked with home care to assimilate information delivery into more efficient processes and align resources to support the new workflow, ultimately achieving real tangible returns.

Digital pathology in clinical use: where are we now and what is holding us back?

PubMed

Griffin, Jon; Treanor, Darren

2017-01-01

Whole slide imaging is being used increasingly in research applications and in frozen section, consultation and external quality assurance practice. Digital pathology, when integrated with other digital tools such as barcoding, specimen tracking and digital dictation, can be integrated into the histopathology workflow, from specimen accession to report sign-out. These elements can bring about improvements in the safety, quality and efficiency of a histopathology department. The present paper reviews the evidence for these benefits. We then discuss the challenges of implementing a fully digital pathology workflow, including the regulatory environment, validation of whole slide imaging and the evidence for the design of a digital pathology workstation. © 2016 John Wiley & Sons Ltd.

Basics of Confocal Microscopy and the Complexity of Diagnosing Skin Tumors: New Imaging Tools in Clinical Practice, Diagnostic Workflows, Cost-Estimate, and New Trends.

PubMed

Que, Syril Keena T; Grant-Kels, Jane M; Longo, Caterina; Pellacani, Giovanni

2016-10-01

The use of reflectance confocal microscopy (RCM) and other noninvasive imaging devices can potentially streamline clinical care, leading to more precise and efficient management of skin cancer. This article explores the potential role of RCM in cutaneous oncology, as an adjunct to more established techniques of detecting and monitoring for skin cancer, such as dermoscopy and total body photography. Discussed are current barriers to the adoption of RCM, diagnostic workflows and standards of care in the United States and Europe, and medicolegal issues. The potential role of RCM and other similar technological innovations in the enhancement of dermatologic care is evaluated. Copyright © 2016 Elsevier Inc. All rights reserved.

Data Provenance in Photogrammetry Through Documentation Protocols

NASA Astrophysics Data System (ADS)

Carboni, N.; Bruseker, G.; Guillem, A.; Bellido Castañeda, D.; Coughenour, C.; Domajnko, M.; de Kramer, M.; Ramos Calles, M. M.; Stathopoulou, E. K.; Suma, R.

2016-06-01

Documenting the relevant aspects in digitisation processes such as photogrammetry in order to provide a robust provenance for their products continues to present a challenge. The creation of a product that can be re-used scientifically requires a framework for consistent, standardised documentation of the entire digitisation pipeline. This article provides an analysis of the problems inherent to such goals and presents a series of protocols to document the various steps of a photogrammetric workflow. We propose this pipeline, with descriptors to track all phases of digital product creation in order to assure data provenance and enable the validation of the operations from an analytic and production perspective. The approach aims to support adopters of the workflow to define procedures with a long term perspective. The conceptual schema we present is founded on an analysis of information and actor exchanges in the digitisation process. The metadata were defined through the synthesis of previous proposals in this area and were tested on a case study. We performed the digitisation of a set of cultural heritage artefacts from an Iron Age burial in Ilmendorf, Germany. The objects were captured and processed using different techniques, including a comparison of different imaging tools and algorithms. This augmented the complexity of the process allowing us to test the flexibility of the schema for documenting complex scenarios. Although we have only presented a photogrammetry digitisation scenario, we claim that our schema is easily applicable to a multitude of 3D documentation processes.

Image fusion pitfalls for cranial radiosurgery.

PubMed

Jonker, Benjamin P

2013-01-01

Stereotactic radiosurgery requires imaging to define both the stereotactic space in which the treatment is delivered and the target itself. Image fusion is the process of using rotation and translation to bring a second image set into alignment with the first image set. This allows the potential concurrent use of multiple image sets to define the target and stereotactic space. While a single magnetic resonance imaging (MRI) sequence alone can be used for delineation of the target and fiducials, there may be significant advantages to using additional imaging sets including other MRI sequences, computed tomography (CT) scans, and advanced imaging sets such as catheter-based angiography, diffusor tension imaging-based fiber tracking and positon emission tomography in order to more accurately define the target and surrounding critical structures. Stereotactic space is usually defined by detection of fiducials on the stereotactic head frame or mask system. Unfortunately MRI sequences are susceptible to geometric distortion, whereas CT scans do not face this problem (although they have poorer resolution of the target in most cases). Thus image fusion can allow the definition of stereotactic space to proceed from the geometrically accurate CT images at the same time as using MRI to define the target. The use of image fusion is associated with risk of error introduced by inaccuracies of the fusion process, as well as workflow changes that if not properly accounted for can mislead the treating clinician. The purpose of this review is to describe the uses of image fusion in stereotactic radiosurgery as well as its potential pitfalls.

Cool Apps: Productivity at Your Fingertips

ERIC Educational Resources Information Center

Flaherty, Bill

2013-01-01

In addition to listing apps and their value, this article focuses on ways people can be more productive by adopting certain workflows in several ways. Apps listed herein include those useful in calendaring, printing, photo-editing, image-recognition, image scanning, electronic signatures, and making and sharing lists and notes.

Digitizing an Analog Radiography Teaching File Under Time Constraint: Trade-Offs in Efficiency and Image Quality.

PubMed

Loehfelm, Thomas W; Prater, Adam B; Debebe, Tequam; Sekhar, Aarti K

2017-02-01

We digitized the radiography teaching file at Black Lion Hospital (Addis Ababa, Ethiopia) during a recent trip, using a standard digital camera and a fluorescent light box. Our goal was to photograph every radiograph in the existing library while optimizing the final image size to the maximum resolution of a high quality tablet computer, preserving the contrast resolution of the radiographs, and minimizing total library file size. A secondary important goal was to minimize the cost and time required to take and process the images. Three workers were able to efficiently remove the radiographs from their storage folders, hang them on the light box, operate the camera, catalog the image, and repack the radiographs back to the storage folder. Zoom, focal length, and film speed were fixed, while aperture and shutter speed were manually adjusted for each image, allowing for efficiency and flexibility in image acquisition. Keeping zoom and focal length fixed, which kept the view box at the same relative position in all of the images acquired during a single photography session, allowed unused space to be batch-cropped, saving considerable time in post-processing, at the expense of final image resolution. We present an analysis of the trade-offs in workflow efficiency and final image quality, and demonstrate that a few people with minimal equipment can efficiently digitize a teaching file library.

Parametric Workflow (BIM) for the Repair Construction of Traditional Historic Architecture in Taiwan

NASA Astrophysics Data System (ADS)

Ma, Y.-P.; Hsu, C. C.; Lin, M.-C.; Tsai, Z.-W.; Chen, J.-Y.

2015-08-01

In Taiwan, numerous existing traditional buildings are constructed with wooden structures, brick structures, and stone structures. This paper will focus on the Taiwan traditional historic architecture and target the traditional wooden structure buildings as the design proposition and process the BIM workflow for modeling complex wooden combination geometry, integrating with more traditional 2D documents and for visualizing repair construction assumptions within the 3D model representation. The goal of this article is to explore the current problems to overcome in wooden historic building conservation, and introduce the BIM technology in the case of conserving, documenting, managing, and creating full engineering drawings and information for effectively support historic conservation. Although BIM is mostly oriented to current construction praxis, there have been some attempts to investigate its applicability in historic conservation projects. This article also illustrates the importance and advantages of using BIM workflow in repair construction process, when comparing with generic workflow.

Absorption Mode FT-ICR Mass Spectrometry Imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Donald F.; Kilgour, David P.; Konijnenburg, Marco

2013-12-03

Fourier transform ion cyclotron resonance mass spectrometry offers the highest mass resolving power for molecular imaging experiments. This high mass resolving power ensures that closely spaced peaks at the same nominal mass are resolved for proper image generation. Typically higher magnetic fields are used to increase mass resolving power. However, a gain in mass resolving power can also be realized by phase correction of the data for absorption mode display. In addition to mass resolving power, absorption mode offers higher mass accuracy and signal-to-noise ratio over the conventional magnitude mode. Here we present the first use of absorption mode formore » Fourier transform ion cyclotron resonance mass spectrometry imaging. The Autophaser algorithm is used to phase correct each spectrum (pixel) in the image and then these parameters are used by the Chameleon work-flow based data processing software to generate absorption mode ?Datacubes? for image and spectral viewing. Absorption mode reveals new mass and spatial features that are not resolved in magnitude mode and results in improved selected ion image contrast.« less

Workspace definition for navigated control functional endoscopic sinus surgery

NASA Astrophysics Data System (ADS)

Gessat, Michael; Hofer, Mathias; Audette, Michael; Dietz, Andreas; Meixensberger, Jürgen; Stauß, Gero; Burgert, Oliver

2007-03-01

For the pre-operative definition of a surgical workspace for Navigated Control ® Functional Endoscopic Sinus Surgery (FESS), we developed a semi-automatic image processing system. Based on observations of surgeons using a manual system, we implemented a workflow-based engineering process that led us to the development of a system reducing time and workload spent during the workspace definition. The system uses a feature based on local curvature to align vertices of a polygonal outline along the bone structures defining the cavities of the inner nose. An anisotropic morphologic operator was developed solve problems arising from artifacts from noise and partial volume effects. We used time measurements and NASA's TLX questionnaire to evaluate our system.

MO-E-BRC-03: Fast Online Replanning Techniques

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, X.

Online adaptive radiation therapy has the potential to ensure delivery of optimal treatment to the patient by accounting for anatomical and potentially functional changes that occur from one fraction to the next and over the course of treatment. While on-line adaptive RT (ART) has been a topic of many publications, discussions, and research, it has until very recently remained largely a concept and not a practical implementation. However, recent advances in on-table imaging, use of deformable image registration for contour generation and dose tracking, faster and more efficient plan optimization, as well as fast quality assurance method has enabled themore » implementation of ART in the clinic in the past couple of years. The introduction of these tools into routine clinical use requires many considerations and progressive knowledge to understand how processes that have historically taken hours/days to complete can now be done in less than 30 minutes. This session will discuss considerations to perform real time contouring, planning and patient specific QA, as well as a practical workflow and the required resources. Learning Objectives: To understand the difficulties, challenges and available technologies for online adaptive RT. To understand how to implement online adaptive therapy in a clinical environment and to understand the workflow and resources required. To understand the limitations and sources of uncertainty in the online adaptive process I have research funding from ViewRay Inc. and Philips Medical Systems.; R. Kashani, I have research funding from ViewRay Inc. and Philips Medical Systems.; X. Li, Research supported by Elekta Inc.« less

MO-E-BRC-00: Online Adaptive Radiotherapy - Considerations for Practical Clinical Implementation

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

Online adaptive radiation therapy has the potential to ensure delivery of optimal treatment to the patient by accounting for anatomical and potentially functional changes that occur from one fraction to the next and over the course of treatment. While on-line adaptive RT (ART) has been a topic of many publications, discussions, and research, it has until very recently remained largely a concept and not a practical implementation. However, recent advances in on-table imaging, use of deformable image registration for contour generation and dose tracking, faster and more efficient plan optimization, as well as fast quality assurance method has enabled themore » implementation of ART in the clinic in the past couple of years. The introduction of these tools into routine clinical use requires many considerations and progressive knowledge to understand how processes that have historically taken hours/days to complete can now be done in less than 30 minutes. This session will discuss considerations to perform real time contouring, planning and patient specific QA, as well as a practical workflow and the required resources. Learning Objectives: To understand the difficulties, challenges and available technologies for online adaptive RT. To understand how to implement online adaptive therapy in a clinical environment and to understand the workflow and resources required. To understand the limitations and sources of uncertainty in the online adaptive process I have research funding from ViewRay Inc. and Philips Medical Systems.; R. Kashani, I have research funding from ViewRay Inc. and Philips Medical Systems.; X. Li, Research supported by Elekta Inc.« less

MO-E-BRC-02: MRI-Guided Online Adaptive Radiotherapy: The UCLA Approach to Quality Management

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lamb, J.

Online adaptive radiation therapy has the potential to ensure delivery of optimal treatment to the patient by accounting for anatomical and potentially functional changes that occur from one fraction to the next and over the course of treatment. While on-line adaptive RT (ART) has been a topic of many publications, discussions, and research, it has until very recently remained largely a concept and not a practical implementation. However, recent advances in on-table imaging, use of deformable image registration for contour generation and dose tracking, faster and more efficient plan optimization, as well as fast quality assurance method has enabled themore » implementation of ART in the clinic in the past couple of years. The introduction of these tools into routine clinical use requires many considerations and progressive knowledge to understand how processes that have historically taken hours/days to complete can now be done in less than 30 minutes. This session will discuss considerations to perform real time contouring, planning and patient specific QA, as well as a practical workflow and the required resources. Learning Objectives: To understand the difficulties, challenges and available technologies for online adaptive RT. To understand how to implement online adaptive therapy in a clinical environment and to understand the workflow and resources required. To understand the limitations and sources of uncertainty in the online adaptive process I have research funding from ViewRay Inc. and Philips Medical Systems.; R. Kashani, I have research funding from ViewRay Inc. and Philips Medical Systems.; X. Li, Research supported by Elekta Inc.« less

PACS-Graz, 1985-2000: from a scientific pilot to a state-wide multimedia radiological information system

NASA Astrophysics Data System (ADS)

Gell, Guenther

2000-05-01

1971/72 began the implementation of a computerized radiological documentation system as the Department of Radiology of the University of Graz, which developed over the years into a full RIS. 1985 started a scientific cooperation with SIEMENS to develop a PACS. The two systems were linked and evolved into a highly integrated RIS-PACS for the state wide hospital system in Styria. During its lifetime the RIS, originally implemented in FORTRAN on a UNIVAC 494 mainframe migrated to a PDP15, on to a PDP11, then VAX and Alphas. The flexible original record structure with variable length fields and the powerful retrieval language were retained. The data acquisition part with the user interface was rewritten several times and many service programs have been added. During our PACS cooperation many ideas like the folder concept or functionalities of the GUI have been designed and tested and were then implemented in the SIENET product. The actual RIS/PACS supports the whole workflow in the Radiology Department. It is installed in a 2.300 bed university hospital and the smaller hospitals of the State of Styria. Modalities from different vendors are connected via DICOM to the RIS (modality worklist) and to the PACS. PACSubsystems from other vendors have been integrated. Images are distributed to referring clinics and for teleconsultation and image processing and reports are available on line to all connected hospitals. We spent great efforts to guarantee optimal support of the workflow and to ensure an enhanced cost/benefit ratio for each user (class). Another special feature is selective image distribution. Using the high level retrieval language individual filters can be constructed easily to implement any image distribution policy agreed upon by radiologists and referring clinicians.

Antibiogramj: A tool for analysing images from disk diffusion tests.

PubMed

Alonso, C A; Domínguez, C; Heras, J; Mata, E; Pascual, V; Torres, C; Zarazaga, M

2017-05-01

Disk diffusion testing, known as antibiogram, is widely applied in microbiology to determine the antimicrobial susceptibility of microorganisms. The measurement of the diameter of the zone of growth inhibition of microorganisms around the antimicrobial disks in the antibiogram is frequently performed manually by specialists using a ruler. This is a time-consuming and error-prone task that might be simplified using automated or semi-automated inhibition zone readers. However, most readers are usually expensive instruments with embedded software that require significant changes in laboratory design and workflow. Based on the workflow employed by specialists to determine the antimicrobial susceptibility of microorganisms, we have designed a software tool that, from images of disk diffusion tests, semi-automatises the process. Standard computer vision techniques are employed to achieve such an automatisation. We present AntibiogramJ, a user-friendly and open-source software tool to semi-automatically determine, measure and categorise inhibition zones of images from disk diffusion tests. AntibiogramJ is implemented in Java and deals with images captured with any device that incorporates a camera, including digital cameras and mobile phones. The fully automatic procedure of AntibiogramJ for measuring inhibition zones achieves an overall agreement of 87% with an expert microbiologist; moreover, AntibiogramJ includes features to easily detect when the automatic reading is not correct and fix it manually to obtain the correct result. AntibiogramJ is a user-friendly, platform-independent, open-source, and free tool that, up to the best of our knowledge, is the most complete software tool for antibiogram analysis without requiring any investment in new equipment or changes in the laboratory. Copyright © 2017 Elsevier B.V. All rights reserved.

MACS-Mar: a real-time remote sensing system for maritime security applications

NASA Astrophysics Data System (ADS)

Brauchle, Jörg; Bayer, Steven; Hein, Daniel; Berger, Ralf; Pless, Sebastian

2018-04-01

The modular aerial camera system (MACS) is a development platform for optical remote sensing concepts, algorithms and special environments. For real-time services for maritime security (EMSec joint project), a new multi-sensor configuration MACS-Mar was realized. It consists of four co-aligned sensor heads in the visible RGB, near infrared (NIR, 700-950 nm), hyperspectral (HS, 450-900 nm) and thermal infrared (TIR, 7.5-14 µm) spectral range, a mid-cost navigation system, a processing unit and two data links. On-board image projection, cropping of redundant data and compression enable the instant generation of direct-georeferenced high-resolution image mosaics, automatic object detection, vectorization and annotation of floating objects on the water surface. The results were transmitted over a distance up to 50 km in real-time via narrow and broadband data links and were visualized in a maritime situation awareness system. For the automatic onboard detection of floating objects, a segmentation and classification workflow based on RGB, IR and TIR information was developed and tested. The completeness of the object detection in the experiment resulted in 95%, the correctness in 53%. Mostly, bright backwash of ships lead to an overestimation of the number of objects, further refinement using water homogeneity in the TIR, as implemented in the workflow, couldn't be carried out due to problems with the TIR sensor, else distinctly better results could have been expected. The absolute positional accuracy of the projected real-time imagery resulted in 2 m without postprocessing of images or navigation data, the relative measurement accuracy of distances is in the range of the image resolution, which is about 12 cm for RGB imagery in the EMSec experiment.

Improving data collection, documentation, and workflow in a dementia screening study

PubMed Central

Read, Kevin B.; LaPolla, Fred Willie Zametkin; Tolea, Magdalena I.; Galvin, James E.; Surkis, Alisa

2017-01-01

Background A clinical study team performing three multicultural dementia screening studies identified the need to improve data management practices and facilitate data sharing. A collaboration was initiated with librarians as part of the National Library of Medicine (NLM) informationist supplement program. The librarians identified areas for improvement in the studies’ data collection, entry, and processing workflows. Case Presentation The librarians’ role in this project was to meet needs expressed by the study team around improving data collection and processing workflows to increase study efficiency and ensure data quality. The librarians addressed the data collection, entry, and processing weaknesses through standardizing and renaming variables, creating an electronic data capture system using REDCap, and developing well-documented, reproducible data processing workflows. Conclusions NLM informationist supplements provide librarians with valuable experience in collaborating with study teams to address their data needs. For this project, the librarians gained skills in project management, REDCap, and understanding of the challenges and specifics of a clinical research study. However, the time and effort required to provide targeted and intensive support for one study team was not scalable to the library’s broader user community. PMID:28377680

Applying lean principles to continuous renal replacement therapy processes.

PubMed

Benfield, C Brett; Brummond, Philip; Lucarotti, Andrew; Villarreal, Maria; Goodwin, Adam; Wonnacott, Rob; Talley, Cheryl; Heung, Michael

2015-02-01

The application of lean principles to continuous renal replacement therapy (CRRT) processes in an academic medical center is described. A manual audit over six consecutive weeks revealed that 133 5-L bags of CRRT solution were discarded after being dispensed from pharmacy but before clinical use. Lean principles were used to examine the workflow for CRRT preparation and develop and implement an intervention. An educational program was developed to encourage and enhance direct communication between nursing and pharmacy about changes in a patient's condition or CRRT order. It was through this education program that the reordering workflow shifted from nurses to pharmacy technicians. The primary outcome was the number of CRRT solution bags delivered in the preintervention and postintervention periods. Nurses and pharmacy technicians were surveyed to determine their satisfaction with the workflow change. After implementation of lean principles, the mean number of CRRT solution bags dispensed per day of CRRT decreased substantially. Respondents' overall satisfaction with the CRRT solution preparation process increased during the postintervention period, and the satisfaction scores for each individual component of the workflow after implementation of lean principles. The decreased solution waste resulted in projected annual cost savings exceeding $70,000 in product alone. The use of lean principles to identify medication waste in the CRRT workflow and implementation of an intervention to shift the workload from intensive care unit nurses to pharmacy technicians led to reduced CRRT solution waste, improved efficiency of CRRT workflow, and increased satisfaction among staff. Copyright © 2015 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

Towards a unified estimate of arctic glaciers contribution to sea level rise since 1972.

NASA Astrophysics Data System (ADS)

Dehecq, A.; Gardner, A. S.; Alexandrov, O.; McMichael, S.

2017-12-01

Glaciers retreat contributed to about 1/3 of the observed sea level rise since 1971 (IPCC). However, long term estimates of glaciers volume changes rely on sparse field observations and region-wide satellite observations are available mostly after 2000. The recently declassified images from the reconnaissance satellite series Hexagon (KH9), that acquired 6 m resolution stereoscopic images from 1971 to 1986, open new possibilities for glaciers observation. But the film-printed images represent a processing challenge. Here we present an automatic workflow developed to generate Digital Elevation Models (DEMs) at 24 m resolution from the raw scanned KH9 images. It includes a preprocessing step to detect fiducial marks and to correct distortions of the film caused by the 40-year storage. An estimate of the unknown satellite position is obtained from a crude geolocation of the images. Each stereo image pair/triplet is then processed using the NASA Ames Stereo Pipeline to derive an unscaled DEM using standard photogrammetric techniques. This DEM is finally aligned to a reference topography, to account for errors in translation, rotation and scaling. In a second part, we present DEMs generated over glaciers in the Canadian Arctic and analyze glaciers volume changes from 1970 to the more recent WorldView ArcticDEM.

Semi-automatic mapping for identifying complex geobodies in seismic images

NASA Astrophysics Data System (ADS)

Domínguez-C, Raymundo; Romero-Salcedo, Manuel; Velasquillo-Martínez, Luis G.; Shemeretov, Leonid

2017-03-01

Seismic images are composed of positive and negative seismic wave traces with different amplitudes (Robein 2010 Seismic Imaging: A Review of the Techniques, their Principles, Merits and Limitations (Houten: EAGE)). The association of these amplitudes together with a color palette forms complex visual patterns. The color intensity of such patterns is directly related to impedance contrasts: the higher the contrast, the higher the color intensity. Generally speaking, low impedance contrasts are depicted with low tone colors, creating zones with different patterns whose features are not evident for a 3D automated mapping option available on commercial software. In this work, a workflow for a semi-automatic mapping of seismic images focused on those areas with low-intensity colored zones that may be associated with geobodies of petroleum interest is proposed. The CIE L*A*B* color space was used to perform the seismic image processing, which helped find small but significant differences between pixel tones. This process generated binary masks that bound color regions to low-intensity colors. The three-dimensional-mask projection allowed the construction of 3D structures for such zones (geobodies). The proposed method was applied to a set of digital images from a seismic cube and tested on four representative study cases. The obtained results are encouraging because interesting geobodies are obtained with a minimum of information.

Optimization of tomographic reconstruction workflows on geographically distributed resources

DOE PAGES

Bicer, Tekin; Gursoy, Doga; Kettimuthu, Rajkumar; ...

2016-01-01

New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modelingmore » of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum resources, which in turn can provide up to 3.13× speedup (on experimented resources). Furthermore, the error rates of the models range between 2.1 and 23.3% (considering workflow execution times), where the accuracy of the model estimations increases with higher computational demands in reconstruction tasks.« less

Optimization of tomographic reconstruction workflows on geographically distributed resources

PubMed Central

Bicer, Tekin; Gürsoy, Doǧa; Kettimuthu, Rajkumar; De Carlo, Francesco; Foster, Ian T.

2016-01-01

New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modeling of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum resources, which in turn can provide up to 3.13× speedup (on experimented resources). Moreover, the error rates of the models range between 2.1 and 23.3% (considering workflow execution times), where the accuracy of the model estimations increases with higher computational demands in reconstruction tasks. PMID:27359149

Optimization of tomographic reconstruction workflows on geographically distributed resources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bicer, Tekin; Gursoy, Doga; Kettimuthu, Rajkumar

New technological advancements in synchrotron light sources enable data acquisitions at unprecedented levels. This emergent trend affects not only the size of the generated data but also the need for larger computational resources. Although beamline scientists and users have access to local computational resources, these are typically limited and can result in extended execution times. Applications that are based on iterative processing as in tomographic reconstruction methods require high-performance compute clusters for timely analysis of data. Here, time-sensitive analysis and processing of Advanced Photon Source data on geographically distributed resources are focused on. Two main challenges are considered: (i) modelingmore » of the performance of tomographic reconstruction workflows and (ii) transparent execution of these workflows on distributed resources. For the former, three main stages are considered: (i) data transfer between storage and computational resources, (i) wait/queue time of reconstruction jobs at compute resources, and (iii) computation of reconstruction tasks. These performance models allow evaluation and estimation of the execution time of any given iterative tomographic reconstruction workflow that runs on geographically distributed resources. For the latter challenge, a workflow management system is built, which can automate the execution of workflows and minimize the user interaction with the underlying infrastructure. The system utilizes Globus to perform secure and efficient data transfer operations. The proposed models and the workflow management system are evaluated by using three high-performance computing and two storage resources, all of which are geographically distributed. Workflows were created with different computational requirements using two compute-intensive tomographic reconstruction algorithms. Experimental evaluation shows that the proposed models and system can be used for selecting the optimum resources, which in turn can provide up to 3.13× speedup (on experimented resources). Furthermore, the error rates of the models range between 2.1 and 23.3% (considering workflow execution times), where the accuracy of the model estimations increases with higher computational demands in reconstruction tasks.« less

Observing System Simulation Experiment (OSSE) for the HyspIRI Spectrometer Mission

NASA Technical Reports Server (NTRS)

Turmon, Michael J.; Block, Gary L.; Green, Robert O.; Hua, Hook; Jacob, Joseph C.; Sobel, Harold R.; Springer, Paul L.; Zhang, Qingyuan

2010-01-01

The OSSE software provides an integrated end-to-end environment to simulate an Earth observing system by iteratively running a distributed modeling workflow based on the HyspIRI Mission, including atmospheric radiative transfer, surface albedo effects, detection, and retrieval for agile exploration of the mission design space. The software enables an Observing System Simulation Experiment (OSSE) and can be used for design trade space exploration of science return for proposed instruments by modeling the whole ground truth, sensing, and retrieval chain and to assess retrieval accuracy for a particular instrument and algorithm design. The OSSE in fra struc ture is extensible to future National Research Council (NRC) Decadal Survey concept missions where integrated modeling can improve the fidelity of coupled science and engineering analyses for systematic analysis and science return studies. This software has a distributed architecture that gives it a distinct advantage over other similar efforts. The workflow modeling components are typically legacy computer programs implemented in a variety of programming languages, including MATLAB, Excel, and FORTRAN. Integration of these diverse components is difficult and time-consuming. In order to hide this complexity, each modeling component is wrapped as a Web Service, and each component is able to pass analysis parameterizations, such as reflectance or radiance spectra, on to the next component downstream in the service workflow chain. In this way, the interface to each modeling component becomes uniform and the entire end-to-end workflow can be run using any existing or custom workflow processing engine. The architecture lets users extend workflows as new modeling components become available, chain together the components using any existing or custom workflow processing engine, and distribute them across any Internet-accessible Web Service endpoints. The workflow components can be hosted on any Internet-accessible machine. This has the advantages that the computations can be distributed to make best use of the available computing resources, and each workflow component can be hosted and maintained by their respective domain experts.

Use of contextual inquiry to understand anatomic pathology workflow: Implications for digital pathology adoption

PubMed Central

Ho, Jonhan; Aridor, Orly; Parwani, Anil V.

2012-01-01

Background: For decades anatomic pathology (AP) workflow have been a highly manual process based on the use of an optical microscope and glass slides. Recent innovations in scanning and digitizing of entire glass slides are accelerating a move toward widespread adoption and implementation of a workflow based on digital slides and their supporting information management software. To support the design of digital pathology systems and ensure their adoption into pathology practice, the needs of the main users within the AP workflow, the pathologists, should be identified. Contextual inquiry is a qualitative, user-centered, social method designed to identify and understand users’ needs and is utilized for collecting, interpreting, and aggregating in-detail aspects of work. Objective: Contextual inquiry was utilized to document current AP workflow, identify processes that may benefit from the introduction of digital pathology systems, and establish design requirements for digital pathology systems that will meet pathologists’ needs. Materials and Methods: Pathologists were observed and interviewed at a large academic medical center according to contextual inquiry guidelines established by Holtzblatt et al. 1998. Notes representing user-provided data were documented during observation sessions. An affinity diagram, a hierarchal organization of the notes based on common themes in the data, was created. Five graphical models were developed to help visualize the data including sequence, flow, artifact, physical, and cultural models. Results: A total of six pathologists were observed by a team of two researchers. A total of 254 affinity notes were documented and organized using a system based on topical hierarchy, including 75 third-level, 24 second-level, and five main-level categories, including technology, communication, synthesis/preparation, organization, and workflow. Current AP workflow was labor intensive and lacked scalability. A large number of processes that may possibly improve following the introduction of digital pathology systems were identified. These work processes included case management, case examination and review, and final case reporting. Furthermore, a digital slide system should integrate with the anatomic pathologic laboratory information system. Conclusions: To our knowledge, this is the first study that utilized the contextual inquiry method to document AP workflow. Findings were used to establish key requirements for the design of digital pathology systems. PMID:23243553

Warpgroup: increased precision of metabolomic data processing by consensus integration bound analysis

PubMed Central

Mahieu, Nathaniel G.; Spalding, Jonathan L.; Patti, Gary J.

2016-01-01

Motivation: Current informatic techniques for processing raw chromatography/mass spectrometry data break down under several common, non-ideal conditions. Importantly, hydrophilic liquid interaction chromatography (a key separation technology for metabolomics) produces data which are especially challenging to process. We identify three critical points of failure in current informatic workflows: compound specific drift, integration region variance, and naive missing value imputation. We implement the Warpgroup algorithm to address these challenges. Results: Warpgroup adds peak subregion detection, consensus integration bound detection, and intelligent missing value imputation steps to the conventional informatic workflow. When compared with the conventional workflow, Warpgroup made major improvements to the processed data. The coefficient of variation for peaks detected in replicate injections of a complex Escherichia Coli extract were halved (a reduction of 19%). Integration regions across samples were much more robust. Additionally, many signals lost by the conventional workflow were ‘rescued’ by the Warpgroup refinement, thereby resulting in greater analyte coverage in the processed data. Availability and implementation: Warpgroup is an open source R package available on GitHub at github.com/nathaniel-mahieu/warpgroup. The package includes example data and XCMS compatibility wrappers for ease of use. Supplementary information: Supplementary data are available at Bioinformatics online. Contact: nathaniel.mahieu@wustl.edu or gjpattij@wustl.edu PMID:26424859

The VERCE platform: Enabling Computational Seismology via Streaming Workflows and Science Gateways

NASA Astrophysics Data System (ADS)

Spinuso, Alessandro; Filgueira, Rosa; Krause, Amrey; Matser, Jonas; Casarotti, Emanuele; Magnoni, Federica; Gemund, Andre; Frobert, Laurent; Krischer, Lion; Atkinson, Malcolm

2015-04-01

The VERCE project is creating an e-Science platform to facilitate innovative data analysis and coding methods that fully exploit the wealth of data in global seismology. One of the technologies developed within the project is the Dispel4Py python library, which allows to describe abstract stream-based workflows for data-intensive applications and to execute them in a distributed environment. At runtime Dispel4Py is able to map workflow descriptions dynamically onto a number of computational resources (Apache Storm clusters, MPI powered clusters, and shared-memory multi-core machines, single-core machines), setting it apart from other workflow frameworks. Therefore, Dispel4Py enables scientists to focus on their computation instead of being distracted by details of the computing infrastructure they use. Among the workflows developed with Dispel4Py in VERCE, we mention here those for Seismic Ambient Noise Cross-Correlation and MISFIT calculation, which address two data-intensive problems that are common in computational seismology. The former, also called Passive Imaging, allows the detection of relative seismic-wave velocity variations during the time of recording, to be associated with the stress-field changes that occurred in the test area. The MISFIT instead, takes as input the synthetic seismograms generated from HPC simulations for a certain Earth model and earthquake and, after a preprocessing stage, compares them with real observations in order to foster subsequent model updates and improvement (Inversion). The VERCE Science Gateway exposes the MISFIT calculation workflow as a service, in combination with the simulation phase. Both phases can be configured, controlled and monitored by the user via a rich user interface which is integrated within the gUSE Science Gateway framework, hiding the complexity of accessing third parties data services, security mechanisms and enactment on the target resources. Thanks to a modular extension to the Dispel4Py framework, the system collects provenance data adopting the W3C-PROV data model. Provenance recordings can be explored and analysed at run time for rapid diagnostic and workflow steering, or later for further validation and comparisons across runs. We will illustrate the interactive services of the gateway and the capabilities of the produced metadata, coupled with the VERCE data management layer based on iRODS. The Cross-Correlation workflow was evaluated on SuperMUC, a supercomputing cluster at the Leibniz Supercomputing Centre in Munich, with 155,656 processor cores in 9400 compute nodes. SuperMUC is based on the Intel Xeon architecture consisting of 18 Thin Node Islands and one Fat Node Island. This work has only had access to the Thin Node Islands, which contain Sandy Bridge nodes, each having 16 cores and 32 GB of memory. In the evaluations we used 1000 stations, and we applied two types of methods (whiten and non-whiten) for pre-processing the data. The workflow was tested on a varying number of cores (16, 32, 64, 128, and 256 cores) using the MPI mapping of Dispel4Py. The results show that Dispel4Py is able to improve the performance by increasing the number of cores without changing the description of the workflow.

Hybrid network modeling and the effect of image resolution on digitally-obtained petrophysical and two-phase flow properties

NASA Astrophysics Data System (ADS)

Aghaei, A.

2017-12-01

Digital imaging and modeling of rocks and subsequent simulation of physical phenomena in digitally-constructed rock models are becoming an integral part of core analysis workflows. One of the inherent limitations of image-based analysis, at any given scale, is image resolution. This limitation becomes more evident when the rock has multiple scales of porosity such as in carbonates and tight sandstones. Multi-scale imaging and constructions of hybrid models that encompass images acquired at multiple scales and resolutions are proposed as a solution to this problem. In this study, we investigate the effect of image resolution and unresolved porosity on petrophysical and two-phase flow properties calculated based on images. A helical X-ray micro-CT scanner with a high cone-angle is used to acquire digital rock images that are free of geometric distortion. To remove subjectivity from the analyses, a semi-automated image processing technique is used to process and segment the acquired data into multiple phases. Direct and pore network based models are used to simulate physical phenomena and obtain absolute permeability, formation factor and two-phase flow properties such as relative permeability and capillary pressure. The effect of image resolution on each property is investigated. Finally a hybrid network model incorporating images at multiple resolutions is built and used for simulations. The results from the hybrid model are compared against results from the model built at the highest resolution and those from laboratory tests.

Automating PACS quality control with the Vanderbilt image processing enterprise resource

NASA Astrophysics Data System (ADS)

Esparza, Michael L.; Welch, E. Brian; Landman, Bennett A.

2012-02-01

Precise image acquisition is an integral part of modern patient care and medical imaging research. Periodic quality control using standardized protocols and phantoms ensures that scanners are operating according to specifications, yet such procedures do not ensure that individual datasets are free from corruption; for example due to patient motion, transient interference, or physiological variability. If unacceptable artifacts are noticed during scanning, a technologist can repeat a procedure. Yet, substantial delays may be incurred if a problematic scan is not noticed until a radiologist reads the scans or an automated algorithm fails. Given scores of slices in typical three-dimensional scans and widevariety of potential use cases, a technologist cannot practically be expected inspect all images. In large-scale research, automated pipeline systems have had great success in achieving high throughput. However, clinical and institutional workflows are largely based on DICOM and PACS technologies; these systems are not readily compatible with research systems due to security and privacy restrictions. Hence, quantitative quality control has been relegated to individual investigators and too often neglected. Herein, we propose a scalable system, the Vanderbilt Image Processing Enterprise Resource (VIPER) to integrate modular quality control and image analysis routines with a standard PACS configuration. This server unifies image processing routines across an institutional level and provides a simple interface so that investigators can collaborate to deploy new analysis technologies. VIPER integrates with high performance computing environments has successfully analyzed all standard scans from our institutional research center over the course of the last 18 months.

Identification of drug metabolites in human plasma or serum integrating metabolite prediction, LC-HRMS and untargeted data processing.

PubMed

Jacobs, Peter L; Ridder, Lars; Ruijken, Marco; Rosing, Hilde; Jager, Nynke Gl; Beijnen, Jos H; Bas, Richard R; van Dongen, William D

2013-09-01

Comprehensive identification of human drug metabolites in first-in-man studies is crucial to avoid delays in later stages of drug development. We developed an efficient workflow for systematic identification of human metabolites in plasma or serum that combines metabolite prediction, high-resolution accurate mass LC-MS and MS vendor independent data processing. Retrospective evaluation of predictions for 14 (14)C-ADME studies published in the period 2007-January 2012 indicates that on average 90% of the major metabolites in human plasma can be identified by searching for accurate masses of predicted metabolites. Furthermore, the workflow can identify unexpected metabolites in the same processing run, by differential analysis of samples of drug-dosed subjects and (placebo-dosed, pre-dose or otherwise blank) control samples. To demonstrate the utility of the workflow we applied it to identify tamoxifen metabolites in serum of a breast cancer patient treated with tamoxifen. Previously published metabolites were confirmed in this study and additional metabolites were identified, two of which are discussed to illustrate the advantages of the workflow.

Biowep: a workflow enactment portal for bioinformatics applications.

PubMed

Romano, Paolo; Bartocci, Ezio; Bertolini, Guglielmo; De Paoli, Flavio; Marra, Domenico; Mauri, Giancarlo; Merelli, Emanuela; Milanesi, Luciano

2007-03-08

The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of effective workflows can significantly improve automation of in-silico analysis. Biowep is available for interested researchers as a reference portal. They are invited to submit their workflows to the workflow repository. Biowep is further being developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics - LITBIO.

Biowep: a workflow enactment portal for bioinformatics applications

PubMed Central

Romano, Paolo; Bartocci, Ezio; Bertolini, Guglielmo; De Paoli, Flavio; Marra, Domenico; Mauri, Giancarlo; Merelli, Emanuela; Milanesi, Luciano

2007-01-01

Background The huge amount of biological information, its distribution over the Internet and the heterogeneity of available software tools makes the adoption of new data integration and analysis network tools a necessity in bioinformatics. ICT standards and tools, like Web Services and Workflow Management Systems (WMS), can support the creation and deployment of such systems. Many Web Services are already available and some WMS have been proposed. They assume that researchers know which bioinformatics resources can be reached through a programmatic interface and that they are skilled in programming and building workflows. Therefore, they are not viable to the majority of unskilled researchers. A portal enabling these to take profit from new technologies is still missing. Results We designed biowep, a web based client application that allows for the selection and execution of a set of predefined workflows. The system is available on-line. Biowep architecture includes a Workflow Manager, a User Interface and a Workflow Executor. The task of the Workflow Manager is the creation and annotation of workflows. These can be created by using either the Taverna Workbench or BioWMS. Enactment of workflows is carried out by FreeFluo for Taverna workflows and by BioAgent/Hermes, a mobile agent-based middleware, for BioWMS ones. Main workflows' processing steps are annotated on the basis of their input and output, elaboration type and application domain by using a classification of bioinformatics data and tasks. The interface supports users authentication and profiling. Workflows can be selected on the basis of users' profiles and can be searched through their annotations. Results can be saved. Conclusion We developed a web system that support the selection and execution of predefined workflows, thus simplifying access for all researchers. The implementation of Web Services allowing specialized software to interact with an exhaustive set of biomedical databases and analysis software and the creation of effective workflows can significantly improve automation of in-silico analysis. Biowep is available for interested researchers as a reference portal. They are invited to submit their workflows to the workflow repository. Biowep is further being developed in the sphere of the Laboratory of Interdisciplinary Technologies in Bioinformatics – LITBIO. PMID:17430563

Wireless Mobile Technology to Improve Workflow and Feasibility of MR-Guided Percutaneous Interventions

PubMed Central

Rube, Martin A.; Holbrook, Andrew B.; Cox, Benjamin F.; Buciuc, Razvan; Melzer, Andreas

2015-01-01

Purpose A wireless interactive display and control device combined with a platform-independent web-based User Interface (UI) was developed to improve the workflow for interventional Magnetic Resonance Imaging (iMRI). Methods The iMRI-UI enables image acquisition of up to three independent slices using various pulse sequences with different contrast weighting. Pulse sequence, scan geometry and related parameters can be changed on the fly via the iMRI-UI using a tablet computer for improved lesion detection and interventional device targeting. The iMRI-UI was validated for core biopsies with a liver phantom (n=40) and Thiel soft-embalmed human cadavers (n=24) in a clinical 1.5T MRI scanner. Results The iMRI-UI components and setup were tested and found conditionally MRI-safe to use according to current ASTM standards. Despite minor temporary touchscreen interference at a close distance to the bore (<20 cm), no other issues regarding quality or imaging artefacts were observed. The 3D root-mean-square distance error was 2.8±1.0 (phantom) / 2.9±0.8 mm (cadaver) and overall procedure times ranged between 12–22 (phantom) / 20–55 minutes (cadaver). Conclusions The wireless iMRI-UI control setup enabled fast and accurate interventional biopsy needle placements along complex trajectories and improved the workflow for percutaneous interventions under MRI guidance in a preclinical trial. PMID:25179151

Localization-based super-resolution imaging meets high-content screening.

PubMed

Beghin, Anne; Kechkar, Adel; Butler, Corey; Levet, Florian; Cabillic, Marine; Rossier, Olivier; Giannone, Gregory; Galland, Rémi; Choquet, Daniel; Sibarita, Jean-Baptiste

2017-12-01

Single-molecule localization microscopy techniques have proven to be essential tools for quantitatively monitoring biological processes at unprecedented spatial resolution. However, these techniques are very low throughput and are not yet compatible with fully automated, multiparametric cellular assays. This shortcoming is primarily due to the huge amount of data generated during imaging and the lack of software for automation and dedicated data mining. We describe an automated quantitative single-molecule-based super-resolution methodology that operates in standard multiwell plates and uses analysis based on high-content screening and data-mining software. The workflow is compatible with fixed- and live-cell imaging and allows extraction of quantitative data like fluorophore photophysics, protein clustering or dynamic behavior of biomolecules. We demonstrate that the method is compatible with high-content screening using 3D dSTORM and DNA-PAINT based super-resolution microscopy as well as single-particle tracking.

Integration of SimSET photon history generator in GATE for efficient Monte Carlo simulations of pinhole SPECT.

PubMed

Chen, Chia-Lin; Wang, Yuchuan; Lee, Jason J S; Tsui, Benjamin M W

2008-07-01

The authors developed and validated an efficient Monte Carlo simulation (MCS) workflow to facilitate small animal pinhole SPECT imaging research. This workflow seamlessly integrates two existing MCS tools: simulation system for emission tomography (SimSET) and GEANT4 application for emission tomography (GATE). Specifically, we retained the strength of GATE in describing complex collimator/detector configurations to meet the anticipated needs for studying advanced pinhole collimation (e.g., multipinhole) geometry, while inserting the fast SimSET photon history generator (PHG) to circumvent the relatively slow GEANT4 MCS code used by GATE in simulating photon interactions inside voxelized phantoms. For validation, data generated from this new SimSET-GATE workflow were compared with those from GATE-only simulations as well as experimental measurements obtained using a commercial small animal pinhole SPECT system. Our results showed excellent agreement (e.g., in system point response functions and energy spectra) between SimSET-GATE and GATE-only simulations, and, more importantly, a significant computational speedup (up to approximately 10-fold) provided by the new workflow. Satisfactory agreement between MCS results and experimental data were also observed. In conclusion, the authors have successfully integrated SimSET photon history generator in GATE for fast and realistic pinhole SPECT simulations, which can facilitate research in, for example, the development and application of quantitative pinhole and multipinhole SPECT for small animal imaging. This integrated simulation tool can also be adapted for studying other preclinical and clinical SPECT techniques.

Scientific Workflows + Provenance = Better (Meta-)Data Management

NASA Astrophysics Data System (ADS)

Ludaescher, B.; Cuevas-Vicenttín, V.; Missier, P.; Dey, S.; Kianmajd, P.; Wei, Y.; Koop, D.; Chirigati, F.; Altintas, I.; Belhajjame, K.; Bowers, S.

2013-12-01

The origin and processing history of an artifact is known as its provenance. Data provenance is an important form of metadata that explains how a particular data product came about, e.g., how and when it was derived in a computational process, which parameter settings and input data were used, etc. Provenance information provides transparency and helps to explain and interpret data products. Other common uses and applications of provenance include quality control, data curation, result debugging, and more generally, 'reproducible science'. Scientific workflow systems (e.g. Kepler, Taverna, VisTrails, and others) provide controlled environments for developing computational pipelines with built-in provenance support. Workflow results can then be explained in terms of workflow steps, parameter settings, input data, etc. using provenance that is automatically captured by the system. Scientific workflows themselves provide a user-friendly abstraction of the computational process and are thus a form of ('prospective') provenance in their own right. The full potential of provenance information is realized when combining workflow-level information (prospective provenance) with trace-level information (retrospective provenance). To this end, the DataONE Provenance Working Group (ProvWG) has developed an extension of the W3C PROV standard, called D-PROV. Whereas PROV provides a 'least common denominator' for exchanging and integrating provenance information, D-PROV adds new 'observables' that described workflow-level information (e.g., the functional steps in a pipeline), as well as workflow-specific trace-level information ( timestamps for each workflow step executed, the inputs and outputs used, etc.) Using examples, we will demonstrate how the combination of prospective and retrospective provenance provides added value in managing scientific data. The DataONE ProvWG is also developing tools based on D-PROV that allow scientists to get more mileage from provenance metadata. DataONE is a federation of member nodes that store data and metadata for discovery and access. By enriching metadata with provenance information, search and reuse of data is enhanced, and the 'social life' of data (being the product of many workflow runs, different people, etc.) is revealed. We are currently prototyping a provenance repository (PBase) to demonstrate what can be achieved with advanced provenance queries. The ProvExplorer and ProPub tools support advanced ad-hoc querying and visualization of provenance as well as customized provenance publications (e.g., to address privacy issues, or to focus provenance to relevant details). In a parallel line of work, we are exploring ways to add provenance support to widely-used scripting platforms (e.g. R and Python) and then expose that information via D-PROV.

geoKepler Workflow Module for Computationally Scalable and Reproducible Geoprocessing and Modeling

NASA Astrophysics Data System (ADS)

Cowart, C.; Block, J.; Crawl, D.; Graham, J.; Gupta, A.; Nguyen, M.; de Callafon, R.; Smarr, L.; Altintas, I.

2015-12-01

The NSF-funded WIFIRE project has developed an open-source, online geospatial workflow platform for unifying geoprocessing tools and models for for fire and other geospatially dependent modeling applications. It is a product of WIFIRE's objective to build an end-to-end cyberinfrastructure for real-time and data-driven simulation, prediction and visualization of wildfire behavior. geoKepler includes a set of reusable GIS components, or actors, for the Kepler Scientific Workflow System (https://kepler-project.org). Actors exist for reading and writing GIS data in formats such as Shapefile, GeoJSON, KML, and using OGC web services such as WFS. The actors also allow for calling geoprocessing tools in other packages such as GDAL and GRASS. Kepler integrates functions from multiple platforms and file formats into one framework, thus enabling optimal GIS interoperability, model coupling, and scalability. Products of the GIS actors can be fed directly to models such as FARSITE and WRF. Kepler's ability to schedule and scale processes using Hadoop and Spark also makes geoprocessing ultimately extensible and computationally scalable. The reusable workflows in geoKepler can be made to run automatically when alerted by real-time environmental conditions. Here, we show breakthroughs in the speed of creating complex data for hazard assessments with this platform. We also demonstrate geoKepler workflows that use Data Assimilation to ingest real-time weather data into wildfire simulations, and for data mining techniques to gain insight into environmental conditions affecting fire behavior. Existing machine learning tools and libraries such as R and MLlib are being leveraged for this purpose in Kepler, as well as Kepler's Distributed Data Parallel (DDP) capability to provide a framework for scalable processing. geoKepler workflows can be executed via an iPython notebook as a part of a Jupyter hub at UC San Diego for sharing and reporting of the scientific analysis and results from various runs of geoKepler workflows. The communication between iPython and Kepler workflow executions is established through an iPython magic function for Kepler that we have implemented. In summary, geoKepler is an ecosystem that makes geospatial processing and analysis of any kind programmable, reusable, scalable and sharable.

Fundamentals of image acquisition and processing in the digital era.

PubMed

Farman, A G

2003-01-01

To review the historic context for digital imaging in dentistry and to outline the fundamental issues related to digital imaging modalities. Digital dental X-ray images can be achieved by scanning analog film radiographs (secondary capture), with photostimulable phosphors, or using solid-state detectors (e.g. charge-coupled device and complementary metal oxide semiconductor). There are four characteristics that are basic to all digital image detectors; namely, size of active area, signal-to-noise ratio, contrast resolution and the spatial resolution. To perceive structure in a radiographic image, there needs to be sufficient difference between contrasting densities. This primarily depends on the differences in the attenuation of the X-ray beam by adjacent tissues. It is also depends on the signal received; therefore, contrast tends to increase with increased exposure. Given adequate signal and sufficient differences in radiodensity, contrast will be sufficient to differentiate between adjacent structures, irrespective of the recording modality and processing used. Where contrast is not sufficient, digital images can sometimes be post-processed to disclose details that would otherwise go undetected. For example, cephalogram isodensity mapping can improve soft tissue detail. It is concluded that it could be a further decade or two before three-dimensional digital imaging systems entirely replace two-dimensional analog films. Such systems need not only to produce prettier images, but also to provide a demonstrable evidence-based higher standard of care at a cost that is not economically prohibitive for the practitioner or society, and which allows efficient and effective workflow within the business of dental practice.

A quality-refinement process for medical imaging applications.

PubMed

Neuhaus, J; Maleike, D; Nolden, M; Kenngott, H-G; Meinzer, H-P; Wolf, I

2009-01-01

To introduce and evaluate a process for refinement of software quality that is suitable to research groups. In order to avoid constraining researchers too much, the quality improvement process has to be designed carefully. The scope of this paper is to present and evaluate a process to advance quality aspects of existing research prototypes in order to make them ready for initial clinical studies. The proposed process is tailored for research environments and therefore more lightweight than traditional quality management processes. Focus on quality criteria that are important at the given stage of the software life cycle. Usage of tools that automate aspects of the process is emphasized. To evaluate the additional effort that comes along with the process, it was exemplarily applied for eight prototypical software modules for medical image processing. The introduced process has been applied to improve the quality of all prototypes so that they could be successfully used in clinical studies. The quality refinement yielded an average of 13 person days of additional effort per project. Overall, 107 bugs were found and resolved by applying the process. Careful selection of quality criteria and the usage of automated process tools lead to a lightweight quality refinement process suitable for scientific research groups that can be applied to ensure a successful transfer of technical software prototypes into clinical research workflows.

CONNJUR Workflow Builder: A software integration environment for spectral reconstruction

PubMed Central

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O.; Ellis, Heidi J.C.; Gryk, Michael R.

2015-01-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses. PMID:26066803

Teaching Workflow Analysis and Lean Thinking via Simulation: A Formative Evaluation

PubMed Central

Campbell, Robert James; Gantt, Laura; Congdon, Tamara

2009-01-01

This article presents the rationale for the design and development of a video simulation used to teach lean thinking and workflow analysis to health services and health information management students enrolled in a course on the management of health information. The discussion includes a description of the design process, a brief history of the use of simulation in healthcare, and an explanation of how video simulation can be used to generate experiential learning environments. Based on the results of a survey given to 75 students as part of a formative evaluation, the video simulation was judged effective because it allowed students to visualize a real-world process (concrete experience), contemplate the scenes depicted in the video along with the concepts presented in class in a risk-free environment (reflection), develop hypotheses about why problems occurred in the workflow process (abstract conceptualization), and develop solutions to redesign a selected process (active experimentation). PMID:19412533

CONNJUR Workflow Builder: a software integration environment for spectral reconstruction.

PubMed

Fenwick, Matthew; Weatherby, Gerard; Vyas, Jay; Sesanker, Colbert; Martyn, Timothy O; Ellis, Heidi J C; Gryk, Michael R

2015-07-01

CONNJUR Workflow Builder (WB) is an open-source software integration environment that leverages existing spectral reconstruction tools to create a synergistic, coherent platform for converting biomolecular NMR data from the time domain to the frequency domain. WB provides data integration of primary data and metadata using a relational database, and includes a library of pre-built workflows for processing time domain data. WB simplifies maximum entropy reconstruction, facilitating the processing of non-uniformly sampled time domain data. As will be shown in the paper, the unique features of WB provide it with novel abilities to enhance the quality, accuracy, and fidelity of the spectral reconstruction process. WB also provides features which promote collaboration, education, parameterization, and non-uniform data sets along with processing integrated with the Rowland NMR Toolkit (RNMRTK) and NMRPipe software packages. WB is available free of charge in perpetuity, dual-licensed under the MIT and GPL open source licenses.

IceProd 2 Usage Experience

NASA Astrophysics Data System (ADS)

Delventhal, D.; Schultz, D.; Diaz Velez, J. C.

2017-10-01

IceProd is a data processing and management framework developed by the IceCube Neutrino Observatory for processing of Monte Carlo simulations, detector data, and data driven analysis. It runs as a separate layer on top of grid and batch systems. This is accomplished by a set of daemons which process job workflow, maintaining configuration and status information on the job before, during, and after processing. IceProd can also manage complex workflow DAGs across distributed computing grids in order to optimize usage of resources. IceProd has recently been rewritten to increase its scaling capabilities, handle user analysis workflows together with simulation production, and facilitate the integration with 3rd party scheduling tools. IceProd 2, the second generation of IceProd, has been running in production for several months now. We share our experience setting up the system and things we’ve learned along the way.

Using AI and Semantic Web Technologies to attack Process Complexity in Open Systems

NASA Astrophysics Data System (ADS)

Thompson, Simon; Giles, Nick; Li, Yang; Gharib, Hamid; Nguyen, Thuc Duong

Recently many vendors and groups have advocated using BPEL and WS-BPEL as a workflow language to encapsulate business logic. While encapsulating workflow and process logic in one place is a sensible architectural decision the implementation of complex workflows suffers from the same problems that made managing and maintaining hierarchical procedural programs difficult. BPEL lacks constructs for logical modularity such as the requirements construct from the STL [12] or the ability to adapt constructs like pure abstract classes for the same purpose. We describe a system that uses semantic web and agent concepts to implement an abstraction layer for BPEL based on the notion of Goals and service typing. AI planning was used to enable process engineers to create and validate systems that used services and goals as first class concepts and compiled processes at run time for execution.

Geomorphic process from topographic form: automating the interpretation of repeat survey data in river valleys

USGS Publications Warehouse

Kasprak, Alan; Caster, Joshua J.; Bangen, Sara G.; Sankey, Joel B.

2017-01-01

The ability to quantify the processes driving geomorphic change in river valley margins is vital to geomorphologists seeking to understand the relative role of transport mechanisms (e.g. fluvial, aeolian, and hillslope processes) in landscape dynamics. High-resolution, repeat topographic data are becoming readily available to geomorphologists. By contrasting digital elevation models derived from repeat surveys, the transport processes driving topographic changes can be inferred, a method termed ‘mechanistic segregation.’ Unfortunately, mechanistic segregation largely relies on subjective and time consuming manual classification, which has implications both for its reproducibility and the practical scale of its application. Here we present a novel computational workflow for the mechanistic segregation of geomorphic transport processes in geospatial datasets. We apply the workflow to seven sites along the Colorado River in the Grand Canyon, where geomorphic transport is driven by a diverse suite of mechanisms. The workflow performs well when compared to field observations, with an overall predictive accuracy of 84% across 113 validation points. The approach most accurately predicts changes due to fluvial processes (100% accuracy) and aeolian processes (96%), with reduced accuracy in predictions of alluvial and colluvial processes (64% and 73%, respectively). Our workflow is designed to be applicable to a diversity of river systems and will likely provide a rapid and objective understanding of the processes driving geomorphic change at the reach and network scales. We anticipate that such an understanding will allow insight into the response of geomorphic transport processes to external forcings, such as shifts in climate, land use, or river regulation, with implications for process-based river management and restoration.

A software tool to analyze clinical workflows from direct observations.

PubMed

Schweitzer, Marco; Lasierra, Nelia; Hoerbst, Alexander

2015-01-01

Observational data of clinical processes need to be managed in a convenient way, so that process information is reliable, valid and viable for further analysis. However, existing tools for allocating observations fail in systematic data collection of specific workflow recordings. We present a software tool which was developed to facilitate the analysis of clinical process observations. The tool was successfully used in the project OntoHealth, to build, store and analyze observations of diabetes routine consultations.

Providing Enterprise Information Services for Multinational Interoperability - The EIM Approach

DTIC Science & Technology

2005-06-01

Federated Search • Document Processing and Archiving • Workflow processing References 1. Perspective on Multinational Information Sharing, Cheryl...layer, with a primary focus on the Application Layers. App Layer Focus Areas Enterprise Content Mgt, Workflow, Business Processes, Federated ... Search Integration Layer – EAI Components Nation 1 Nation 2 Nation 3 … Nation N Silo 1 Silo 2 Silo 3 S ilo N Silo 1 Silo 1 Silo 2 Silo 2 Silo 3 Silo 3 S

Pathology economic model tool: a novel approach to workflow and budget cost analysis in an anatomic pathology laboratory.

PubMed

Muirhead, David; Aoun, Patricia; Powell, Michael; Juncker, Flemming; Mollerup, Jens

2010-08-01

The need for higher efficiency, maximum quality, and faster turnaround time is a continuous focus for anatomic pathology laboratories and drives changes in work scheduling, instrumentation, and management control systems. To determine the costs of generating routine, special, and immunohistochemical microscopic slides in a large, academic anatomic pathology laboratory using a top-down approach. The Pathology Economic Model Tool was used to analyze workflow processes at The Nebraska Medical Center's anatomic pathology laboratory. Data from the analysis were used to generate complete cost estimates, which included not only materials, consumables, and instrumentation but also specific labor and overhead components for each of the laboratory's subareas. The cost data generated by the Pathology Economic Model Tool were compared with the cost estimates generated using relative value units. Despite the use of automated systems for different processes, the workflow in the laboratory was found to be relatively labor intensive. The effect of labor and overhead on per-slide costs was significantly underestimated by traditional relative-value unit calculations when compared with the Pathology Economic Model Tool. Specific workflow defects with significant contributions to the cost per slide were identified. The cost of providing routine, special, and immunohistochemical slides may be significantly underestimated by traditional methods that rely on relative value units. Furthermore, a comprehensive analysis may identify specific workflow processes requiring improvement.

Adaptive platform for fluorescence microscopy-based high-content screening

NASA Astrophysics Data System (ADS)

Geisbauer, Matthias; Röder, Thorsten; Chen, Yang; Knoll, Alois; Uhl, Rainer

2010-04-01

Fluorescence microscopy has become a widely used tool for the study of medically relevant intra- and intercellular processes. Extracting meaningful information out of a bulk of acquired images is usually performed during a separate post-processing task. Thus capturing raw data results in an unnecessary huge number of images, whereas usually only a few images really show the particular information that is searched for. Here we propose a novel automated high-content microscope system, which enables experiments to be carried out with only a minimum of human interaction. It facilitates a huge speed-increase for cell biology research and its applications compared to the widely performed workflows. Our fluorescence microscopy system can automatically execute application-dependent data processing algorithms during the actual experiment. They are used for image contrast enhancement, cell segmentation and/or cell property evaluation. On-the-fly retrieved information is used to reduce data and concomitantly control the experiment process in real-time. Resulting in a closed loop of perception and action the system can greatly decrease the amount of stored data on one hand and increases the relative valuable data content on the other hand. We demonstrate our approach by addressing the problem of automatically finding cells with a particular combination of labeled receptors and then selectively stimulate them with antagonists or agonists. The results are then compared against the results of traditional, static systems.

a Standardized Approach to Topographic Data Processing and Workflow Management

NASA Astrophysics Data System (ADS)

Wheaton, J. M.; Bailey, P.; Glenn, N. F.; Hensleigh, J.; Hudak, A. T.; Shrestha, R.; Spaete, L.

2013-12-01

An ever-increasing list of options exist for collecting high resolution topographic data, including airborne LIDAR, terrestrial laser scanners, bathymetric SONAR and structure-from-motion. An equally rich, arguably overwhelming, variety of tools exists with which to organize, quality control, filter, analyze and summarize these data. However, scientists are often left to cobble together their analysis as a series of ad hoc steps, often using custom scripts and one-time processes that are poorly documented and rarely shared with the community. Even when literature-cited software tools are used, the input and output parameters differ from tool to tool. These parameters are rarely archived and the steps performed lost, making the analysis virtually impossible to replicate precisely. What is missing is a coherent, robust, framework for combining reliable, well-documented topographic data-processing steps into a workflow that can be repeated and even shared with others. We have taken several popular topographic data processing tools - including point cloud filtering and decimation as well as DEM differencing - and defined a common protocol for passing inputs and outputs between them. This presentation describes a free, public online portal that enables scientists to create custom workflows for processing topographic data using a number of popular topographic processing tools. Users provide the inputs required for each tool and in what sequence they want to combine them. This information is then stored for future reuse (and optionally sharing with others) before the user then downloads a single package that contains all the input and output specifications together with the software tools themselves. The user then launches the included batch file that executes the workflow on their local computer against their topographic data. This ZCloudTools architecture helps standardize, automate and archive topographic data processing. It also represents a forum for discovering and sharing effective topographic processing workflows.

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

PubMed Central

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A.; Caron, Christophe

2015-01-01

Summary: The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. Availability and implementation: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). Contact: contact@workflow4metabolomics.org PMID:25527831

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.

PubMed

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A; Caron, Christophe

2015-05-01

The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). contact@workflow4metabolomics.org. © The Author 2014. Published by Oxford University Press.

PANORAMA: An approach to performance modeling and diagnosis of extreme-scale workflows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Deelman, Ewa; Carothers, Christopher; Mandal, Anirban

Here we report that computational science is well established as the third pillar of scientific discovery and is on par with experimentation and theory. However, as we move closer toward the ability to execute exascale calculations and process the ensuing extreme-scale amounts of data produced by both experiments and computations alike, the complexity of managing the compute and data analysis tasks has grown beyond the capabilities of domain scientists. Therefore, workflow management systems are absolutely necessary to ensure current and future scientific discoveries. A key research question for these workflow management systems concerns the performance optimization of complex calculation andmore » data analysis tasks. The central contribution of this article is a description of the PANORAMA approach for modeling and diagnosing the run-time performance of complex scientific workflows. This approach integrates extreme-scale systems testbed experimentation, structured analytical modeling, and parallel systems simulation into a comprehensive workflow framework called Pegasus for understanding and improving the overall performance of complex scientific workflows.« less

PANORAMA: An approach to performance modeling and diagnosis of extreme-scale workflows

DOE PAGES

Deelman, Ewa; Carothers, Christopher; Mandal, Anirban; ...

2015-07-14

Here we report that computational science is well established as the third pillar of scientific discovery and is on par with experimentation and theory. However, as we move closer toward the ability to execute exascale calculations and process the ensuing extreme-scale amounts of data produced by both experiments and computations alike, the complexity of managing the compute and data analysis tasks has grown beyond the capabilities of domain scientists. Therefore, workflow management systems are absolutely necessary to ensure current and future scientific discoveries. A key research question for these workflow management systems concerns the performance optimization of complex calculation andmore » data analysis tasks. The central contribution of this article is a description of the PANORAMA approach for modeling and diagnosing the run-time performance of complex scientific workflows. This approach integrates extreme-scale systems testbed experimentation, structured analytical modeling, and parallel systems simulation into a comprehensive workflow framework called Pegasus for understanding and improving the overall performance of complex scientific workflows.« less

FISSA: A neuropil decontamination toolbox for calcium imaging signals.

PubMed

Keemink, Sander W; Lowe, Scott C; Pakan, Janelle M P; Dylda, Evelyn; van Rossum, Mark C W; Rochefort, Nathalie L

2018-02-22

In vivo calcium imaging has become a method of choice to image neuronal population activity throughout the nervous system. These experiments generate large sequences of images. Their analysis is computationally intensive and typically involves motion correction, image segmentation into regions of interest (ROIs), and extraction of fluorescence traces from each ROI. Out of focus fluorescence from surrounding neuropil and other cells can strongly contaminate the signal assigned to a given ROI. In this study, we introduce the FISSA toolbox (Fast Image Signal Separation Analysis) for neuropil decontamination. Given pre-defined ROIs, the FISSA toolbox automatically extracts the surrounding local neuropil and performs blind-source separation with non-negative matrix factorization. Using both simulated and in vivo data, we show that this toolbox performs similarly or better than existing published methods. FISSA requires only little RAM, and allows for fast processing of large datasets even on a standard laptop. The FISSA toolbox is available in Python, with an option for MATLAB format outputs, and can easily be integrated into existing workflows. It is available from Github and the standard Python repositories.

Overcoming Barriers to Technology Adoption in Small Manufacturing Enterprises (SMEs)

DTIC Science & Technology

2003-06-01

automates quote-generation, order - processing workflow management, perform- ance analysis, and accounting functions. Ultimately, it will enable Magdic...that Magdic imple- ment an MES instead. The MES, in addition to solving the problem of document manage- ment, would automate quote-generation, order ... processing , workflow management, perform- ance analysis, and accounting functions. To help Magdic personnel learn about the MES, TIDE personnel provided

Human Systems Integration Design Environment (HSIDE)

DTIC Science & Technology

2012-04-09

quality of the resulting HSI products. 15. SUBJECT TERMS HSI , Manning Estimation and Validation , Risk Assessment, I POE, PLM, BPMN , Workflow...business process model in Business Process Modeling Notation ( BPMN ) or the actual workflow template associated with the specific functional area, again...as filtered by the user settings in the high level interface. Figure 3 shows the initial screen which allows the user to select either the BPMN or

WE-AB-BRA-07: Quantitative Evaluation of 2D-2D and 2D-3D Image Guided Radiation Therapy for Clinical Trial Credentialing, NRG Oncology/RTOG

DOE Office of Scientific and Technical Information (OSTI.GOV)

Giaddui, T; Yu, J; Xiao, Y

Purpose: 2D-2D kV image guided radiation therapy (IGRT) credentialing evaluation for clinical trial qualification was historically qualitative through submitting screen captures of the fusion process. However, as quantitative DICOM 2D-2D and 2D-3D image registration tools are implemented in clinical practice for better precision, especially in centers that treat patients with protons, better IGRT credentialing techniques are needed. The aim of this work is to establish methodologies for quantitatively reviewing IGRT submissions based on DICOM 2D-2D and 2D-3D image registration and to test the methodologies in reviewing 2D-2D and 2D-3D IGRT submissions for RTOG/NRG Oncology clinical trials qualifications. Methods: DICOM 2D-2Dmore » and 2D-3D automated and manual image registration have been tested using the Harmony tool in MIM software. 2D kV orthogonal portal images are fused with the reference digital reconstructed radiographs (DRR) in the 2D-2D registration while the 2D portal images are fused with DICOM planning CT image in the 2D-3D registration. The Harmony tool allows alignment of the two images used in the registration process and also calculates the required shifts. Shifts calculated using MIM are compared with those submitted by institutions for IGRT credentialing. Reported shifts are considered to be acceptable if differences are less than 3mm. Results: Several tests have been performed on the 2D-2D and 2D-3D registration. The results indicated good agreement between submitted and calculated shifts. A workflow for reviewing these IGRT submissions has been developed and will eventually be used to review IGRT submissions. Conclusion: The IROC Philadelphia RTQA center has developed and tested a new workflow for reviewing DICOM 2D-2D and 2D-3D IGRT credentialing submissions made by different cancer clinical centers, especially proton centers. NRG Center for Innovation in Radiation Oncology (CIRO) and IROC RTQA center continue their collaborative efforts to enhance quality assurance services and to be consistently adaptive to the new advances in radiation therapy. This project was supported by NCI grants U10CA180868, U10CA180822, U24CA180803, U24CA12014 and PA CURE Grant.« less

ibex: An open infrastructure software platform to facilitate collaborative work in radiomics

PubMed Central

Zhang, Lifei; Fried, David V.; Fave, Xenia J.; Hunter, Luke A.; Court, Laurence E.

2015-01-01

Purpose: Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (ibex), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. Methods: The ibex software package was developed using the matlab and c/c++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, ibex is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, ibex provides an integrated development environment on top of matlab and c/c++, so users are not limited to its built-in functions. In the ibex developer studio, users can plug in, debug, and test new algorithms, extending ibex’s functionality. ibex also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the ibex workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Results: Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the ibex software to be intuitive, powerful, and easy to use. ibex can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone ibex and ibex’s source code can be downloaded. Conclusions: The authors successfully implemented ibex, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation. PMID:25735289

STSE: Spatio-Temporal Simulation Environment Dedicated to Biology.

PubMed

Stoma, Szymon; Fröhlich, Martina; Gerber, Susanne; Klipp, Edda

2011-04-28

Recently, the availability of high-resolution microscopy together with the advancements in the development of biomarkers as reporters of biomolecular interactions increased the importance of imaging methods in molecular cell biology. These techniques enable the investigation of cellular characteristics like volume, size and geometry as well as volume and geometry of intracellular compartments, and the amount of existing proteins in a spatially resolved manner. Such detailed investigations opened up many new areas of research in the study of spatial, complex and dynamic cellular systems. One of the crucial challenges for the study of such systems is the design of a well stuctured and optimized workflow to provide a systematic and efficient hypothesis verification. Computer Science can efficiently address this task by providing software that facilitates handling, analysis, and evaluation of biological data to the benefit of experimenters and modelers. The Spatio-Temporal Simulation Environment (STSE) is a set of open-source tools provided to conduct spatio-temporal simulations in discrete structures based on microscopy images. The framework contains modules to digitize, represent, analyze, and mathematically model spatial distributions of biochemical species. Graphical user interface (GUI) tools provided with the software enable meshing of the simulation space based on the Voronoi concept. In addition, it supports to automatically acquire spatial information to the mesh from the images based on pixel luminosity (e.g. corresponding to molecular levels from microscopy images). STSE is freely available either as a stand-alone version or included in the linux live distribution Systems Biology Operational Software (SB.OS) and can be downloaded from http://www.stse-software.org/. The Python source code as well as a comprehensive user manual and video tutorials are also offered to the research community. We discuss main concepts of the STSE design and workflow. We demonstrate it's usefulness using the example of a signaling cascade leading to formation of a morphological gradient of Fus3 within the cytoplasm of the mating yeast cell Saccharomyces cerevisiae. STSE is an efficient and powerful novel platform, designed for computational handling and evaluation of microscopic images. It allows for an uninterrupted workflow including digitization, representation, analysis, and mathematical modeling. By providing the means to relate the simulation to the image data it allows for systematic, image driven model validation or rejection. STSE can be scripted and extended using the Python language. STSE should be considered rather as an API together with workflow guidelines and a collection of GUI tools than a stand alone application. The priority of the project is to provide an easy and intuitive way of extending and customizing software using the Python language.

IBEX: an open infrastructure software platform to facilitate collaborative work in radiomics.

PubMed

Zhang, Lifei; Fried, David V; Fave, Xenia J; Hunter, Luke A; Yang, Jinzhong; Court, Laurence E

2015-03-01

Radiomics, which is the high-throughput extraction and analysis of quantitative image features, has been shown to have considerable potential to quantify the tumor phenotype. However, at present, a lack of software infrastructure has impeded the development of radiomics and its applications. Therefore, the authors developed the imaging biomarker explorer (IBEX), an open infrastructure software platform that flexibly supports common radiomics workflow tasks such as multimodality image data import and review, development of feature extraction algorithms, model validation, and consistent data sharing among multiple institutions. The IBEX software package was developed using the MATLAB and c/c++ programming languages. The software architecture deploys the modern model-view-controller, unit testing, and function handle programming concepts to isolate each quantitative imaging analysis task, to validate if their relevant data and algorithms are fit for use, and to plug in new modules. On one hand, IBEX is self-contained and ready to use: it has implemented common data importers, common image filters, and common feature extraction algorithms. On the other hand, IBEX provides an integrated development environment on top of MATLAB and c/c++, so users are not limited to its built-in functions. In the IBEX developer studio, users can plug in, debug, and test new algorithms, extending IBEX's functionality. IBEX also supports quality assurance for data and feature algorithms: image data, regions of interest, and feature algorithm-related data can be reviewed, validated, and/or modified. More importantly, two key elements in collaborative workflows, the consistency of data sharing and the reproducibility of calculation result, are embedded in the IBEX workflow: image data, feature algorithms, and model validation including newly developed ones from different users can be easily and consistently shared so that results can be more easily reproduced between institutions. Researchers with a variety of technical skill levels, including radiation oncologists, physicists, and computer scientists, have found the IBEX software to be intuitive, powerful, and easy to use. IBEX can be run at any computer with the windows operating system and 1GB RAM. The authors fully validated the implementation of all importers, preprocessing algorithms, and feature extraction algorithms. Windows version 1.0 beta of stand-alone IBEX and IBEX's source code can be downloaded. The authors successfully implemented IBEX, an open infrastructure software platform that streamlines common radiomics workflow tasks. Its transparency, flexibility, and portability can greatly accelerate the pace of radiomics research and pave the way toward successful clinical translation.

Phantom-less bone mineral density (BMD) measurement using dual energy computed tomography-based 3-material decomposition

NASA Astrophysics Data System (ADS)

Hofmann, Philipp; Sedlmair, Martin; Krauss, Bernhard; Wichmann, Julian L.; Bauer, Ralf W.; Flohr, Thomas G.; Mahnken, Andreas H.

2016-03-01

Osteoporosis is a degenerative bone disease usually diagnosed at the manifestation of fragility fractures, which severely endanger the health of especially the elderly. To ensure timely therapeutic countermeasures, noninvasive and widely applicable diagnostic methods are required. Currently the primary quantifiable indicator for bone stability, bone mineral density (BMD), is obtained either by DEXA (Dual-energy X-ray absorptiometry) or qCT (quantitative CT). Both have respective advantages and disadvantages, with DEXA being considered as gold standard. For timely diagnosis of osteoporosis, another CT-based method is presented. A Dual Energy CT reconstruction workflow is being developed to evaluate BMD by evaluating lumbar spine (L1-L4) DE-CT images. The workflow is ROI-based and automated for practical use. A dual energy 3-material decomposition algorithm is used to differentiate bone from soft tissue and fat attenuation. The algorithm uses material attenuation coefficients on different beam energy levels. The bone fraction of the three different tissues is used to calculate the amount of hydroxylapatite in the trabecular bone of the corpus vertebrae inside a predefined ROI. Calibrations have been performed to obtain volumetric bone mineral density (vBMD) without having to add a calibration phantom or to use special scan protocols or hardware. Accuracy and precision are dependent on image noise and comparable to qCT images. Clinical indications are in accordance with the DEXA gold standard. The decomposition-based workflow shows bone degradation effects normally not visible on standard CT images which would induce errors in normal qCT results.

SF3M software: 3-D photo-reconstruction for non-expert users and its application to a gully network

NASA Astrophysics Data System (ADS)

Castillo, C.; James, M. R.; Redel-Macías, M. D.; Pérez, R.; Gómez, J. A.

2015-08-01

Three-dimensional photo-reconstruction (PR) techniques have been successfully used to produce high-resolution surface models for different applications and over different spatial scales. However, innovative approaches are required to overcome some limitations that this technique may present for field image acquisition in challenging scene geometries. Here, we evaluate SF3M, a new graphical user interface for implementing a complete PR workflow based on freely available software (including external calls to VisualSFM and CloudCompare), in combination with a low-cost survey design for the reconstruction of a several-hundred-metres-long gully network. SF3M provided a semi-automated workflow for 3-D reconstruction requiring ~ 49 h (of which only 17 % required operator assistance) for obtaining a final gully network model of > 17 million points over a gully plan area of 4230 m2. We show that a walking itinerary along the gully perimeter using two lightweight automatic cameras (1 s time-lapse mode) and a 6 m long pole is an efficient method for 3-D monitoring of gullies, at a low cost (~ EUR 1000 budget for the field equipment) and the time requirements (~ 90 min for image collection). A mean error of 6.9 cm at the ground control points was found, mainly due to model deformations derived from the linear geometry of the gully and residual errors in camera calibration. The straightforward image collection and processing approach can be of great benefit for non-expert users working on gully erosion assessment.

Automatic segmentation and supervised learning-based selection of nuclei in cancer tissue images.

PubMed

Nandy, Kaustav; Gudla, Prabhakar R; Amundsen, Ryan; Meaburn, Karen J; Misteli, Tom; Lockett, Stephen J

2012-09-01

Analysis of preferential localization of certain genes within the cell nuclei is emerging as a new technique for the diagnosis of breast cancer. Quantitation requires accurate segmentation of 100-200 cell nuclei in each tissue section to draw a statistically significant result. Thus, for large-scale analysis, manual processing is too time consuming and subjective. Fortuitously, acquired images generally contain many more nuclei than are needed for analysis. Therefore, we developed an integrated workflow that selects, following automatic segmentation, a subpopulation of accurately delineated nuclei for positioning of fluorescence in situ hybridization-labeled genes of interest. Segmentation was performed by a multistage watershed-based algorithm and screening by an artificial neural network-based pattern recognition engine. The performance of the workflow was quantified in terms of the fraction of automatically selected nuclei that were visually confirmed as well segmented and by the boundary accuracy of the well-segmented nuclei relative to a 2D dynamic programming-based reference segmentation method. Application of the method was demonstrated for discriminating normal and cancerous breast tissue sections based on the differential positioning of the HES5 gene. Automatic results agreed with manual analysis in 11 out of 14 cancers, all four normal cases, and all five noncancerous breast disease cases, thus showing the accuracy and robustness of the proposed approach. Published 2012 Wiley Periodicals, Inc.

Running Neuroimaging Applications on Amazon Web Services: How, When, and at What Cost?

PubMed

Madhyastha, Tara M; Koh, Natalie; Day, Trevor K M; Hernández-Fernández, Moises; Kelley, Austin; Peterson, Daniel J; Rajan, Sabreena; Woelfer, Karl A; Wolf, Jonathan; Grabowski, Thomas J

2017-01-01

The contribution of this paper is to identify and describe current best practices for using Amazon Web Services (AWS) to execute neuroimaging workflows "in the cloud." Neuroimaging offers a vast set of techniques by which to interrogate the structure and function of the living brain. However, many of the scientists for whom neuroimaging is an extremely important tool have limited training in parallel computation. At the same time, the field is experiencing a surge in computational demands, driven by a combination of data-sharing efforts, improvements in scanner technology that allow acquisition of images with higher image resolution, and by the desire to use statistical techniques that stress processing requirements. Most neuroimaging workflows can be executed as independent parallel jobs and are therefore excellent candidates for running on AWS, but the overhead of learning to do so and determining whether it is worth the cost can be prohibitive. In this paper we describe how to identify neuroimaging workloads that are appropriate for running on AWS, how to benchmark execution time, and how to estimate cost of running on AWS. By benchmarking common neuroimaging applications, we show that cloud computing can be a viable alternative to on-premises hardware. We present guidelines that neuroimaging labs can use to provide a cluster-on-demand type of service that should be familiar to users, and scripts to estimate cost and create such a cluster.

Design requirements for radiology workstations.

PubMed

Moise, Adrian; Atkins, M Stella

2004-06-01

This article stresses the importance of capturing feedback from representative users in the early stages of product development. We present our solution to producing quality requirement specifications for radiology workstations, specifications that remain valid over time because we successfully anticipated the industry trends and the user's needs. We present the results from a user study performed in December 1999 in a radiology clinic equipped with state-of-the-art Picture Archiving and Communications Systems (PACS) and imaging scanners. The study involved eight radiologists who answered questions and provided comments on three complementary research topics. First, we asked our subjects to enumerate the advantages and the disadvantages for both softcopy and hardcopy reading. We identified the two major factors for productivity improvement through the use of PACS workstations: workflow re-engineering and process automation. Second, we collected radiologist feedback on the use of hanging protocols (HPs). The results indicated the high importance of automatic image organization through HPs, with the potential effect of reducing the interpretation time by 10-20%. Our subjects estimated that 10-15 HPs would cover about 85%-95% of the regular radiological examinations. Third, we investigated the impact of the display devices on the radiologist's workflow. Our results indicated that the number and the properties of the monitors is a modality-specific requirement. The main results from this study on key functional requirements for softcopy interpretation only recently were incorporated in most of the current, successful PACS workstations.

Scientific workflows as productivity tools for drug discovery.

PubMed

Shon, John; Ohkawa, Hitomi; Hammer, Juergen

2008-05-01

Large pharmaceutical companies annually invest tens to hundreds of millions of US dollars in research informatics to support their early drug discovery processes. Traditionally, most of these investments are designed to increase the efficiency of drug discovery. The introduction of do-it-yourself scientific workflow platforms has enabled research informatics organizations to shift their efforts toward scientific innovation, ultimately resulting in a possible increase in return on their investments. Unlike the handling of most scientific data and application integration approaches, researchers apply scientific workflows to in silico experimentation and exploration, leading to scientific discoveries that lie beyond automation and integration. This review highlights some key requirements for scientific workflow environments in the pharmaceutical industry that are necessary for increasing research productivity. Examples of the application of scientific workflows in research and a summary of recent platform advances are also provided.

A Computational Workflow for the Automated Generation of Models of Genetic Designs.

PubMed

Misirli, Göksel; Nguyen, Tramy; McLaughlin, James Alastair; Vaidyanathan, Prashant; Jones, Timothy S; Densmore, Douglas; Myers, Chris; Wipat, Anil

2018-06-05

Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modeling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs. Despite several automated model construction approaches, computational methodologies to bridge knowledge in design repositories and the process of creating computational models have still not been established. This paper describes a workflow for automatic generation of computational models of genetic circuits from data stored in design repositories using existing standards. This workflow leverages the software tool SBOLDesigner to build structural models that are then enriched by the Virtual Parts Repository API using Systems Biology Open Language (SBOL) data fetched from the SynBioHub design repository. The iBioSim software tool is then utilized to convert this SBOL description into a computational model encoded using the Systems Biology Markup Language (SBML). Finally, this SBML model can be simulated using a variety of methods. This workflow provides synthetic biologists with easy to use tools to create predictable biological systems, hiding away the complexity of building computational models. This approach can further be incorporated into other computational workflows for design automation.

Accessing eSDO Solar Image Processing and Visualization through AstroGrid

NASA Astrophysics Data System (ADS)

Auden, E.; Dalla, S.

2008-08-01

The eSDO project is funded by the UK's Science and Technology Facilities Council (STFC) to integrate Solar Dynamics Observatory (SDO) data, algorithms, and visualization tools with the UK's Virtual Observatory project, AstroGrid. In preparation for the SDO launch in January 2009, the eSDO team has developed nine algorithms covering coronal behaviour, feature recognition, and global / local helioseismology. Each of these algorithms has been deployed as an AstroGrid Common Execution Architecture (CEA) application so that they can be included in complex VO workflows. In addition, the PLASTIC-enabled eSDO "Streaming Tool" online movie application allows users to search multi-instrument solar archives through AstroGrid web services and visualise the image data through galleries, an interactive movie viewing applet, and QuickTime movies generated on-the-fly.

Intelligent services for discovery of complex geospatial features from remote sensing imagery

NASA Astrophysics Data System (ADS)

Yue, Peng; Di, Liping; Wei, Yaxing; Han, Weiguo

2013-09-01

Remote sensing imagery has been commonly used by intelligence analysts to discover geospatial features, including complex ones. The overwhelming volume of routine image acquisition requires automated methods or systems for feature discovery instead of manual image interpretation. The methods of extraction of elementary ground features such as buildings and roads from remote sensing imagery have been studied extensively. The discovery of complex geospatial features, however, is still rather understudied. A complex feature, such as a Weapon of Mass Destruction (WMD) proliferation facility, is spatially composed of elementary features (e.g., buildings for hosting fuel concentration machines, cooling towers, transportation roads, and fences). Such spatial semantics, together with thematic semantics of feature types, can be used to discover complex geospatial features. This paper proposes a workflow-based approach for discovery of complex geospatial features that uses geospatial semantics and services. The elementary features extracted from imagery are archived in distributed Web Feature Services (WFSs) and discoverable from a catalogue service. Using spatial semantics among elementary features and thematic semantics among feature types, workflow-based service chains can be constructed to locate semantically-related complex features in imagery. The workflows are reusable and can provide on-demand discovery of complex features in a distributed environment.

Study on user interface of pathology picture archiving and communication system.

PubMed

Kim, Dasueran; Kang, Peter; Yun, Jungmin; Park, Sung-Hye; Seo, Jeong-Wook; Park, Peom

2014-01-01

It is necessary to improve the pathology workflow. A workflow task analysis was performed using a pathology picture archiving and communication system (pathology PACS) in order to propose a user interface for the Pathology PACS considering user experience. An interface analysis of the Pathology PACS in Seoul National University Hospital and a task analysis of the pathology workflow were performed by observing recorded video. Based on obtained results, a user interface for the Pathology PACS was proposed. Hierarchical task analysis of Pathology PACS was classified into 17 tasks including 1) pre-operation, 2) text, 3) images, 4) medical record viewer, 5) screen transition, 6) pathology identification number input, 7) admission date input, 8) diagnosis doctor, 9) diagnosis code, 10) diagnosis, 11) pathology identification number check box, 12) presence or absence of images, 13) search, 14) clear, 15) Excel save, 16) search results, and 17) re-search. And frequently used menu items were identified and schematized. A user interface for the Pathology PACS considering user experience could be proposed as a preliminary step, and this study may contribute to the development of medical information systems based on user experience and usability.

Meta-manager: a requirements analysis.

PubMed

Cook, J F; Rozenblit, J W; Chacko, A K; Martinez, R; Timboe, H L

1999-05-01

The digital imaging network-picture-archiving and communications system (DIN-PACS) will be implemented in ten sites within the Great Plains Regional Medical Command (GPRMC). This network of PACS and teleradiology technology over a shared T1 network has opened the door for round the clock radiology coverage of all sites. However, the concept of a virtual radiology environment poses new issues for military medicine. A new workflow management system must be developed. This workflow management system will allow us to efficiently resolve these issues including quality of care, availability, severe capitation, and quality of the workforce. The design process of this management system must employ existing technology, operate over various telecommunication networks and protocols, be independent of platform operating systems, be flexible and scaleable, and involve the end user at the outset in the design process for which it is developed. Using the unified modeling language (UML), the specifications for this new business management system were created in concert between the University of Arizona and the GPRMC. These specifications detail a management system operating through a common object request brokered architecture (CORBA) environment. In this presentation, we characterize the Meta-Manager management system including aspects of intelligence, interfacility routing, fail-safe operations, and expected improvements in patient care and efficiency.

A filmless radiology department in a full digital regional hospital: quantitative evaluation of the increased quality and efficiency.

PubMed

Nitrosi, Andrea; Borasi, Giovanni; Nicoli, Franco; Modigliani, Gino; Botti, Andrea; Bertolini, Marco; Notari, Pietro

2007-06-01

Reggio Emilia hospital installed Picture Archiving and Communications Systems (PACS) as the final step towards a completely digital clinical environment completing the HIS/EMR and 1,400 web/terminals for patient information access. Financial benefits throughout the hospital were assessed upfront and measured periodically. Key indicators (radiology exam turnaround time, number of radiology procedures performed, inpatients length of stay before and after the PACS implementation, etc.) were analyzed and values were statistically tested to assess workflow and productivity improvements. The hospital went "filmless" in 28 weeks. Between the half of 2004 and the respective period in 2003, overall Radiology Department productivity increased by 12%, TAT improved by more than 60%. Timelier patient care resulted in decreased lengths of stay. Neurology alone experienced a 12% improvement in average patient stay. To quantify the impact of PACS on the average hospital stays and the expected productivity benefits to inpatient productivity were used a "high level" and a "detailed" business model. Annual financial upsides have exceeded $1.9 millions/year. A well-planned PACS deployment simplifies imaging workflow and improves patient care throughout the hospital while delivering substantial financial benefits. Staff buy-in was the key in this process and on-going training and process monitoring are a must.

AtomPy: an open atomic-data curation environment

NASA Astrophysics Data System (ADS)

Bautista, Manuel; Mendoza, Claudio; Boswell, Josiah S; Ajoku, Chukwuemeka

2014-06-01

We present a cloud-computing environment for atomic data curation, networking among atomic data providers and users, teaching-and-learning, and interfacing with spectral modeling software. The system is based on Google-Drive Sheets, Pandas (Python Data Analysis Library) DataFrames, and IPython Notebooks for open community-driven curation of atomic data for scientific and technological applications. The atomic model for each ionic species is contained in a multi-sheet Google-Drive workbook, where the atomic parameters from all known public sources are progressively stored. Metadata (provenance, community discussion, etc.) accompanying every entry in the database are stored through Notebooks. Education tools on the physics of atomic processes as well as their relevance to plasma and spectral modeling are based on IPython Notebooks that integrate written material, images, videos, and active computer-tool workflows. Data processing workflows and collaborative software developments are encouraged and managed through the GitHub social network. Relevant issues this platform intends to address are: (i) data quality by allowing open access to both data producers and users in order to attain completeness, accuracy, consistency, provenance and currentness; (ii) comparisons of different datasets to facilitate accuracy assessment; (iii) downloading to local data structures (i.e. Pandas DataFrames) for further manipulation and analysis by prospective users; and (iv) data preservation by avoiding the discard of outdated sets.

Numerical modelling of fluid-rock interactions: Lessons learnt from carbonate rocks diagenesis studies

NASA Astrophysics Data System (ADS)

Nader, Fadi; Bachaud, Pierre; Michel, Anthony

2015-04-01

Quantitative assessment of fluid-rock interactions and their impact on carbonate host-rocks has recently become a very attractive research topic within academic and industrial realms. Today, a common operational workflow that aims at predicting the relevant diagenetic processes on the host rocks (i.e. fluid-rock interactions) consists of three main stages: i) constructing a conceptual diagenesis model including inferred preferential fluids pathways; ii) quantifying the resulted diagenetic phases (e.g. depositing cements, dissolved and recrystallized minerals); and iii) numerical modelling of diagenetic processes. Most of the concepts of diagenetic processes operate at the larger, basin-scale, however, the description of the diagenetic phases (products of such processes) and their association with the overall petrophysical evolution of sedimentary rocks remain at reservoir (and even outcrop/ well core) scale. Conceptual models of diagenetic processes are thereafter constructed based on studying surface-exposed rocks and well cores (e.g. petrography, geochemistry, fluid inclusions). We are able to quantify the diagenetic products with various evolving techniques and on varying scales (e.g. point-counting, 2D and 3D image analysis, XRD, micro-CT and pore network models). Geochemical modelling makes use of thermodynamic and kinetic rules as well as data-bases to simulate chemical reactions and fluid-rock interactions. This can be through a 0D model, whereby a certain process is tested (e.g. the likelihood of a certain chemical reaction to operate under specific conditions). Results relate to the fluids and mineral phases involved in the chemical reactions. They could be used as arguments to support or refute proposed outcomes of fluid-rock interactions. Coupling geochemical modelling with transport (reactive transport model; 1D, 2D and 3D) is another possibility, attractive as it provides forward simulations of diagenetic processes and resulting phases. This contribution is based on several studies that were undertaken on carbonate rocks diagenesis in some of the major reservoir rocks in the Middle East and outcrop analogues in Europe. Here, the main processes at hand are related to fracture-related dolomitization and carbonate dissolution. We would like to present the workflows we have followed and the questioning that resulted for a series of case studies. The way forward, seems evident as the integration of workflows and numerical modelling tools at different scales, bringing better constrains on the boundary data and less uncertainty.

Workflow Automation: A Collective Case Study

ERIC Educational Resources Information Center

Harlan, Jennifer

2013-01-01

Knowledge management has proven to be a sustainable competitive advantage for many organizations. Knowledge management systems are abundant, with multiple functionalities. The literature reinforces the use of workflow automation with knowledge management systems to benefit organizations; however, it was not known if process automation yielded…

Device and methods for "gold standard" registration of clinical 3D and 2D cerebral angiograms

NASA Astrophysics Data System (ADS)

Madan, Hennadii; Likar, Boštjan; Pernuš, Franjo; Å piclin, Žiga

2015-03-01

Translation of any novel and existing 3D-2D image registration methods into clinical image-guidance systems is limited due to lack of their objective validation on clinical image datasets. The main reason is that, besides the calibration of the 2D imaging system, a reference or "gold standard" registration is very difficult to obtain on clinical image datasets. In the context of cerebral endovascular image-guided interventions (EIGIs), we present a calibration device in the form of a headband with integrated fiducial markers and, secondly, propose an automated pipeline comprising 3D and 2D image processing, analysis and annotation steps, the result of which is a retrospective calibration of the 2D imaging system and an optimal, i.e., "gold standard" registration of 3D and 2D images. The device and methods were used to create the "gold standard" on 15 datasets of 3D and 2D cerebral angiograms, whereas each dataset was acquired on a patient undergoing EIGI for either aneurysm coiling or embolization of arteriovenous malformation. The use of the device integrated seamlessly in the clinical workflow of EIGI. While the automated pipeline eliminated all manual input or interactive image processing, analysis or annotation. In this way, the time to obtain the "gold standard" was reduced from 30 to less than one minute and the "gold standard" of 3D-2D registration on all 15 datasets of cerebral angiograms was obtained with a sub-0.1 mm accuracy.

Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data.

PubMed

Davidson, Robert L; Weber, Ralf J M; Liu, Haoyu; Sharma-Oates, Archana; Viant, Mark R

2016-01-01

Metabolomics is increasingly recognized as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other omics fields. To achieve its full potential, including the integration of multiple omics modalities, the accessibility, standardization and reproducibility of computational metabolomics tools must be improved significantly. Here we present our end-to-end mass spectrometry metabolomics workflow in the widely used platform, Galaxy. Named Galaxy-M, our workflow has been developed for both direct infusion mass spectrometry (DIMS) and liquid chromatography mass spectrometry (LC-MS) metabolomics. The range of tools presented spans from processing of raw data, e.g. peak picking and alignment, through data cleansing, e.g. missing value imputation, to preparation for statistical analysis, e.g. normalization and scaling, and principal components analysis (PCA) with associated statistical evaluation. We demonstrate the ease of using these Galaxy workflows via the analysis of DIMS and LC-MS datasets, and provide PCA scores and associated statistics to help other users to ensure that they can accurately repeat the processing and analysis of these two datasets. Galaxy and data are all provided pre-installed in a virtual machine (VM) that can be downloaded from the GigaDB repository. Additionally, source code, executables and installation instructions are available from GitHub. The Galaxy platform has enabled us to produce an easily accessible and reproducible computational metabolomics workflow. More tools could be added by the community to expand its functionality. We recommend that Galaxy-M workflow files are included within the supplementary information of publications, enabling metabolomics studies to achieve greater reproducibility.

Evaluation of Standardization of Transfer of Accountability between Inpatient Pharmacists.

PubMed

Tsoi, Vivian; Dewhurst, Norman; Tom, Elaine

2018-01-01

A compelling body of evidence supports the notion that transfer of accountability (TOA) improves communication, continuity of care, and patient safety. TOA involves the transmission and receipt of information between clinicians at each transition of care. Without a notification system alerting pharmacists to patient transfers, pharmacists' ability to seek out and complete TOA may be hindered. A standardized policy and process for TOA, with automated workflow, was implemented at the study hospital in 2015, to ensure consistency and timeliness of documentation by pharmacists. To evaluate pharmacists' adherence to and satisfaction with the TOA policy and process. A retrospective audit was conducted, using a random sample of individuals who were inpatients between June 2014 and February 2016. Transition points for TOA were identified, and the computerized pharmacy system was reviewed to determine whether TOA had been documented at each transition point. After the audit, an online survey was distributed to assess pharmacists' response to and satisfaction with the TOA policy and workflow. Before the TOA workflow was implemented, TOA documentation by pharmacists ranged from 11% (10/93) to 43% (48/111) of transitions. Eight months after implementation of the workflow, the rate of TOA documentation was 87% (68/78), exceeding the institution's target of 70%. Of the 32 pharmacists surveyed, most were satisfied with the TOA policy and agreed that the standardized workflow was simple to use, increased the number of TOAs provided and received, and improved the quality of completed TOAs. Respondents also indicated that the TOA workflow had improved patient care (mean score 4.09/5, standard deviation 0.64). The standardized TOA policy and process were well received by pharmacists, and resulted in consistent TOA documentation and a TOA documentation rate that exceeded the institutional target.

KNIME for reproducible cross-domain analysis of life science data.

PubMed

Fillbrunn, Alexander; Dietz, Christian; Pfeuffer, Julianus; Rahn, René; Landrum, Gregory A; Berthold, Michael R

2017-11-10

Experiments in the life sciences often involve tools from a variety of domains such as mass spectrometry, next generation sequencing, or image processing. Passing the data between those tools often involves complex scripts for controlling data flow, data transformation, and statistical analysis. Such scripts are not only prone to be platform dependent, they also tend to grow as the experiment progresses and are seldomly well documented, a fact that hinders the reproducibility of the experiment. Workflow systems such as KNIME Analytics Platform aim to solve these problems by providing a platform for connecting tools graphically and guaranteeing the same results on different operating systems. As an open source software, KNIME allows scientists and programmers to provide their own extensions to the scientific community. In this review paper we present selected extensions from the life sciences that simplify data exploration, analysis, and visualization and are interoperable due to KNIME's unified data model. Additionally, we name other workflow systems that are commonly used in the life sciences and highlight their similarities and differences to KNIME. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

The Symbiotic Relationship between Scientific Workflow and Provenance (Invited)

NASA Astrophysics Data System (ADS)

Stephan, E.

2010-12-01

The purpose of this presentation is to describe the symbiotic nature of scientific workflows and provenance. We will also discuss the current trends and real world challenges facing these two distinct research areas. Although motivated differently, the needs of the international science communities are the glue that binds this relationship together. Understanding and articulating the science drivers to these communities is paramount as these technologies evolve and mature. Originally conceived for managing business processes, workflows are now becoming invaluable assets in both computational and experimental sciences. These reconfigurable, automated systems provide essential technology to perform complex analyses by coupling together geographically distributed disparate data sources and applications. As a result, workflows are capable of higher throughput in a shorter amount of time than performing the steps manually. Today many different workflow products exist; these could include Kepler and Taverna or similar products like MeDICI, developed at PNNL, that are standardized on the Business Process Execution Language (BPEL). Provenance, originating from the French term Provenir “to come from”, is used to describe the curation process of artwork as art is passed from owner to owner. The concept of provenance was adopted by digital libraries as a means to track the lineage of documents while standards such as the DublinCore began to emerge. In recent years the systems science community has increasingly expressed the need to expand the concept of provenance to formally articulate the history of scientific data. Communities such as the International Provenance and Annotation Workshop (IPAW) have formalized a provenance data model. The Open Provenance Model, and the W3C is hosting a provenance incubator group featuring the Proof Markup Language. Although both workflows and provenance have risen from different communities and operate independently, their mutual success is tied together, forming a symbiotic relationship where research and development advances in one effort can provide tremendous benefits to the other. For example, automating provenance extraction within scientific applications is still a relatively new concept; the workflow engine provides the framework to capture application specific operations, inputs, and resulting data. It provides a description of the process history and data flow by wrapping workflow components around the applications and data sources. On the other hand, a lack of cooperation between workflows and provenance can inhibit usefulness of both to science. Blindly tracking the execution history without having a true understanding of what kinds of questions end users may have makes the provenance indecipherable to the target users. Over the past nine years PNNL has been actively involved in provenance research in support of computational chemistry, molecular dynamics, biology, hydrology, and climate. PNNL has also been actively involved in efforts by the international community to develop open standards for provenance and the development of architectures to support provenance capture, storage, and querying. This presentation will provide real world use cases of how provenance and workflow can be leveraged and implemented to meet different needs and the challenges that lie ahead.

A Community-Driven Workflow Recommendations and Reuse Infrastructure

NASA Astrophysics Data System (ADS)

Zhang, J.; Votava, P.; Lee, T. J.; Lee, C.; Xiao, S.; Nemani, R. R.; Foster, I.

2013-12-01

Aiming to connect the Earth science community to accelerate the rate of discovery, NASA Earth Exchange (NEX) has established an online repository and platform, so that researchers can publish and share their tools and models with colleagues. In recent years, workflow has become a popular technique at NEX for Earth scientists to define executable multi-step procedures for data processing and analysis. The ability to discover and reuse knowledge (sharable workflows or workflow) is critical to the future advancement of science. However, as reported in our earlier study, the reusability of scientific artifacts at current time is very low. Scientists often do not feel confident in using other researchers' tools and utilities. One major reason is that researchers are often unaware of the existence of others' data preprocessing processes. Meanwhile, researchers often do not have time to fully document the processes and expose them to others in a standard way. These issues cannot be overcome by the existing workflow search technologies used in NEX and other data projects. Therefore, this project aims to develop a proactive recommendation technology based on collective NEX user behaviors. In this way, we aim to promote and encourage process and workflow reuse within NEX. Particularly, we focus on leveraging peer scientists' best practices to support the recommendation of artifacts developed by others. Our underlying theoretical foundation is rooted in the social cognitive theory, which declares people learn by watching what others do. Our fundamental hypothesis is that sharable artifacts have network properties, much like humans in social networks. More generally, reusable artifacts form various types of social relationships (ties), and may be viewed as forming what organizational sociologists who use network analysis to study human interactions call a 'knowledge network.' In particular, we will tackle two research questions: R1: What hidden knowledge may be extracted from usage history to help Earth scientists better understand existing artifacts and how to use them in a proper manner? R2: Informed by insights derived from their computing contexts, how could such hidden knowledge be used to facilitate artifact reuse by Earth scientists? Our study of the two research questions will provide answers to three technical questions aiming to assist NEX users during workflow development: 1) How to determine what topics interest the researcher? 2) How to find appropriate artifacts? and 3) How to advise the researcher in artifact reuse? In this paper, we report our on-going efforts of leveraging social networking theory and analysis techniques to provide dynamic advice on artifact reuse to NEX users based on their surrounding contexts. As a proof of concept, we have designed and developed a plug-in to the VisTrails workflow design tool. When users develop workflows using VisTrails, our plug-in will proactively recommend most relevant sub-workflows to the users.

Scientific Workflow Management in Proteomics

PubMed Central

de Bruin, Jeroen S.; Deelder, André M.; Palmblad, Magnus

2012-01-01

Data processing in proteomics can be a challenging endeavor, requiring extensive knowledge of many different software packages, all with different algorithms, data format requirements, and user interfaces. In this article we describe the integration of a number of existing programs and tools in Taverna Workbench, a scientific workflow manager currently being developed in the bioinformatics community. We demonstrate how a workflow manager provides a single, visually clear and intuitive interface to complex data analysis tasks in proteomics, from raw mass spectrometry data to protein identifications and beyond. PMID:22411703

Ergonomic design for dental offices.

PubMed

Ahearn, David J; Sanders, Martha J; Turcotte, Claudia

2010-01-01

The increasing complexity of the dental office environment influences productivity and workflow for dental clinicians. Advances in technology, and with it the range of products needed to provide services, have led to sprawl in operatory setups and the potential for awkward postures for dental clinicians during the delivery of oral health services. Although ergonomics often addresses the prevention of musculoskeletal disorders for specific populations of workers, concepts of workflow and productivity are integral to improved practice in work environments. This article provides suggestions for improving workflow and productivity for dental clinicians. The article applies ergonomic principles to dental practice issues such as equipment and supply management, office design, and workflow management. Implications for improved ergonomic processes and future research are explored.