Platform for Quantitative Evaluation of Spatial Intratumoral Heterogeneity in Multiplexed Fluorescence Images.

PubMed

Spagnolo, Daniel M; Al-Kofahi, Yousef; Zhu, Peihong; Lezon, Timothy R; Gough, Albert; Stern, Andrew M; Lee, Adrian V; Ginty, Fiona; Sarachan, Brion; Taylor, D Lansing; Chennubhotla, S Chakra

2017-11-01

We introduce THRIVE (Tumor Heterogeneity Research Interactive Visualization Environment), an open-source tool developed to assist cancer researchers in interactive hypothesis testing. The focus of this tool is to quantify spatial intratumoral heterogeneity (ITH), and the interactions between different cell phenotypes and noncellular constituents. Specifically, we foresee applications in phenotyping cells within tumor microenvironments, recognizing tumor boundaries, identifying degrees of immune infiltration and epithelial/stromal separation, and identification of heterotypic signaling networks underlying microdomains. The THRIVE platform provides an integrated workflow for analyzing whole-slide immunofluorescence images and tissue microarrays, including algorithms for segmentation, quantification, and heterogeneity analysis. THRIVE promotes flexible deployment, a maintainable code base using open-source libraries, and an extensible framework for customizing algorithms with ease. THRIVE was designed with highly multiplexed immunofluorescence images in mind, and, by providing a platform to efficiently analyze high-dimensional immunofluorescence signals, we hope to advance these data toward mainstream adoption in cancer research. Cancer Res; 77(21); e71-74. ©2017 AACR . ©2017 American Association for Cancer Research.

Constraint processing in our extensible language for cooperative imaging system

NASA Astrophysics Data System (ADS)

Aoki, Minoru; Murao, Yo; Enomoto, Hajime

1996-02-01

The extensible WELL (Window-based elaboration language) has been developed using the concept of common platform, where both client and server can communicate with each other with support from a communication manager. This extensible language is based on an object oriented design by introducing constraint processing. Any kind of services including imaging in the extensible language is controlled by the constraints. Interactive functions between client and server are extended by introducing agent functions including a request-respond relation. Necessary service integrations are satisfied with some cooperative processes using constraints. Constraints are treated similarly to data, because the system should have flexibilities in the execution of many kinds of services. The similar control process is defined by using intentional logic. There are two kinds of constraints, temporal and modal constraints. Rendering the constraints, the predicate format as the relation between attribute values can be a warrant for entities' validity as data. As an imaging example, a processing procedure of interaction between multiple objects is shown as an image application for the extensible system. This paper describes how the procedure proceeds in the system, and that how the constraints work for generating moving pictures.

ART-ML - a novel XML format for the biological procedures modeling and the representation of blood flow simulation.

PubMed

Karvounis, E C; Tsakanikas, V D; Fotiou, E; Fotiadis, D I

2010-01-01

The paper proposes a novel Extensible Markup Language (XML) based format called ART-ML that aims at supporting the interoperability and the reuse of models of blood flow, mass transport and plaque formation, exported by ARTool. ARTool is a platform for the automatic processing of various image modalities of coronary and carotid arteries. The images and their content are fused to develop morphological models of the arteries in easy to handle 3D representations. The platform incorporates efficient algorithms which are able to perform blood flow simulation. In addition atherosclerotic plaque development is estimated taking into account morphological, flow and genetic factors. ART-ML provides a XML format that enables the representation and management of embedded models within the ARTool platform and the storage and interchange of well-defined information. This approach influences in the model creation, model exchange, model reuse and result evaluation.

The Open Microscopy Environment: open image informatics for the biological sciences

NASA Astrophysics Data System (ADS)

Blackburn, Colin; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gault, David; Gillen, Kenneth; Leigh, Roger; Leo, Simone; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, Josh; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Swedlow, Jason R.

2016-07-01

Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

A new tool for supervised classification of satellite images available on web servers: Google Maps as a case study

NASA Astrophysics Data System (ADS)

García-Flores, Agustín.; Paz-Gallardo, Abel; Plaza, Antonio; Li, Jun

2016-10-01

This paper describes a new web platform dedicated to the classification of satellite images called Hypergim. The current implementation of this platform enables users to perform classification of satellite images from any part of the world thanks to the worldwide maps provided by Google Maps. To perform this classification, Hypergim uses unsupervised algorithms like Isodata and K-means. Here, we present an extension of the original platform in which we adapt Hypergim in order to use supervised algorithms to improve the classification results. This involves a significant modification of the user interface, providing the user with a way to obtain samples of classes present in the images to use in the training phase of the classification process. Another main goal of this development is to improve the runtime of the image classification process. To achieve this goal, we use a parallel implementation of the Random Forest classification algorithm. This implementation is a modification of the well-known CURFIL software package. The use of this type of algorithms to perform image classification is widespread today thanks to its precision and ease of training. The actual implementation of Random Forest was developed using CUDA platform, which enables us to exploit the potential of several models of NVIDIA graphics processing units using them to execute general purpose computing tasks as image classification algorithms. As well as CUDA, we use other parallel libraries as Intel Boost, taking advantage of the multithreading capabilities of modern CPUs. To ensure the best possible results, the platform is deployed in a cluster of commodity graphics processing units (GPUs), so that multiple users can use the tool in a concurrent way. The experimental results indicate that this new algorithm widely outperform the previous unsupervised algorithms implemented in Hypergim, both in runtime as well as precision of the actual classification of the images.

BIRD: Bio-Image Referral Database. Design and implementation of a new web based and patient multimedia data focused system for effective medical diagnosis and therapy.

PubMed

Pinciroli, Francesco; Masseroli, Marco; Acerbo, Livio A; Bonacina, Stefano; Ferrari, Roberto; Marchente, Mario

2004-01-01

This paper presents a low cost software platform prototype supporting health care personnel in retrieving patient referral multimedia data. These information are centralized in a server machine and structured by using a flexible eXtensible Markup Language (XML) Bio-Image Referral Database (BIRD). Data are distributed on demand to requesting client in an Intranet network and transformed via eXtensible Stylesheet Language (XSL) to be visualized in an uniform way on market browsers. The core server operation software has been developed in PHP Hypertext Preprocessor scripting language, which is very versatile and useful for crafting a dynamic Web environment.

LesionTracker: Extensible Open-Source Zero-Footprint Web Viewer for Cancer Imaging Research and Clinical Trials.

PubMed

Urban, Trinity; Ziegler, Erik; Lewis, Rob; Hafey, Chris; Sadow, Cheryl; Van den Abbeele, Annick D; Harris, Gordon J

2017-11-01

Oncology clinical trials have become increasingly dependent upon image-based surrogate endpoints for determining patient eligibility and treatment efficacy. As therapeutics have evolved and multiplied in number, the tumor metrics criteria used to characterize therapeutic response have become progressively more varied and complex. The growing intricacies of image-based response evaluation, together with rising expectations for rapid and consistent results reporting, make it difficult for site radiologists to adequately address local and multicenter imaging demands. These challenges demonstrate the need for advanced cancer imaging informatics tools that can help ensure protocol-compliant image evaluation while simultaneously promoting reviewer efficiency. LesionTracker is a quantitative imaging package optimized for oncology clinical trial workflows. The goal of the project is to create an open source zero-footprint viewer for image analysis that is designed to be extensible as well as capable of being integrated into third-party systems for advanced imaging tools and clinical trials informatics platforms. Cancer Res; 77(21); e119-22. ©2017 AACR . ©2017 American Association for Cancer Research.

ImagePy: an open-source, Python-based and platform-independent software package for boimage analysis.

PubMed

Wang, Anliang; Yan, Xiaolong; Wei, Zhijun

2018-04-27

This note presents the design of a scalable software package named ImagePy for analysing biological images. Our contribution is concentrated on facilitating extensibility and interoperability of the software through decoupling the data model from the user interface. Especially with assistance from the Python ecosystem, this software framework makes modern computer algorithms easier to be applied in bioimage analysis. ImagePy is free and open source software, with documentation and code available at https://github.com/Image-Py/imagepy under the BSD license. It has been tested on the Windows, Mac and Linux operating systems. wzjdlut@dlut.edu.cn or yxdragon@imagepy.org.

Aptamer-Targeted Gold Nanoparticles As Molecular-Specific Contrast Agents for Reflectance Imaging

PubMed Central

2008-01-01

Targeted metallic nanoparticles have shown potential as a platform for development of molecular-specific contrast agents. Aptamers have recently been demonstrated as ideal candidates for molecular targeting applications. In this study, we investigated the development of aptamer-based gold nanoparticles as contrast agents, using aptamers as targeting agents and gold nanoparticles as imaging agents. We devised a novel conjugation approach using an extended aptamer design where the extension is complementary to an oligonucleotide sequence attached to the surface of the gold nanoparticles. The chemical and optical properties of the aptamer−gold conjugates were characterized using size measurements and oligonucleotide quantitation assays. We demonstrate this conjugation approach to create a contrast agent designed for detection of prostate-specific membrane antigen (PSMA), obtaining reflectance images of PSMA(+) and PSMA(−) cell lines treated with the anti-PSMA aptamer−gold conjugates. This design strategy can easily be modified to incorporate multifunctional agents as part of a multimodal platform for reflectance imaging applications. PMID:18512972

Ultrahigh phase-stable swept-source optical coherence tomography as a cardiac imaging platform (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ling, Yuye; Hendon, Christine P.

2016-02-01

Functional extensions to optical coherence tomography (OCT) provide useful imaging contrasts that are complementary to conventional OCT. Our goal is to characterize tissue types within the myocardial due to remodeling and therapy. High-speed imaging is necessary to extract mechanical properties and dynamics of fiber orientation changes in a beating heart. Functional extensions of OCT such as polarization sensitive and optical coherence elastography (OCE) require high phase stability of the system, which is a drawback of current mechanically tuned swept source OCT systems. Here we present a high-speed functional imaging platform, which includes an ultrahigh-phase-stable swept source equipped with KTN deflector from NTT-AT. The swept source does not require mechanical movements during the wavelength sweeping; it is electrically tuned. The inter-sweep phase variance of the system was measured to be less than 300 ps at a path length difference of ~2 mm. The axial resolution of the system is 20 µm and the -10 dB fall-off depth is about 3.2 mm. The sample arm has an 8 mmx8 mm field of view with a lateral resolution of approximately 18 µm. The sample arm uses a two-axis MEMS mirror, which is programmable and capable of scanning arbitrary patterns at a sampling rate of 50 kHz. Preliminary imaging results showed differences in polarization properties and image penetration in ablated and normal myocardium. In the future, we will conduct dynamic stretching experiments with strips of human myocardial tissue to characterize mechanical properties using OCE. With high speed imaging of 200 kHz and an all-fiber design, we will work towards catheter-based functional imaging.

3D Slicer as an Image Computing Platform for the Quantitative Imaging Network

PubMed Central

Fedorov, Andriy; Beichel, Reinhard; Kalpathy-Cramer, Jayashree; Finet, Julien; Fillion-Robin, Jean-Christophe; Pujol, Sonia; Bauer, Christian; Jennings, Dominique; Fennessy, Fiona; Sonka, Milan; Buatti, John; Aylward, Stephen; Miller, James V.; Pieper, Steve; Kikinis, Ron

2012-01-01

Quantitative analysis has tremendous but mostly unrealized potential in healthcare to support objective and accurate interpretation of the clinical imaging. In 2008, the National Cancer Institute began building the Quantitative Imaging Network (QIN) initiative with the goal of advancing quantitative imaging in the context of personalized therapy and evaluation of treatment response. Computerized analysis is an important component contributing to reproducibility and efficiency of the quantitative imaging techniques. The success of quantitative imaging is contingent on robust analysis methods and software tools to bring these methods from bench to bedside. 3D Slicer is a free open source software application for medical image computing. As a clinical research tool, 3D Slicer is similar to a radiology workstation that supports versatile visualizations but also provides advanced functionality such as automated segmentation and registration for a variety of application domains. Unlike a typical radiology workstation, 3D Slicer is free and is not tied to specific hardware. As a programming platform, 3D Slicer facilitates translation and evaluation of the new quantitative methods by allowing the biomedical researcher to focus on the implementation of the algorithm, and providing abstractions for the common tasks of data communication, visualization and user interface development. Compared to other tools that provide aspects of this functionality, 3D Slicer is fully open source and can be readily extended and redistributed. In addition, 3D Slicer is designed to facilitate the development of new functionality in the form of 3D Slicer extensions. In this paper, we present an overview of 3D Slicer as a platform for prototyping, development and evaluation of image analysis tools for clinical research applications. To illustrate the utility of the platform in the scope of QIN, we discuss several use cases of 3D Slicer by the existing QIN teams, and we elaborate on the future directions that can further facilitate development and validation of imaging biomarkers using 3D Slicer. PMID:22770690

Quantitative Radiomics System Decoding the Tumor Phenotype | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Our goal is to construct a publicly available computational radiomics system for the objective and automated extraction of quantitative imaging features that we believe will yield biomarkers of greater prognostic value compared with routinely extracted descriptors of tumor size. We will create a generalized, open, portable, and extensible radiomics platform that is widely applicable across cancer types and imaging modalities and describe how we will use lung and head and neck cancers as models to validate our developments.

WiseEye: Next Generation Expandable and Programmable Camera Trap Platform for Wildlife Research.

PubMed

Nazir, Sajid; Newey, Scott; Irvine, R Justin; Verdicchio, Fabio; Davidson, Paul; Fairhurst, Gorry; Wal, René van der

2017-01-01

The widespread availability of relatively cheap, reliable and easy to use digital camera traps has led to their extensive use for wildlife research, monitoring and public outreach. Users of these units are, however, often frustrated by the limited options for controlling camera functions, the generation of large numbers of images, and the lack of flexibility to suit different research environments and questions. We describe the development of a user-customisable open source camera trap platform named 'WiseEye', designed to provide flexible camera trap technology for wildlife researchers. The novel platform is based on a Raspberry Pi single-board computer and compatible peripherals that allow the user to control its functions and performance. We introduce the concept of confirmatory sensing, in which the Passive Infrared triggering is confirmed through other modalities (i.e. radar, pixel change) to reduce the occurrence of false positives images. This concept, together with user-definable metadata, aided identification of spurious images and greatly reduced post-collection processing time. When tested against a commercial camera trap, WiseEye was found to reduce the incidence of false positive images and false negatives across a range of test conditions. WiseEye represents a step-change in camera trap functionality, greatly increasing the value of this technology for wildlife research and conservation management.

WiseEye: Next Generation Expandable and Programmable Camera Trap Platform for Wildlife Research

PubMed Central

Nazir, Sajid; Newey, Scott; Irvine, R. Justin; Verdicchio, Fabio; Davidson, Paul; Fairhurst, Gorry; van der Wal, René

2017-01-01

The widespread availability of relatively cheap, reliable and easy to use digital camera traps has led to their extensive use for wildlife research, monitoring and public outreach. Users of these units are, however, often frustrated by the limited options for controlling camera functions, the generation of large numbers of images, and the lack of flexibility to suit different research environments and questions. We describe the development of a user-customisable open source camera trap platform named ‘WiseEye’, designed to provide flexible camera trap technology for wildlife researchers. The novel platform is based on a Raspberry Pi single-board computer and compatible peripherals that allow the user to control its functions and performance. We introduce the concept of confirmatory sensing, in which the Passive Infrared triggering is confirmed through other modalities (i.e. radar, pixel change) to reduce the occurrence of false positives images. This concept, together with user-definable metadata, aided identification of spurious images and greatly reduced post-collection processing time. When tested against a commercial camera trap, WiseEye was found to reduce the incidence of false positive images and false negatives across a range of test conditions. WiseEye represents a step-change in camera trap functionality, greatly increasing the value of this technology for wildlife research and conservation management. PMID:28076444

An all-optronic synthetic aperture lidar

NASA Astrophysics Data System (ADS)

Turbide, Simon; Marchese, Linda; Terroux, Marc; Babin, François; Bergeron, Alain

2012-09-01

Synthetic Aperture Radar (SAR) is a mature technology that overcomes the diffraction limit of an imaging system's real aperture by taking advantage of the platform motion to coherently sample multiple sections of an aperture much larger than the physical one. Synthetic Aperture Lidar (SAL) is the extension of SAR to much shorter wavelengths (1.5 μm vs 5 cm). This new technology can offer higher resolution images in day or night time as well as in certain adverse conditions. It could be a powerful tool for Earth monitoring (ship detection, frontier surveillance, ocean monitoring) from aircraft, unattended aerial vehicle (UAV) or spatial platforms. A continuous flow of high-resolution images covering large areas would however produce a large amount of data involving a high cost in term of post-processing computational time. This paper presents a laboratory demonstration of a SAL system complete with image reconstruction based on optronic processing. This differs from the more traditional digital approach by its real-time processing capability. The SAL system is discussed and images obtained from a non-metallic diffuse target at ranges up to 3m are shown, these images being processed by a real-time optronic SAR processor origiinally designed to reconstruct SAR images from ENVISAT/ASAR data.

Development of a phenotyping platform for high throughput screening of nodal root angle in sorghum.

PubMed

Joshi, Dinesh C; Singh, Vijaya; Hunt, Colleen; Mace, Emma; van Oosterom, Erik; Sulman, Richard; Jordan, David; Hammer, Graeme

2017-01-01

In sorghum, the growth angle of nodal roots is a major component of root system architecture. It strongly influences the spatial distribution of roots of mature plants in the soil profile, which can impact drought adaptation. However, selection for nodal root angle in sorghum breeding programs has been restricted by the absence of a suitable high throughput phenotyping platform. The aim of this study was to develop a phenotyping platform for the rapid, non-destructive and digital measurement of nodal root angle of sorghum at the seedling stage. The phenotyping platform comprises of 500 soil filled root chambers (50 × 45 × 0.3 cm in size), made of transparent perspex sheets that were placed in metal tubs and covered with polycarbonate sheets. Around 3 weeks after sowing, once the first flush of nodal roots was visible, roots were imaged in situ using an imaging box that included two digital cameras that were remotely controlled by two android tablets. Free software ( openGelPhoto.tcl ) allowed precise measurement of nodal root angle from the digital images. The reliability and efficiency of the platform was evaluated by screening a large nested association mapping population of sorghum and a set of hybrids in six independent experimental runs that included up to 500 plants each. The platform revealed extensive genetic variation and high heritability (repeatability) for nodal root angle. High genetic correlations and consistent ranking of genotypes across experimental runs confirmed the reproducibility of the platform. This low cost, high throughput root phenotyping platform requires no sophisticated equipment, is adaptable to most glasshouse environments and is well suited to dissect the genetic control of nodal root angle of sorghum. The platform is suitable for use in sorghum breeding programs aiming to improve drought adaptation through root system architecture manipulation.

Imaging of karsts on buried carbonate platform in Central Luconia Province, Malaysia

NASA Astrophysics Data System (ADS)

Nur Fathiyah Jamaludin, Siti; Mubin, Mukhriz; Latiff, Abdul Halim Abdul

2017-10-01

Imaging of carbonate rocks in the subsurface through seismic method is always challenging due to its heterogeneity and fast velocity compared to the other rock types. Existence of karsts features on the carbonate rocks make it more complicated to interpret the reflectors. Utilization of modern interpretation software such as PETREL and GeoTeric® to image the karsts morphology make it possible to model the karst network within the buried carbonate platform used in this study. Using combination of different seismic attributes such as Variance, Conformance, Continuity, Amplitude, Frequency and Edge attributes, we are able to image the karsts features that are available in the proven gas-field in Central Luconia Province, Malaysia. The mentioned attributes are excellent in visualize and image the stratigraphic features based on the difference in their acoustic impedance as well as structural features, which include karst. 2D & 3D Karst Models were developed to give a better understanding on the characteristics of the identified karsts. From the models, it is found that the karsts are concentrated in the top part of the carbonate reservoir (epikarst) and the middle layer with some of them becomes extensive and create karst networks, either laterally or vertically. Most of the vertical network karst are related to the existence of faults that displaced all the horizons in the carbonate platform.

Imaging of earthquake faults using small UAVs as a pathfinder for air and space observations

USGS Publications Warehouse

Donnellan, Andrea; Green, Joseph; Ansar, Adnan; Aletky, Joseph; Glasscoe, Margaret; Ben-Zion, Yehuda; Arrowsmith, J. Ramón; DeLong, Stephen B.

2017-01-01

Large earthquakes cause billions of dollars in damage and extensive loss of life and property. Geodetic and topographic imaging provide measurements of transient and long-term crustal deformation needed to monitor fault zones and understand earthquakes. Earthquake-induced strain and rupture characteristics are expressed in topographic features imprinted on the landscapes of fault zones. Small UAVs provide an efficient and flexible means to collect multi-angle imagery to reconstruct fine scale fault zone topography and provide surrogate data to determine requirements for and to simulate future platforms for air- and space-based multi-angle imaging.

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 InSAR Scientific Computing Environment

NASA Technical Reports Server (NTRS)

Rosen, Paul A.; Gurrola, Eric; Sacco, Gian Franco; Zebker, Howard

2012-01-01

We have developed a flexible and extensible Interferometric SAR (InSAR) Scientific Computing Environment (ISCE) for geodetic image processing. ISCE was designed from the ground up as a geophysics community tool for generating stacks of interferograms that lend themselves to various forms of time-series analysis, with attention paid to accuracy, extensibility, and modularity. The framework is python-based, with code elements rigorously componentized by separating input/output operations from the processing engines. This allows greater flexibility and extensibility in the data models, and creates algorithmic code that is less susceptible to unnecessary modification when new data types and sensors are available. In addition, the components support provenance and checkpointing to facilitate reprocessing and algorithm exploration. The algorithms, based on legacy processing codes, have been adapted to assume a common reference track approach for all images acquired from nearby orbits, simplifying and systematizing the geometry for time-series analysis. The framework is designed to easily allow user contributions, and is distributed for free use by researchers. ISCE can process data from the ALOS, ERS, EnviSAT, Cosmo-SkyMed, RadarSAT-1, RadarSAT-2, and TerraSAR-X platforms, starting from Level-0 or Level 1 as provided from the data source, and going as far as Level 3 geocoded deformation products. With its flexible design, it can be extended with raw/meta data parsers to enable it to work with radar data from other platforms

CellShape: A user-friendly image analysis tool for quantitative visualization of bacterial cell factories inside.

PubMed

Goñi-Moreno, Ángel; Kim, Juhyun; de Lorenzo, Víctor

2017-02-01

Visualization of the intracellular constituents of individual bacteria while performing as live biocatalysts is in principle doable through more or less sophisticated fluorescence microscopy. Unfortunately, rigorous quantitation of the wealth of data embodied in the resulting images requires bioinformatic tools that are not widely extended within the community-let alone that they are often subject to licensing that impedes software reuse. In this context we have developed CellShape, a user-friendly platform for image analysis with subpixel precision and double-threshold segmentation system for quantification of fluorescent signals stemming from single-cells. CellShape is entirely coded in Python, a free, open-source programming language with widespread community support. For a developer, CellShape enhances extensibility (ease of software improvements) by acting as an interface to access and use existing Python modules; for an end-user, CellShape presents standalone executable files ready to open without installation. We have adopted this platform to analyse with an unprecedented detail the tridimensional distribution of the constituents of the gene expression flow (DNA, RNA polymerase, mRNA and ribosomal proteins) in individual cells of the industrial platform strain Pseudomonas putida KT2440. While the CellShape first release version (v0.8) is readily operational, users and/or developers are enabled to expand the platform further. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

Apte, A; Veeraraghavan, H; Oh, J

Purpose: To present an open source and free platform to facilitate radiomics research — The “Radiomics toolbox” in CERR. Method: There is scarcity of open source tools that support end-to-end modeling of image features to predict patient outcomes. The “Radiomics toolbox” strives to fill the need for such a software platform. The platform supports (1) import of various kinds of image modalities like CT, PET, MR, SPECT, US. (2) Contouring tools to delineate structures of interest. (3) Extraction and storage of image based features like 1st order statistics, gray-scale co-occurrence and zonesize matrix based texture features and shape features andmore » (4) Statistical Analysis. Statistical analysis of the extracted features is supported with basic functionality that includes univariate correlations, Kaplan-Meir curves and advanced functionality that includes feature reduction and multivariate modeling. The graphical user interface and the data management are performed with Matlab for the ease of development and readability of code and features for wide audience. Open-source software developed with other programming languages is integrated to enhance various components of this toolbox. For example: Java-based DCM4CHE for import of DICOM, R for statistical analysis. Results: The Radiomics toolbox will be distributed as an open source, GNU copyrighted software. The toolbox was prototyped for modeling Oropharyngeal PET dataset at MSKCC. The analysis will be presented in a separate paper. Conclusion: The Radiomics Toolbox provides an extensible platform for extracting and modeling image features. To emphasize new uses of CERR for radiomics and image-based research, we have changed the name from the “Computational Environment for Radiotherapy Research” to the “Computational Environment for Radiological Research”.« less

FIRE: an open-software suite for real-time 2D/3D image registration for image guided radiotherapy research

NASA Astrophysics Data System (ADS)

Furtado, H.; Gendrin, C.; Spoerk, J.; Steiner, E.; Underwood, T.; Kuenzler, T.; Georg, D.; Birkfellner, W.

2016-03-01

Radiotherapy treatments have changed at a tremendously rapid pace. Dose delivered to the tumor has escalated while organs at risk (OARs) are better spared. The impact of moving tumors during dose delivery has become higher due to very steep dose gradients. Intra-fractional tumor motion has to be managed adequately to reduce errors in dose delivery. For tumors with large motion such as tumors in the lung, tracking is an approach that can reduce position uncertainty. Tumor tracking approaches range from purely image intensity based techniques to motion estimation based on surrogate tracking. Research efforts are often based on custom designed software platforms which take too much time and effort to develop. To address this challenge we have developed an open software platform especially focusing on tumor motion management. FLIRT is a freely available open-source software platform. The core method for tumor tracking is purely intensity based 2D/3D registration. The platform is written in C++ using the Qt framework for the user interface. The performance critical methods are implemented on the graphics processor using the CUDA extension. One registration can be as fast as 90ms (11Hz). This is suitable to track tumors moving due to respiration (~0.3Hz) or heartbeat (~1Hz). Apart from focusing on high performance, the platform is designed to be flexible and easy to use. Current use cases range from tracking feasibility studies, patient positioning and method validation. Such a framework has the potential of enabling the research community to rapidly perform patient studies or try new methods.

Facile characterization of aptamer kinetic and equilibrium binding properties using surface plasmon resonance

PubMed Central

Chang, Andrew L.; McKeague, Maureen; Smolke, Christina D.

2015-01-01

Nucleic acid aptamers find widespread use as targeting and sensing agents in nature and biotechnology. Their ability to bind an extensive range of molecular targets, including small molecules, proteins, and ions, with high affinity and specificity enables their use in diverse diagnostic, therapeutic, imaging, and gene-regulatory applications. Here, we describe methods for characterizing aptamer kinetic and equilibrium binding properties using a surface plasmon resonance-based platform. This aptamer characterization platform is broadly useful for studying aptamer–ligand interactions, comparing aptamer properties, screening functional aptamers during in vitro selection processes, and prototyping aptamers for integration into nucleic acid devices. PMID:25432760

Three-dimensional scene reconstruction from a two-dimensional image

NASA Astrophysics Data System (ADS)

Parkins, Franz; Jacobs, Eddie

2017-05-01

We propose and simulate a method of reconstructing a three-dimensional scene from a two-dimensional image for developing and augmenting world models for autonomous navigation. This is an extension of the Perspective-n-Point (PnP) method which uses a sampling of the 3D scene, 2D image point parings, and Random Sampling Consensus (RANSAC) to infer the pose of the object and produce a 3D mesh of the original scene. Using object recognition and segmentation, we simulate the implementation on a scene of 3D objects with an eye to implementation on embeddable hardware. The final solution will be deployed on the NVIDIA Tegra platform.

Integrating medical imaging analyses through a high-throughput bundled resource imaging system

NASA Astrophysics Data System (ADS)

Covington, Kelsie; Welch, E. Brian; Jeong, Ha-Kyu; Landman, Bennett A.

2011-03-01

Exploitation of advanced, PACS-centric image analysis and interpretation pipelines provides well-developed storage, retrieval, and archival capabilities along with state-of-the-art data providence, visualization, and clinical collaboration technologies. However, pursuit of integrated medical imaging analysis through a PACS environment can be limiting in terms of the overhead required to validate, evaluate and integrate emerging research technologies. Herein, we address this challenge through presentation of a high-throughput bundled resource imaging system (HUBRIS) as an extension to the Philips Research Imaging Development Environment (PRIDE). HUBRIS enables PACS-connected medical imaging equipment to invoke tools provided by the Java Imaging Science Toolkit (JIST) so that a medical imaging platform (e.g., a magnetic resonance imaging scanner) can pass images and parameters to a server, which communicates with a grid computing facility to invoke the selected algorithms. Generated images are passed back to the server and subsequently to the imaging platform from which the images can be sent to a PACS. JIST makes use of an open application program interface layer so that research technologies can be implemented in any language capable of communicating through a system shell environment (e.g., Matlab, Java, C/C++, Perl, LISP, etc.). As demonstrated in this proof-of-concept approach, HUBRIS enables evaluation and analysis of emerging technologies within well-developed PACS systems with minimal adaptation of research software, which simplifies evaluation of new technologies in clinical research and provides a more convenient use of PACS technology by imaging scientists.

Imaging Complex Protein Metabolism in Live Organisms by Stimulated Raman Scattering Microscopy with Isotope Labeling

PubMed Central

2016-01-01

Protein metabolism, consisting of both synthesis and degradation, is highly complex, playing an indispensable regulatory role throughout physiological and pathological processes. Over recent decades, extensive efforts, using approaches such as autoradiography, mass spectrometry, and fluorescence microscopy, have been devoted to the study of protein metabolism. However, noninvasive and global visualization of protein metabolism has proven to be highly challenging, especially in live systems. Recently, stimulated Raman scattering (SRS) microscopy coupled with metabolic labeling of deuterated amino acids (D-AAs) was demonstrated for use in imaging newly synthesized proteins in cultured cell lines. Herein, we significantly generalize this notion to develop a comprehensive labeling and imaging platform for live visualization of complex protein metabolism, including synthesis, degradation, and pulse–chase analysis of two temporally defined populations. First, the deuterium labeling efficiency was optimized, allowing time-lapse imaging of protein synthesis dynamics within individual live cells with high spatial–temporal resolution. Second, by tracking the methyl group (CH3) distribution attributed to pre-existing proteins, this platform also enables us to map protein degradation inside live cells. Third, using two subsets of structurally and spectroscopically distinct D-AAs, we achieved two-color pulse–chase imaging, as demonstrated by observing aggregate formation of mutant hungtingtin proteins. Finally, going beyond simple cell lines, we demonstrated the imaging ability of protein synthesis in brain tissues, zebrafish, and mice in vivo. Hence, the presented labeling and imaging platform would be a valuable tool to study complex protein metabolism with high sensitivity, resolution, and biocompatibility for a broad spectrum of systems ranging from cells to model animals and possibly to humans. PMID:25560305

A multimodal imaging platform with integrated simultaneous photoacoustic microscopy, optical coherence tomography, optical Doppler tomography and fluorescence microscopy

NASA Astrophysics Data System (ADS)

Dadkhah, Arash; Zhou, Jun; Yeasmin, Nusrat; Jiao, Shuliang

2018-02-01

Various optical imaging modalities with different optical contrast mechanisms have been developed over the past years. Although most of these imaging techniques are being used in many biomedical applications and researches, integration of these techniques will allow researchers to reach the full potential of these technologies. Nevertheless, combining different imaging techniques is always challenging due to the difference in optical and hardware requirements for different imaging systems. Here, we developed a multimodal optical imaging system with the capability of providing comprehensive structural, functional and molecular information of living tissue in micrometer scale. This imaging system integrates photoacoustic microscopy (PAM), optical coherence tomography (OCT), optical Doppler tomography (ODT) and fluorescence microscopy in one platform. Optical-resolution PAM (OR-PAM) provides absorption-based imaging of biological tissues. Spectral domain OCT is able to provide structural information based on the scattering property of biological sample with no need for exogenous contrast agents. In addition, ODT is a functional extension of OCT with the capability of measurement and visualization of blood flow based on the Doppler effect. Fluorescence microscopy allows to reveal molecular information of biological tissue using autofluoresce or exogenous fluorophores. In-vivo as well as ex-vivo imaging studies demonstrated the capability of our multimodal imaging system to provide comprehensive microscopic information on biological tissues. Integrating all the aforementioned imaging modalities for simultaneous multimodal imaging has promising potential for preclinical research and clinical practice in the near future.

A MULTICORE BASED PARALLEL IMAGE REGISTRATION METHOD

PubMed Central

Yang, Lin; Gong, Leiguang; Zhang, Hong; Nosher, John L.; Foran, David J.

2012-01-01

Image registration is a crucial step for many image-assisted clinical applications such as surgery planning and treatment evaluation. In this paper we proposed a landmark based nonlinear image registration algorithm for matching 2D image pairs. The algorithm was shown to be effective and robust under conditions of large deformations. In landmark based registration, the most important step is establishing the correspondence among the selected landmark points. This usually requires an extensive search which is often computationally expensive. We introduced a nonregular data partition algorithm using the K-means clustering algorithm to group the landmarks based on the number of available processing cores. The step optimizes the memory usage and data transfer. We have tested our method using IBM Cell Broadband Engine (Cell/B.E.) platform. PMID:19964921

Low-dose, high-resolution and high-efficiency ptychography at STXM beamline of SSRF

NASA Astrophysics Data System (ADS)

Xu, Zijian; Wang, Chunpeng; Liu, Haigang; Tao, Xulei; Tai, Renzhong

2017-06-01

Ptychography is a diffraction-based X-ray microscopy method that can image extended samples quantitatively while remove the resolution limit imposed by image-forming optical elements. As a natural extension of scanning transmission X-ray microscopy (STXM) imaging method, we developed soft X-ray ptychographic coherent diffraction imaging (PCDI) method at the STXM endstation of BL08U beamline of Shanghai Synchrotron Radiation Facility. Compared to the traditional STXM imaging, the new PCDI method has resulted in significantly lower dose, higher resolution and higher efficiency imaging in our platform. In the demonstration experiments shown here, a spatial resolution of sub-10 nm was obtained for a gold nanowires sample, which is much better than the limit resolution 30 nm of the STXM method, while the radiation dose is only 1/12 of STXM.

The Medical Imaging Interaction Toolkit: challenges and advances : 10 years of open-source development.

PubMed

Nolden, Marco; Zelzer, Sascha; Seitel, Alexander; Wald, Diana; Müller, Michael; Franz, Alfred M; Maleike, Daniel; Fangerau, Markus; Baumhauer, Matthias; Maier-Hein, Lena; Maier-Hein, Klaus H; Meinzer, Hans-Peter; Wolf, Ivo

2013-07-01

The Medical Imaging Interaction Toolkit (MITK) has been available as open-source software for almost 10 years now. In this period the requirements of software systems in the medical image processing domain have become increasingly complex. The aim of this paper is to show how MITK evolved into a software system that is able to cover all steps of a clinical workflow including data retrieval, image analysis, diagnosis, treatment planning, intervention support, and treatment control. MITK provides modularization and extensibility on different levels. In addition to the original toolkit, a module system, micro services for small, system-wide features, a service-oriented architecture based on the Open Services Gateway initiative (OSGi) standard, and an extensible and configurable application framework allow MITK to be used, extended and deployed as needed. A refined software process was implemented to deliver high-quality software, ease the fulfillment of regulatory requirements, and enable teamwork in mixed-competence teams. MITK has been applied by a worldwide community and integrated into a variety of solutions, either at the toolkit level or as an application framework with custom extensions. The MITK Workbench has been released as a highly extensible and customizable end-user application. Optional support for tool tracking, image-guided therapy, diffusion imaging as well as various external packages (e.g. CTK, DCMTK, OpenCV, SOFA, Python) is available. MITK has also been used in several FDA/CE-certified applications, which demonstrates the high-quality software and rigorous development process. MITK provides a versatile platform with a high degree of modularization and interoperability and is well suited to meet the challenging tasks of today's and tomorrow's clinically motivated research.

The ImageJ ecosystem: an open platform for biomedical image analysis

PubMed Central

Schindelin, Johannes; Rueden, Curtis T.; Hiner, Mark C.; Eliceiri, Kevin W.

2015-01-01

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available – from commercial to academic, special-purpose to Swiss army knife, small to large–but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts life science, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. PMID:26153368

The ImageJ ecosystem: An open platform for biomedical image analysis.

PubMed

Schindelin, Johannes; Rueden, Curtis T; Hiner, Mark C; Eliceiri, Kevin W

2015-01-01

Technology in microscopy advances rapidly, enabling increasingly affordable, faster, and more precise quantitative biomedical imaging, which necessitates correspondingly more-advanced image processing and analysis techniques. A wide range of software is available-from commercial to academic, special-purpose to Swiss army knife, small to large-but a key characteristic of software that is suitable for scientific inquiry is its accessibility. Open-source software is ideal for scientific endeavors because it can be freely inspected, modified, and redistributed; in particular, the open-software platform ImageJ has had a huge impact on the life sciences, and continues to do so. From its inception, ImageJ has grown significantly due largely to being freely available and its vibrant and helpful user community. Scientists as diverse as interested hobbyists, technical assistants, students, scientific staff, and advanced biology researchers use ImageJ on a daily basis, and exchange knowledge via its dedicated mailing list. Uses of ImageJ range from data visualization and teaching to advanced image processing and statistical analysis. The software's extensibility continues to attract biologists at all career stages as well as computer scientists who wish to effectively implement specific image-processing algorithms. In this review, we use the ImageJ project as a case study of how open-source software fosters its suites of software tools, making multitudes of image-analysis technology easily accessible to the scientific community. We specifically explore what makes ImageJ so popular, how it impacts the life sciences, how it inspires other projects, and how it is self-influenced by coevolving projects within the ImageJ ecosystem. © 2015 Wiley Periodicals, Inc.

CONRAD—A software framework for cone-beam imaging in radiology

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

Maier, Andreas; Choi, Jang-Hwan; Riess, Christian

2013-11-15

Purpose: In the community of x-ray imaging, there is a multitude of tools and applications that are used in scientific practice. Many of these tools are proprietary and can only be used within a certain lab. Often the same algorithm is implemented multiple times by different groups in order to enable comparison. In an effort to tackle this problem, the authors created CONRAD, a software framework that provides many of the tools that are required to simulate basic processes in x-ray imaging and perform image reconstruction with consideration of nonlinear physical effects.Methods: CONRAD is a Java-based state-of-the-art software platform withmore » extensive documentation. It is based on platform-independent technologies. Special libraries offer access to hardware acceleration such as OpenCL. There is an easy-to-use interface for parallel processing. The software package includes different simulation tools that are able to generate up to 4D projection and volume data and respective vector motion fields. Well known reconstruction algorithms such as FBP, DBP, and ART are included. All algorithms in the package are referenced to a scientific source.Results: A total of 13 different phantoms and 30 processing steps have already been integrated into the platform at the time of writing. The platform comprises 74.000 nonblank lines of code out of which 19% are used for documentation. The software package is available for download at http://conrad.stanford.edu. To demonstrate the use of the package, the authors reconstructed images from two different scanners, a table top system and a clinical C-arm system. Runtimes were evaluated using the RabbitCT platform and demonstrate state-of-the-art runtimes with 2.5 s for the 256 problem size and 12.4 s for the 512 problem size.Conclusions: As a common software framework, CONRAD enables the medical physics community to share algorithms and develop new ideas. In particular this offers new opportunities for scientific collaboration and quantitative performance comparison between the methods of different groups.« less

Immersion and dry scanner extensions for sub-10nm production nodes

NASA Astrophysics Data System (ADS)

Weichselbaum, Stefan; Bornebroek, Frank; de Kort, Toine; Droste, Richard; de Graaf, Roelof F.; van Ballegoij, Rob; Botter, Herman; McLaren, Matthew G.; de Boeij, Wim P.

2015-03-01

Progressing towards the 10nm and 7nm imaging node, pattern-placement and layer-to-layer overlay requirements keep on scaling down and drives system improvements in immersion (ArFi) and dry (ArF/KrF) scanners. A series of module enhancements in the NXT platform have been introduced; among others, the scanner is equipped with exposure stages with better dynamics and thermal control. Grid accuracy improvements with respect to calibration, setup, stability, and layout dependency tighten MMO performance and enable mix and match scanner operation. The same platform improvements also benefit focus control. Improvements in detectability and reproducibility of low contrast alignment marks enhance the alignment solution window for 10nm logic processes and beyond. The system's architecture allows dynamic use of high-order scanner optimization based on advanced actuators of projection lens and scanning stages. This enables a holistic optimization approach for the scanner, the mask, and the patterning process. Productivity scanner design modifications esp. stage speeds and optimization in metrology schemes provide lower layer costs for customers using immersion lithography as well as conventional dry technology. Imaging, overlay, focus, and productivity data is presented, that demonstrates 10nm and 7nm node litho-capability for both (immersion & dry) platforms.

AstroCloud: An Agile platform for data visualization and specific analyzes in 2D and 3D

NASA Astrophysics Data System (ADS)

Molina, F. Z.; Salgado, R.; Bergel, A.; Infante, A.

2017-07-01

Nowadays, astronomers commonly run their own tools, or distributed computational packages, for data analysis and then visualizing the results with generic applications. This chain of processes comes at high cost: (a) analyses are manually applied, they are therefore difficult to be automatized, and (b) data have to be serialized, thus increasing the cost of parsing and saving intermediary data. We are developing AstroCloud, an agile visualization multipurpose platform intended for specific analyses of astronomical images (https://astrocloudy.wordpress.com). This platform incorporates domain-specific languages which make it easily extensible. AstroCloud supports customized plug-ins, which translate into time reduction on data analysis. Moreover, it also supports 2D and 3D rendering, including interactive features in real time. AstroCloud is under development, we are currently implementing different choices for data reduction and physical analyzes.

Assessing UAV platform types and optical sensor specifications

NASA Astrophysics Data System (ADS)

Altena, B.; Goedemé, T.

2014-05-01

Photogrammetric acquisition with unmanned aerial vehicles (UAV) has grown extensively over the last couple of years. Such mobile platforms and their processing software have matured, resulting in a market which offers off-the-shelf mapping solutions to surveying companies and geospatial enterprises. Different approaches in platform type and optical instruments exist, though its resulting products have similar specifications. To demonstrate differences in acquisitioning practice, a case study over an open mine was flown with two different off-the-shelf UAVs (a fixed-wing and a multi-rotor). The resulting imagery is analyzed to clarify the differences in collection quality. We look at image settings, and stress the fact of photographic experience if manual setting are applied. For mapping production it might be safest to set the camera on automatic. Furthermore, we try to estimate if blur is present due to image motion. A subtle trend seems to be present, for the fast flying platform though its extent is of similar order to the slow moving one. It shows both systems operate at their limits. Finally, the lens distortion is assessed with special attention to chromatic aberration. Here we see that through calibration such aberrations could be present, however detecting this phenomena directly on imagery is not straightforward. For such effects a normal lens is sufficient, though a better lens and collimator does give significant improvement.

Far Ultraviolet Imaging from the Image Spacecraft

NASA Technical Reports Server (NTRS)

Mende, S. B.; Heetderks, H.; Frey, H. U.; Lampton, M.; Geller, S. P.; Stock, J. M.; Abiad, R.; Siegmund, O. H. W.; Tremsin, A. S.; Habraken, S.

2000-01-01

Direct imaging of the magnetosphere by the IMAGE spacecraft will be supplemented by observation of the global aurora. The IMAGE satellite instrument complement includes three Far Ultraviolet (FUV) instruments. The Wideband Imaging Camera (WIC) will provide broad band ultraviolet images of the aurora for maximum spatial and temporal resolution by imaging the LBH N2 bands of the aurora. The Spectrographic Imager (SI), a novel form of monochromatic imager, will image the aurora, filtered by wavelength. The proton-induced component of the aurora will be imaged separately by measuring the Doppler-shifted Lyman-a. Finally, the GEO instrument will observe the distribution of the geocoronal emission to obtain the neutral background density source for charge exchange in the magnetosphere. The FUV instrument complement looks radially outward from the rotating IMAGE satellite and, therefore, it spends only a short time observing the aurora and the Earth during each spin. To maximize photon collection efficiency and use efficiently the short time available for exposures the FUV auroral imagers WIC and SI both have wide fields of view and take data continuously as the auroral region proceeds through the field of view. To minimize data volume, the set of multiple images are electronically co-added by suitably shifting each image to compensate for the spacecraft rotation. In order to minimize resolution loss, the images have to be distort ion-corrected in real time. The distortion correction is accomplished using high speed look up tables that are pre-generated by least square fitting to polynomial functions by the on-orbit processor. The instruments were calibrated individually while on stationary platforms, mostly in vacuum chambers. Extensive ground-based testing was performed with visible and near UV simulators mounted on a rotating platform to emulate their performance on a rotating spacecraft.

Methods for analyzing optical observations of tsunami-induced signatures in airglow emissions from ground-based and space-based platforms

NASA Astrophysics Data System (ADS)

Grawe, M.; Makela, J. J.

2016-12-01

Airglow imaging of the 630.0-nm redline emission has emerged as a useful tool for studying the properties of tsunami-ionospheric coupling in recent years, offering spatially continuous coverage of the sky with a single instrument. Past studies have shown that airglow signatures induced by tsunamis are inherently anisotropic due to the observation geometry and effects from the geomagnetic field. Here, we present details behind the techniques used to determine the parameters of the signature (orientation, wavelength, etc) with potential extensions to real or quasi-real time and a tool for interpreting the location and strength of the signatures in the field of view. We demonstrate application of the techniques to ground-based optical measurements of several tsunami-induced signatures taking place over the past five years from an imaging system in Hawaii. Additionally, these methods are extended for use on space-based observation platforms, offering advantages over ground-based installations.

3-D interactive visualisation tools for Hi spectral line imaging

NASA Astrophysics Data System (ADS)

van der Hulst, J. M.; Punzo, D.; Roerdink, J. B. T. M.

2017-06-01

Upcoming HI surveys will deliver such large datasets that automated processing using the full 3-D information to find and characterize HI objects is unavoidable. Full 3-D visualization is an essential tool for enabling qualitative and quantitative inspection and analysis of the 3-D data, which is often complex in nature. Here we present SlicerAstro, an open-source extension of 3DSlicer, a multi-platform open source software package for visualization and medical image processing, which we developed for the inspection and analysis of HI spectral line data. We describe its initial capabilities, including 3-D filtering, 3-D selection and comparative modelling.

76 FR 61750 - Vehicle-Mounted Elevating and Rotating Work Platforms (Aerial Lifts); Extension of the Office of...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-05

...] Vehicle-Mounted Elevating and Rotating Work Platforms (Aerial Lifts); Extension of the Office of... requirement contained in the Standard on Vehicle-Mounted Elevating and Rotating Work Platforms (Aerial Lifts... by ensuring that aerial lifts are in safe operating condition. DATES: Comments must be submitted...

Magnetic Levitation Coupled with Portable Imaging and Analysis for Disease Diagnostics.

PubMed

Knowlton, Stephanie M; Yenilmez, Bekir; Amin, Reza; Tasoglu, Savas

2017-02-19

Currently, many clinical diagnostic procedures are complex, costly, inefficient, and inaccessible to a large population in the world. The requirements for specialized equipment and trained personnel require that many diagnostic tests be performed at remote, centralized clinical laboratories. Magnetic levitation is a simple yet powerful technique and can be applied to levitate cells, which are suspended in a paramagnetic solution and placed in a magnetic field, at a position determined by equilibrium between a magnetic force and a buoyancy force. Here, we present a versatile platform technology designed for point-of-care diagnostics which uses magnetic levitation coupled to microscopic imaging and automated analysis to determine the density distribution of a patient's cells as a useful diagnostic indicator. We present two platforms operating on this principle: (i) a smartphone-compatible version of the technology, where the built-in smartphone camera is used to image cells in the magnetic field and a smartphone application processes the images and to measures the density distribution of the cells and (ii) a self-contained version where a camera board is used to capture images and an embedded processing unit with attached thin-film-transistor (TFT) screen measures and displays the results. Demonstrated applications include: (i) measuring the altered distribution of a cell population with a disease phenotype compared to a healthy phenotype, which is applied to sickle cell disease diagnosis, and (ii) separation of different cell types based on their characteristic densities, which is applied to separate white blood cells from red blood cells for white blood cell cytometry. These applications, as well as future extensions of the essential density-based measurements enabled by this portable, user-friendly platform technology, will significantly enhance disease diagnostic capabilities at the point of care.

76 FR 1192 - Standard on Powered Platforms for Building Maintenance; Extension of the Office of Management and...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-07

...] Standard on Powered Platforms for Building Maintenance; Extension of the Office of Management and Budget's... specified in its Standard on Powered Platforms for Building Maintenance (29 CFR 1910.66). DATES: Comments... Building Maintenance (29 CFR 1910.66). The Agency is requesting to retain its current burden hour total of...

A cross-platform freeware tool for digital reconstruction of neuronal arborizations from image stacks.

PubMed

Brown, Kerry M; Donohue, Duncan E; D'Alessandro, Giampaolo; Ascoli, Giorgio A

2005-01-01

Digital reconstruction of neuronal arborizations is an important step in the quantitative investigation of cellular neuroanatomy. In this process, neurites imaged by microscopy are semi-manually traced through the use of specialized computer software and represented as binary trees of branching cylinders (or truncated cones). Such form of the reconstruction files is efficient and parsimonious, and allows extensive morphometric analysis as well as the implementation of biophysical models of electrophysiology. Here, we describe Neuron_ Morpho, a plugin for the popular Java application ImageJ that mediates the digital reconstruction of neurons from image stacks. Both the executable and code of Neuron_ Morpho are freely distributed (www.maths. soton.ac.uk/staff/D'Alessandro/morpho or www.krasnow.gmu.edu/L-Neuron), and are compatible with all major computer platforms (including Windows, Mac, and Linux). We tested Neuron_Morpho by reconstructing two neurons from each of the two preparations representing different brain areas (hippocampus and cerebellum), neuritic type (pyramidal cell dendrites and olivar axonal projection terminals), and labeling method (rapid Golgi impregnation and anterograde dextran amine), and quantitatively comparing the resulting morphologies to those of the same cells reconstructed with the standard commercial system, Neurolucida. None of the numerous morphometric measures that were analyzed displayed any significant or systematic difference between the two reconstructing systems.

Simulation of nanoparticle-mediated near-infrared thermal therapy using GATE

PubMed Central

Cuplov, Vesna; Pain, Frédéric; Jan, Sébastien

2017-01-01

Application of nanotechnology for biomedicine in cancer therapy allows for direct delivery of anticancer agents to tumors. An example of such therapies is the nanoparticle-mediated near-infrared hyperthermia treatment. In order to investigate the influence of nanoparticle properties on the spatial distribution of heat in the tumor and healthy tissues, accurate simulations are required. The Geant4 Application for Emission Tomography (GATE) open-source simulation platform, based on the Geant4 toolkit, is widely used by the research community involved in molecular imaging, radiotherapy and optical imaging. We present an extension of GATE that can model nanoparticle-mediated hyperthermal therapy as well as simple heat diffusion in biological tissues. This new feature of GATE combined with optical imaging allows for the simulation of a theranostic scenario in which the patient is injected with theranostic nanosystems that can simultaneously deliver therapeutic (i.e. hyperthermia therapy) and imaging agents (i.e. fluorescence imaging). PMID:28663855

AGScan: a pluggable microarray image quantification software based on the ImageJ library.

PubMed

Cathelin, R; Lopez, F; Klopp, Ch

2007-01-15

Many different programs are available to analyze microarray images. Most programs are commercial packages, some are free. In the latter group only few propose automatic grid alignment and batch mode. More often than not a program implements only one quantification algorithm. AGScan is an open source program that works on all major platforms. It is based on the ImageJ library [Rasband (1997-2006)] and offers a plug-in extension system to add new functions to manipulate images, align grid and quantify spots. It is appropriate for daily laboratory use and also as a framework for new algorithms. The program is freely distributed under X11 Licence. The install instructions can be found in the user manual. The software can be downloaded from http://mulcyber.toulouse.inra.fr/projects/agscan/. The questions and plug-ins can be sent to the contact listed below.

Validation of ALFIA: a platform for quantifying near-infrared fluorescent images of lymphatic propulsion in humans

NASA Astrophysics Data System (ADS)

Rasmussen, John C.; Bautista, Merrick; Tan, I.-Chih; Adams, Kristen E.; Aldrich, Melissa; Marshall, Milton V.; Fife, Caroline E.; Maus, Erik A.; Smith, Latisha A.; Zhang, Jingdan; Xiang, Xiaoyan; Zhou, Shaohua Kevin; Sevick-Muraca, Eva M.

2011-02-01

Recently, we demonstrated near-infrared (NIR) fluorescence imaging for quantifying real-time lymphatic propulsion in humans following intradermal injections of microdose amounts of indocyanine green. However computational methods for image analysis are underdeveloped, hindering the translation and clinical adaptation of NIR fluorescent lymphatic imaging. In our initial work we used ImageJ and custom MatLab programs to manually identify lymphatic vessels and individual propulsion events using the temporal transit of the fluorescent dye. In addition, we extracted the apparent velocities of contractile propagation and time periods between propulsion events. Extensive time and effort were required to analyze the 6-8 gigabytes of NIR fluorescent images obtained for each subject. To alleviate this bottleneck, we commenced development of ALFIA, an integrated software platform which will permit automated, near real-time analysis of lymphatic function using NIR fluorescent imaging. However, prior to automation, the base algorithms calculating the apparent velocity and period must be validated to verify that they produce results consistent with the proof-of-concept programs. To do this, both methods were used to analyze NIR fluorescent images of two subjects and the number of propulsive events identified, the average apparent velocities, and the average periods for each subject were compared. Paired Student's t-tests indicate that the differences between their average results are not significant. With the base algorithms validated, further development and automation of ALFIA can be realized, significantly reducing the amount of user interaction required, and potentially enabling the near real-time, clinical evaluation of NIR fluorescent lymphatic imaging.

A high-performance spatial database based approach for pathology imaging algorithm evaluation

PubMed Central

Wang, Fusheng; Kong, Jun; Gao, Jingjing; Cooper, Lee A.D.; Kurc, Tahsin; Zhou, Zhengwen; Adler, David; Vergara-Niedermayr, Cristobal; Katigbak, Bryan; Brat, Daniel J.; Saltz, Joel H.

2013-01-01

Background: Algorithm evaluation provides a means to characterize variability across image analysis algorithms, validate algorithms by comparison with human annotations, combine results from multiple algorithms for performance improvement, and facilitate algorithm sensitivity studies. The sizes of images and image analysis results in pathology image analysis pose significant challenges in algorithm evaluation. We present an efficient parallel spatial database approach to model, normalize, manage, and query large volumes of analytical image result data. This provides an efficient platform for algorithm evaluation. Our experiments with a set of brain tumor images demonstrate the application, scalability, and effectiveness of the platform. Context: The paper describes an approach and platform for evaluation of pathology image analysis algorithms. The platform facilitates algorithm evaluation through a high-performance database built on the Pathology Analytic Imaging Standards (PAIS) data model. Aims: (1) Develop a framework to support algorithm evaluation by modeling and managing analytical results and human annotations from pathology images; (2) Create a robust data normalization tool for converting, validating, and fixing spatial data from algorithm or human annotations; (3) Develop a set of queries to support data sampling and result comparisons; (4) Achieve high performance computation capacity via a parallel data management infrastructure, parallel data loading and spatial indexing optimizations in this infrastructure. Materials and Methods: We have considered two scenarios for algorithm evaluation: (1) algorithm comparison where multiple result sets from different methods are compared and consolidated; and (2) algorithm validation where algorithm results are compared with human annotations. We have developed a spatial normalization toolkit to validate and normalize spatial boundaries produced by image analysis algorithms or human annotations. The validated data were formatted based on the PAIS data model and loaded into a spatial database. To support efficient data loading, we have implemented a parallel data loading tool that takes advantage of multi-core CPUs to accelerate data injection. The spatial database manages both geometric shapes and image features or classifications, and enables spatial sampling, result comparison, and result aggregation through expressive structured query language (SQL) queries with spatial extensions. To provide scalable and efficient query support, we have employed a shared nothing parallel database architecture, which distributes data homogenously across multiple database partitions to take advantage of parallel computation power and implements spatial indexing to achieve high I/O throughput. Results: Our work proposes a high performance, parallel spatial database platform for algorithm validation and comparison. This platform was evaluated by storing, managing, and comparing analysis results from a set of brain tumor whole slide images. The tools we develop are open source and available to download. Conclusions: Pathology image algorithm validation and comparison are essential to iterative algorithm development and refinement. One critical component is the support for queries involving spatial predicates and comparisons. In our work, we develop an efficient data model and parallel database approach to model, normalize, manage and query large volumes of analytical image result data. Our experiments demonstrate that the data partitioning strategy and the grid-based indexing result in good data distribution across database nodes and reduce I/O overhead in spatial join queries through parallel retrieval of relevant data and quick subsetting of datasets. The set of tools in the framework provide a full pipeline to normalize, load, manage and query analytical results for algorithm evaluation. PMID:23599905

Digital Image Support in the ROADNet Real-time Monitoring Platform

NASA Astrophysics Data System (ADS)

Lindquist, K. G.; Hansen, T. S.; Newman, R. L.; Vernon, F. L.; Nayak, A.; Foley, S.; Fricke, T.; Orcutt, J.; Rajasekar, A.

2004-12-01

The ROADNet real-time monitoring infrastructure has allowed researchers to integrate geophysical monitoring data from a wide variety of signal domains. Antelope-based data transport, relational-database buffering and archiving, backup/replication/archiving through the Storage Resource Broker, and a variety of web-based distribution tools create a powerful monitoring platform. In this work we discuss our use of the ROADNet system for the collection and processing of digital image data. Remote cameras have been deployed at approximately 32 locations as of September 2004, including the SDSU Santa Margarita Ecological Reserve, the Imperial Beach pier, and the Pinon Flats geophysical observatory. Fire monitoring imagery has been obtained through a connection to the HPWREN project. Near-real-time images obtained from the R/V Roger Revelle include records of seafloor operations by the JASON submersible, as part of a maintenance mission for the H2O underwater seismic observatory. We discuss acquisition mechanisms and the packet architecture for image transport via Antelope orbservers, including multi-packet support for arbitrarily large images. Relational database storage supports archiving of timestamped images, image-processing operations, grouping of related images and cameras, support for motion-detect triggers, thumbnail images, pre-computed video frames, support for time-lapse movie generation and storage of time-lapse movies. Available ROADNet monitoring tools include both orbserver-based display of incoming real-time images and web-accessible searching and distribution of images and movies driven by the relational database (http://mercali.ucsd.edu/rtapps/rtimbank.php). An extension to the Kepler Scientific Workflow System also allows real-time image display via the Ptolemy project. Custom time-lapse movies may be made from the ROADNet web pages.

mantisGRID: a grid platform for DICOM medical images management in Colombia and Latin America.

PubMed

Garcia Ruiz, Manuel; Garcia Chaves, Alvin; Ruiz Ibañez, Carlos; Gutierrez Mazo, Jorge Mario; Ramirez Giraldo, Juan Carlos; Pelaez Echavarria, Alejandro; Valencia Diaz, Edison; Pelaez Restrepo, Gustavo; Montoya Munera, Edwin Nelson; Garcia Loaiza, Bernardo; Gomez Gonzalez, Sebastian

2011-04-01

This paper presents the mantisGRID project, an interinstitutional initiative from Colombian medical and academic centers aiming to provide medical grid services for Colombia and Latin America. The mantisGRID is a GRID platform, based on open source grid infrastructure that provides the necessary services to access and exchange medical images and associated information following digital imaging and communications in medicine (DICOM) and health level 7 standards. The paper focuses first on the data abstraction architecture, which is achieved via Open Grid Services Architecture Data Access and Integration (OGSA-DAI) services and supported by the Globus Toolkit. The grid currently uses a 30-Mb bandwidth of the Colombian High Technology Academic Network, RENATA, connected to Internet 2. It also includes a discussion on the relational database created to handle the DICOM objects that were represented using Extensible Markup Language Schema documents, as well as other features implemented such as data security, user authentication, and patient confidentiality. Grid performance was tested using the three current operative nodes and the results demonstrated comparable query times between the mantisGRID (OGSA-DAI) and Distributed mySQL databases, especially for a large number of records.

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.

Remote sensing image segmentation based on Hadoop cloud platform

NASA Astrophysics Data System (ADS)

Li, Jie; Zhu, Lingling; Cao, Fubin

2018-01-01

To solve the problem that the remote sensing image segmentation speed is slow and the real-time performance is poor, this paper studies the method of remote sensing image segmentation based on Hadoop platform. On the basis of analyzing the structural characteristics of Hadoop cloud platform and its component MapReduce programming, this paper proposes a method of image segmentation based on the combination of OpenCV and Hadoop cloud platform. Firstly, the MapReduce image processing model of Hadoop cloud platform is designed, the input and output of image are customized and the segmentation method of the data file is rewritten. Then the Mean Shift image segmentation algorithm is implemented. Finally, this paper makes a segmentation experiment on remote sensing image, and uses MATLAB to realize the Mean Shift image segmentation algorithm to compare the same image segmentation experiment. The experimental results show that under the premise of ensuring good effect, the segmentation rate of remote sensing image segmentation based on Hadoop cloud Platform has been greatly improved compared with the single MATLAB image segmentation, and there is a great improvement in the effectiveness of image segmentation.

Surface-functionalized nanoparticles for biosensing and imaging-guided therapeutics

NASA Astrophysics Data System (ADS)

Jiang, Shan; Win, Khin Yin; Liu, Shuhua; Teng, Choon Peng; Zheng, Yuangang; Han, Ming-Yong

2013-03-01

In this article, the very recent progress of various functional inorganic nanomaterials is reviewed including their unique properties, surface functionalization strategies, and applications in biosensing and imaging-guided therapeutics. The proper surface functionalization renders them with stability, biocompatibility and functionality in physiological environments, and further enables their targeted use in bioapplications after bioconjugation via selective and specific recognition. The surface-functionalized nanoprobes using the most actively studied nanoparticles (i.e., gold nanoparticles, quantum dots, upconversion nanoparticles, and magnetic nanoparticles) make them an excellent platform for a wide range of bioapplications. With more efforts in recent years, they have been widely developed as labeling probes to detect various biological species such as proteins, nucleic acids and ions, and extensively employed as imaging probes to guide therapeutics such as drug/gene delivery and photothermal/photodynamic therapy.

Raspberry Pi-powered imaging for plant phenotyping.

PubMed

Tovar, Jose C; Hoyer, J Steen; Lin, Andy; Tielking, Allison; Callen, Steven T; Elizabeth Castillo, S; Miller, Michael; Tessman, Monica; Fahlgren, Noah; Carrington, James C; Nusinow, Dmitri A; Gehan, Malia A

2018-03-01

Image-based phenomics is a powerful approach to capture and quantify plant diversity. However, commercial platforms that make consistent image acquisition easy are often cost-prohibitive. To make high-throughput phenotyping methods more accessible, low-cost microcomputers and cameras can be used to acquire plant image data. We used low-cost Raspberry Pi computers and cameras to manage and capture plant image data. Detailed here are three different applications of Raspberry Pi-controlled imaging platforms for seed and shoot imaging. Images obtained from each platform were suitable for extracting quantifiable plant traits (e.g., shape, area, height, color) en masse using open-source image processing software such as PlantCV. This protocol describes three low-cost platforms for image acquisition that are useful for quantifying plant diversity. When coupled with open-source image processing tools, these imaging platforms provide viable low-cost solutions for incorporating high-throughput phenomics into a wide range of research programs.

NecroQuant: quantitative assessment of radiological necrosis

NASA Astrophysics Data System (ADS)

Hwang, Darryl H.; Mohamed, Passant; Varghese, Bino A.; Cen, Steven Y.; Duddalwar, Vinay

2017-11-01

Clinicians can now objectively quantify tumor necrosis by Hounsfield units and enhancement characteristics from multiphase contrast enhanced CT imaging. NecroQuant has been designed to work as part of a radiomics pipelines. The software is a departure from the conventional qualitative assessment of tumor necrosis, as it provides the user (radiologists and researchers) a simple interface to precisely and interactively define and measure necrosis in contrast-enhanced CT images. Although, the software is tested here on renal masses, it can be re-configured to assess tumor necrosis across variety of tumors from different body sites, providing a generalized, open, portable, and extensible quantitative analysis platform that is widely applicable across cancer types to quantify tumor necrosis.

DataViewer3D: An Open-Source, Cross-Platform Multi-Modal Neuroimaging Data Visualization Tool

PubMed Central

Gouws, André; Woods, Will; Millman, Rebecca; Morland, Antony; Green, Gary

2008-01-01

Integration and display of results from multiple neuroimaging modalities [e.g. magnetic resonance imaging (MRI), magnetoencephalography, EEG] relies on display of a diverse range of data within a common, defined coordinate frame. DataViewer3D (DV3D) is a multi-modal imaging data visualization tool offering a cross-platform, open-source solution to simultaneous data overlay visualization requirements of imaging studies. While DV3D is primarily a visualization tool, the package allows an analysis approach where results from one imaging modality can guide comparative analysis of another modality in a single coordinate space. DV3D is built on Python, a dynamic object-oriented programming language with support for integration of modular toolkits, and development of cross-platform software for neuroimaging. DV3D harnesses the power of the Visualization Toolkit (VTK) for two-dimensional (2D) and 3D rendering, calling VTK's low level C++ functions from Python. Users interact with data via an intuitive interface that uses Python to bind wxWidgets, which in turn calls the user's operating system dialogs and graphical user interface tools. DV3D currently supports NIfTI-1, ANALYZE™ and DICOM formats for MRI data display (including statistical data overlay). Formats for other data types are supported. The modularity of DV3D and ease of use of Python allows rapid integration of additional format support and user development. DV3D has been tested on Mac OSX, RedHat Linux and Microsoft Windows XP. DV3D is offered for free download with an extensive set of tutorial resources and example data. PMID:19352444

ESPAS: the European e-science platform to access near-Earth space data (Invited)

NASA Astrophysics Data System (ADS)

Belehaki, A.; Hapgood, M. A.; Ritschel, B.; Manola, N.

2013-12-01

The aim of ESPAS platform is to integrate heterogeneous data from the earth's thermosphere, ionosphere, plasmasphere and magnetosphere. ESPAS supports the systematic exploration of multipoint measurements from the near-Earth space through homogenised access to multi-instrument data. It provides access to more than 40 datasets: Cluster, EISCAT, GIRO, DIAS, SWACI, CHAMP, SuperDARN, FPI, magnetometers INGV, SGO, DTU, IMAGE, TGO, IMAGE/RPI, ACE, SOHO, PROBA2, NOAA/POES, etc. The concept of extensibility to new data sets is an important element in the ESPAS architecture. Within the first year of the project, the main components of the system have been developed, namely, the data model, the XML schemas for metadata exchange format, the ontology, the wrapper installed at the data nodes so that the main platform harvest the metadata, the main platform built on the D-NET framework and the GUI with its designed workflows. The first working prototype supports the search for datasets among a selected number of databases (i.e., EDAM, DIAS, Cluster, SWACI data). The next immediate step would be the implementation of search for characteristics within the datasets. For the second release we are planning to deploy tools for conjunctions between ground-space and space-space and for coincidences. For the final phase of the project the ESPAS infrastructure will be extensively tested through the application of several use cases, designed to serve the needs of the wide interdisciplinary users and producers communities, such as the ionospheric, thermospheric, magnetospheric, space weather and space climate communities, the geophysics community, the space communications engineering, HF users, satellite operators, navigation and surveillance systems, and space agencies. The final ESPAS platform is expected to be delivered in 2015. The abstract is submitted on behalf of the ESPAS-FP7EU team (http://www.espas-fp7.eu): Mike Hapgood, Anna Belehaki, Spiros Ventouras, Natalia Manola, Antonis Lebesis, Bruno Zolesi, Tatjana Gerzen, Ingemar Häggström, Anna Charisi, Ivan Galkin, Jurgen Watermann, Matthew Angling, Timo Asikainen, Alan Aylward, Henrike Barkmann, Peter Bergqvist, Andrew Bushell, Fabien Darrouzet, Dimitris Dialetis, Carl-Fredrik Enell, Daniel Heynderickx, Norbert Jakowski, Magnar Johnsen, Jean Lilensten, Ian McCrea, Kalevi Mursula, Bogdan Nicula, Michael Pezzopane, Viviane Pierrard, Bodo Reinisch, Bernd Ritschel, Luca Spogli, Iwona Stanislawska, Claudia Stolle, Eija Tanskanen, Ioanna Tsagouri, Esa Turunen, Thomas Ulich, Matthew Wild, Tim Yeoman

Innovative Extension Models and Smallholders: How ICT platforms can Deliver Timely Information to Farmers in India.

NASA Astrophysics Data System (ADS)

Nagothu, U. S.

2016-12-01

Agricultural extension services, among others, contribute to improving rural livelihoods and enhancing economic development. Knowledge development and transfer from the cognitive science point of view, is about, how farmers use and apply their experiential knowledge as well as acquired new knowledge to solve new problems. This depends on the models adopted, the way knowledge is generated and delivered. New extension models based on ICT platforms and smart phones are promising. Results from a 5-year project (www.climaadapt.org) in India shows that farmer led-on farm validations of technologies and knowledge exchange through ICT based platforms outperformed state operated linear extension programs. Innovation here depends on the connectivity, net-working between stakeholders that are involved in generating, transferring and using the knowledge. Key words: Smallholders, Knowledge, Extension, Innovation, India

Simultaneous dual modality optical and MR imaging of mouse dorsal skin-fold window chamber

NASA Astrophysics Data System (ADS)

Salek, Mir Farrokh; Pagel, Mark D.; Gmitro, Arthur F.

2011-02-01

Optical imaging and MRI have both been used extensively to study tumor microenvironment. The two imaging modalities are complementary and can be used to cross-validate one another for specific measurements. We have developed a modular platform that is capable of doing optical microscopy inside an MRI instrument. To do this, an optical relay system transfers the image to outside of the MR bore to a commercial grade CCD camera. This enables simultaneous optical and MR imaging of the same tissue and thus creates the ideal situation for comparative or complementary studies using both modalities. Initial experiments have been done using GFP labeled prostate cancer cells implanted in mouse dorsal skin fold window chamber. Vascular hemodynamics and vascular permeability were studied using our imaging system. Towards this goal, we developed a dual MR-Optical contrast agent by labeling BSA with both Gd-DTPA and Alexa Fluor. Overall system design and results of these preliminary vascular studies are presented.

Data dictionary services in XNAT and the Human Connectome Project.

PubMed

Herrick, Rick; McKay, Michael; Olsen, Timothy; Horton, William; Florida, Mark; Moore, Charles J; Marcus, Daniel S

2014-01-01

The XNAT informatics platform is an open source data management tool used by biomedical imaging researchers around the world. An important feature of XNAT is its highly extensible architecture: users of XNAT can add new data types to the system to capture the imaging and phenotypic data generated in their studies. Until recently, XNAT has had limited capacity to broadcast the meaning of these data extensions to users, other XNAT installations, and other software. We have implemented a data dictionary service for XNAT, which is currently being used on ConnectomeDB, the Human Connectome Project (HCP) public data sharing website. The data dictionary service provides a framework to define key relationships between data elements and structures across the XNAT installation. This includes not just core data representing medical imaging data or subject or patient evaluations, but also taxonomical structures, security relationships, subject groups, and research protocols. The data dictionary allows users to define metadata for data structures and their properties, such as value types (e.g., textual, integers, floats) and valid value templates, ranges, or field lists. The service provides compatibility and integration with other research data management services by enabling easy migration of XNAT data to standards-based formats such as the Resource Description Framework (RDF), JavaScript Object Notation (JSON), and Extensible Markup Language (XML). It also facilitates the conversion of XNAT's native data schema into standard neuroimaging vocabularies and structures.

Data dictionary services in XNAT and the Human Connectome Project

PubMed Central

Herrick, Rick; McKay, Michael; Olsen, Timothy; Horton, William; Florida, Mark; Moore, Charles J.; Marcus, Daniel S.

2014-01-01

The XNAT informatics platform is an open source data management tool used by biomedical imaging researchers around the world. An important feature of XNAT is its highly extensible architecture: users of XNAT can add new data types to the system to capture the imaging and phenotypic data generated in their studies. Until recently, XNAT has had limited capacity to broadcast the meaning of these data extensions to users, other XNAT installations, and other software. We have implemented a data dictionary service for XNAT, which is currently being used on ConnectomeDB, the Human Connectome Project (HCP) public data sharing website. The data dictionary service provides a framework to define key relationships between data elements and structures across the XNAT installation. This includes not just core data representing medical imaging data or subject or patient evaluations, but also taxonomical structures, security relationships, subject groups, and research protocols. The data dictionary allows users to define metadata for data structures and their properties, such as value types (e.g., textual, integers, floats) and valid value templates, ranges, or field lists. The service provides compatibility and integration with other research data management services by enabling easy migration of XNAT data to standards-based formats such as the Resource Description Framework (RDF), JavaScript Object Notation (JSON), and Extensible Markup Language (XML). It also facilitates the conversion of XNAT's native data schema into standard neuroimaging vocabularies and structures. PMID:25071542

Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets.

PubMed

Scharfe, Michael; Pielot, Rainer; Schreiber, Falk

2010-01-11

Solving bioinformatics tasks often requires extensive computational power. Recent trends in processor architecture combine multiple cores into a single chip to improve overall performance. The Cell Broadband Engine (CBE), a heterogeneous multi-core processor, provides power-efficient and cost-effective high-performance computing. One application area is image analysis and visualisation, in particular registration of 2D cross-sections into 3D image datasets. Such techniques can be used to put different image modalities into spatial correspondence, for example, 2D images of histological cuts into morphological 3D frameworks. We evaluate the CBE-driven PlayStation 3 as a high performance, cost-effective computing platform by adapting a multimodal alignment procedure to several characteristic hardware properties. The optimisations are based on partitioning, vectorisation, branch reducing and loop unrolling techniques with special attention to 32-bit multiplies and limited local storage on the computing units. We show how a typical image analysis and visualisation problem, the multimodal registration of 2D cross-sections and 3D datasets, benefits from the multi-core based implementation of the alignment algorithm. We discuss several CBE-based optimisation methods and compare our results to standard solutions. More information and the source code are available from http://cbe.ipk-gatersleben.de. The results demonstrate that the CBE processor in a PlayStation 3 accelerates computational intensive multimodal registration, which is of great importance in biological/medical image processing. The PlayStation 3 as a low cost CBE-based platform offers an efficient option to conventional hardware to solve computational problems in image processing and bioinformatics.

Conquering the Dark Side: Colloidal Iron Oxide Nanoparticles

PubMed Central

Senpan, Angana; Caruthers, Shelton D.; Rhee, Ilsu; Mauro, Nicholas A.; Pan, Dipanjan; Hu, Grace; Scott, Michael J.; Fuhrhop, Ralph W.; Gaffney, Patrick J.; Wickline, Samuel A.; Lanza, Gregory M.

2009-01-01

Nanomedicine approaches to atherosclerotic disease will have significant impact on the practice and outcomes of cardiovascular medicine. Iron oxide nanoparticles have been extensively used for nontargeted and targeted imaging applications based upon highly sensitive T2* imaging properties, which typically result in negative contrast effects that can only be imaged 24 or more hours after systemic administration due to persistent blood pool interference. Although recent advances involving MR pulse sequences have converted these dark contrast voxels into bright ones, the marked delays in imaging from persistent magnetic background interference and prominent dipole blooming effects of the magnetic susceptibility remain barriers to overcome. We report a T1-weighted (T1w) theranostic colloidal iron oxide nanoparticle platform, CION, which is achieved by entrapping oleate-coated magnetite particles within a cross-linked phospholipid nanoemulsion. Contrary to expectations, this formulation decreased T2 effects thus allowing positive T1w contrast detection down to low nanomolar concentrations. CION, a vascular constrained nanoplatform administered in vivo permitted T1w molecular imaging 1 hour after treatment without blood pool interference, although some T2 shortening effects on blood, induced by the superparamagnetic particles persisted. Moreover, CION was shown to encapsulate antiangiogenic drugs, like fumagillin, and retained them under prolonged dissolution, suggesting significant theranostic functionality. Overall, CION is a platform technology, developed with generally recognized as safe components, that overcomes the temporal and spatial imaging challenges associated with current iron oxide nanoparticle T2 imaging agents, and which has theranostic potential in vascular diseases for detecting unstable ruptured plaque or treating atherosclerotic angiogenesis. PMID:19908850

A software platform for phase contrast x-ray breast imaging research.

PubMed

Bliznakova, K; Russo, P; Mettivier, G; Requardt, H; Popov, P; Bravin, A; Buliev, I

2015-06-01

To present and validate a computer-based simulation platform dedicated for phase contrast x-ray breast imaging research. The software platform, developed at the Technical University of Varna on the basis of a previously validated x-ray imaging software simulator, comprises modules for object creation and for x-ray image formation. These modules were updated to take into account the refractive index for phase contrast imaging as well as implementation of the Fresnel-Kirchhoff diffraction theory of the propagating x-ray waves. Projection images are generated in an in-line acquisition geometry. To test and validate the platform, several phantoms differing in their complexity were constructed and imaged at 25 keV and 60 keV at the beamline ID17 of the European Synchrotron Radiation Facility. The software platform was used to design computational phantoms that mimic those used in the experimental study and to generate x-ray images in absorption and phase contrast modes. The visual and quantitative results of the validation process showed an overall good correlation between simulated and experimental images and show the potential of this platform for research in phase contrast x-ray imaging of the breast. The application of the platform is demonstrated in a feasibility study for phase contrast images of complex inhomogeneous and anthropomorphic breast phantoms, compared to x-ray images generated in absorption mode. The improved visibility of mammographic structures suggests further investigation and optimisation of phase contrast x-ray breast imaging, especially when abnormalities are present. The software platform can be exploited also for educational purposes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Motion systems providing three or four degrees of freedom

NASA Technical Reports Server (NTRS)

Chou, Richard C. (Inventor)

1982-01-01

A motion system is provided by a platform generally parallel to a base and connected thereto by a column and powered and controlled extensible members, at least three of which are connected between distributed points around the column. In a three degree of freedom device, the column is conical, rigidly supported at its base with a universal joint at its top. The points of attachment define triangles in the base and in the platform surrounding the column with one extensible member connected between each. In the four degree of freedom version, the column is modified by making it effectively a column which is pivoted or guided at the base or contains an extensible member, preferably retains its triangular shape and its universal joint connection to the platform at its apex. For stability four powered and controlled extensible members are provided between points in the base and platform distributed around the column, a preferred pattern of arrangement being a square with the column at the center.

General Astrophysics with the HabEx Workhorse Camera

NASA Astrophysics Data System (ADS)

Stern, Daniel; Clarke, John; Gaudi, B. Scott; Kiessling, Alina; Krause, Oliver; Martin, Stefan; Scowen, Paul; Somerville, Rachel; HabEx STDT

2018-01-01

The Habitable Exoplanet Imaging Mission (HabEx) concept has been designed to enable an extensive suite of science, broadly put under the rubric of General Astrophysics, in addition to its exoplanet direct imaging science. General astrophysics directly addresses multiple NASA programmatic branches, and HabEx will enable investigations ranging from cosmology, to galaxy evolution, to stellar population studies, to exoplanet transit spectroscopy, to Solar System studies. This poster briefly describes one of the two primary HabEx General Astrophysics instruments, the HabEx Workhorse Camera (HWC). HWC will be a dual-detector UV-to-near-IR imager and multi-object grism spectrometer with a microshutter array and a moderate (3' x 3') field-of-view. We detail some of the key science we expect HWC to undertake, emphasizing unique capabilities enabled by a large-aperture, highly stable space-borne platform at these wavelengths.

Molecular Optical Simulation Environment (MOSE): A Platform for the Simulation of Light Propagation in Turbid Media

PubMed Central

Ren, Shenghan; Chen, Xueli; Wang, Hailong; Qu, Xiaochao; Wang, Ge; Liang, Jimin; Tian, Jie

2013-01-01

The study of light propagation in turbid media has attracted extensive attention in the field of biomedical optical molecular imaging. In this paper, we present a software platform for the simulation of light propagation in turbid media named the “Molecular Optical Simulation Environment (MOSE)”. Based on the gold standard of the Monte Carlo method, MOSE simulates light propagation both in tissues with complicated structures and through free-space. In particular, MOSE synthesizes realistic data for bioluminescence tomography (BLT), fluorescence molecular tomography (FMT), and diffuse optical tomography (DOT). The user-friendly interface and powerful visualization tools facilitate data analysis and system evaluation. As a major measure for resource sharing and reproducible research, MOSE aims to provide freeware for research and educational institutions, which can be downloaded at http://www.mosetm.net. PMID:23577215

Tools for Creating Mobile Applications for Extension

ERIC Educational Resources Information Center

Drill, Sabrina L.

2012-01-01

Considerations and tools for developing mobile applications for Extension include evaluating the topic, purpose, and audience. Different computing platforms may be used, and apps designed as modified Web pages or implicitly programmed for a particular platform. User privacy is another important consideration, especially for data collection apps.…

A software platform for the analysis of dermatology images

NASA Astrophysics Data System (ADS)

Vlassi, Maria; Mavraganis, Vlasios; Asvestas, Panteleimon

2017-11-01

The purpose of this paper is to present a software platform developed in Python programming environment that can be used for the processing and analysis of dermatology images. The platform provides the capability for reading a file that contains a dermatology image. The platform supports image formats such as Windows bitmaps, JPEG, JPEG2000, portable network graphics, TIFF. Furthermore, it provides suitable tools for selecting, either manually or automatically, a region of interest (ROI) on the image. The automated selection of a ROI includes filtering for smoothing the image and thresholding. The proposed software platform has a friendly and clear graphical user interface and could be a useful second-opinion tool to a dermatologist. Furthermore, it could be used to classify images including from other anatomical parts such as breast or lung, after proper re-training of the classification algorithms.

Automatic Atlas Based Electron Density and Structure Contouring for MRI-based Prostate Radiation Therapy on the Cloud

NASA Astrophysics Data System (ADS)

Dowling, J. A.; Burdett, N.; Greer, P. B.; Sun, J.; Parker, J.; Pichler, P.; Stanwell, P.; Chandra, S.; Rivest-Hénault, D.; Ghose, S.; Salvado, O.; Fripp, J.

2014-03-01

Our group have been developing methods for MRI-alone prostate cancer radiation therapy treatment planning. To assist with clinical validation of the workflow we are investigating a cloud platform solution for research purposes. Benefits of cloud computing can include increased scalability, performance and extensibility while reducing total cost of ownership. In this paper we demonstrate the generation of DICOM-RT directories containing an automatic average atlas based electron density image and fast pelvic organ contouring from whole pelvis MR scans.

Design and development of C-arm based cone-beam CT for image-guided interventions: initial results

NASA Astrophysics Data System (ADS)

Chen, Guang-Hong; Zambelli, Joseph; Nett, Brian E.; Supanich, Mark; Riddell, Cyril; Belanger, Barry; Mistretta, Charles A.

2006-03-01

X-ray cone-beam computed tomography (CBCT) is of importance in image-guided intervention (IGI) and image-guided radiation therapy (IGRT). In this paper, we present a cone-beam CT data acquisition system using a GE INNOVA 4100 (GE Healthcare Technologies, Waukesha, Wisconsin) clinical system. This new cone-beam data acquisition mode was developed for research purposes without interfering with any clinical function of the system. It provides us a basic imaging pipeline for more advanced cone-beam data acquisition methods. It also provides us a platform to study and overcome the limiting factors such as cone-beam artifacts and limiting low contrast resolution in current C-arm based cone-beam CT systems. A geometrical calibration method was developed to experimentally determine parameters of the scanning geometry to correct the image reconstruction for geometric non-idealities. Extensive phantom studies and some small animal studies have been conducted to evaluate the performance of our cone-beam CT data acquisition system.

HelioScan: a software framework for controlling in vivo microscopy setups with high hardware flexibility, functional diversity and extendibility.

PubMed

Langer, Dominik; van 't Hoff, Marcel; Keller, Andreas J; Nagaraja, Chetan; Pfäffli, Oliver A; Göldi, Maurice; Kasper, Hansjörg; Helmchen, Fritjof

2013-04-30

Intravital microscopy such as in vivo imaging of brain dynamics is often performed with custom-built microscope setups controlled by custom-written software to meet specific requirements. Continuous technological advancement in the field has created a need for new control software that is flexible enough to support the biological researcher with innovative imaging techniques and provide the developer with a solid platform for quickly and easily implementing new extensions. Here, we introduce HelioScan, a software package written in LabVIEW, as a platform serving this dual role. HelioScan is designed as a collection of components that can be flexibly assembled into microscope control software tailored to the particular hardware and functionality requirements. Moreover, HelioScan provides a software framework, within which new functionality can be implemented in a quick and structured manner. A specific HelioScan application assembles at run-time from individual software components, based on user-definable configuration files. Due to its component-based architecture, HelioScan can exploit synergies of multiple developers working in parallel on different components in a community effort. We exemplify the capabilities and versatility of HelioScan by demonstrating several in vivo brain imaging modes, including camera-based intrinsic optical signal imaging for functional mapping of cortical areas, standard two-photon laser-scanning microscopy using galvanometric mirrors, and high-speed in vivo two-photon calcium imaging using either acousto-optic deflectors or a resonant scanner. We recommend HelioScan as a convenient software framework for the in vivo imaging community. Copyright © 2013 Elsevier B.V. All rights reserved.

A Noninvasive Platform for Imaging and Quantifying Oil Storage in Submillimeter Tobacco Seed1[W][OA

PubMed Central

Fuchs, Johannes; Neuberger, Thomas; Rolletschek, Hardy; Schiebold, Silke; Nguyen, Thuy Ha; Borisjuk, Nikolai; Börner, Andreas; Melkus, Gerd; Jakob, Peter; Borisjuk, Ljudmilla

2013-01-01

While often thought of as a smoking drug, tobacco (Nicotiana spp.) is now considered as a plant of choice for molecular farming and biofuel production. Here, we describe a noninvasive means of deriving both the distribution of lipid and the microtopology of the submillimeter tobacco seed, founded on nuclear magnetic resonance (NMR) technology. Our platform enables counting of seeds inside the intact tobacco capsule to measure seed sizes, to model the seed interior in three dimensions, to quantify the lipid content, and to visualize lipid gradients. Hundreds of seeds can be simultaneously imaged at an isotropic resolution of 25 µm, sufficient to assess each individual seed. The relative contributions of the embryo and the endosperm to both seed size and total lipid content could be assessed. The extension of the platform to a range of wild and cultivated Nicotiana species demonstrated certain evolutionary trends in both seed topology and pattern of lipid storage. The NMR analysis of transgenic tobacco plants with seed-specific ectopic expression of the plastidial phosphoenolpyruvate/phosphate translocator, displayed a trade off between seed size and oil concentration. The NMR-based assay of seed lipid content and topology has a number of potential applications, in particular providing a means to test and optimize transgenic strategies aimed at the manipulation of seed size, seed number, and lipid content in tobacco and other species with submillimeter seeds. PMID:23232144

A fully automatic approach to register mobile mapping and airborne imagery to support the correction of platform trajectories in GNSS-denied urban areas

NASA Astrophysics Data System (ADS)

Jende, Phillipp; Nex, Francesco; Gerke, Markus; Vosselman, George

2018-07-01

Mobile Mapping (MM) solutions have become a significant extension to traditional data acquisition methods over the last years. Independently from the sensor carried by a platform, may it be laser scanners or cameras, high-resolution data postings are opposing a poor absolute localisation accuracy in urban areas due to GNSS occlusions and multipath effects. Potentially inaccurate position estimations are propagated by IMUs which are furthermore prone to drift effects. Thus, reliable and accurate absolute positioning on a par with MM's high-quality data remains an open issue. Multiple and diverse approaches have shown promising potential to mitigate GNSS errors in urban areas, but cannot achieve decimetre accuracy, require manual effort, or have limitations with respect to costs and availability. This paper presents a fully automatic approach to support the correction of MM imaging data based on correspondences with airborne nadir images. These correspondences can be employed to correct the MM platform's orientation by an adjustment solution. Unlike MM as such, aerial images do not suffer from GNSS occlusions, and their accuracy is usually verified by employing well-established methods using ground control points. However, a registration between MM and aerial images is a non-standard matching scenario, and requires several strategies to yield reliable and accurate correspondences. Scale, perspective and content strongly vary between both image sources, thus traditional feature matching methods may fail. To this end, the registration process is designed to focus on common and clearly distinguishable elements, such as road markings, manholes, or kerbstones. With a registration accuracy of about 98%, reliable tie information between MM and aerial data can be derived. Even though, the adjustment strategy is not covered in its entirety in this paper, accuracy results after adjustment will be presented. It will be shown that a decimetre accuracy is well achievable in a real data test scenario.

Cloud computing in medical imaging.

PubMed

Kagadis, George C; Kloukinas, Christos; Moore, Kevin; Philbin, Jim; Papadimitroulas, Panagiotis; Alexakos, Christos; Nagy, Paul G; Visvikis, Dimitris; Hendee, William R

2013-07-01

Over the past century technology has played a decisive role in defining, driving, and reinventing procedures, devices, and pharmaceuticals in healthcare. Cloud computing has been introduced only recently but is already one of the major topics of discussion in research and clinical settings. The provision of extensive, easily accessible, and reconfigurable resources such as virtual systems, platforms, and applications with low service cost has caught the attention of many researchers and clinicians. Healthcare researchers are moving their efforts to the cloud, because they need adequate resources to process, store, exchange, and use large quantities of medical data. This Vision 20/20 paper addresses major questions related to the applicability of advanced cloud computing in medical imaging. The paper also considers security and ethical issues that accompany cloud computing.

Artificial Structural Color Pixels: A Review

PubMed Central

Zhao, Yuqian; Zhao, Yong; Hu, Sheng; Lv, Jiangtao; Ying, Yu; Gervinskas, Gediminas; Si, Guangyuan

2017-01-01

Inspired by natural photonic structures (Morpho butterfly, for instance), researchers have demonstrated varying artificial color display devices using different designs. Photonic-crystal/plasmonic color filters have drawn increasing attention most recently. In this review article, we show the developing trend of artificial structural color pixels from photonic crystals to plasmonic nanostructures. Such devices normally utilize the distinctive optical features of photonic/plasmon resonance, resulting in high compatibility with current display and imaging technologies. Moreover, dynamical color filtering devices are highly desirable because tunable optical components are critical for developing new optical platforms which can be integrated or combined with other existing imaging and display techniques. Thus, extensive promising potential applications have been triggered and enabled including more abundant functionalities in integrated optics and nanophotonics. PMID:28805736

ClearedLeavesDB: an online database of cleared plant leaf images

PubMed Central

2014-01-01

Background Leaf vein networks are critical to both the structure and function of leaves. A growing body of recent work has linked leaf vein network structure to the physiology, ecology and evolution of land plants. In the process, multiple institutions and individual researchers have assembled collections of cleared leaf specimens in which vascular bundles (veins) are rendered visible. In an effort to facilitate analysis and digitally preserve these specimens, high-resolution images are usually created, either of entire leaves or of magnified leaf subsections. In a few cases, collections of digital images of cleared leaves are available for use online. However, these collections do not share a common platform nor is there a means to digitally archive cleared leaf images held by individual researchers (in addition to those held by institutions). Hence, there is a growing need for a digital archive that enables online viewing, sharing and disseminating of cleared leaf image collections held by both institutions and individual researchers. Description The Cleared Leaf Image Database (ClearedLeavesDB), is an online web-based resource for a community of researchers to contribute, access and share cleared leaf images. ClearedLeavesDB leverages resources of large-scale, curated collections while enabling the aggregation of small-scale collections within the same online platform. ClearedLeavesDB is built on Drupal, an open source content management platform. It allows plant biologists to store leaf images online with corresponding meta-data, share image collections with a user community and discuss images and collections via a common forum. We provide tools to upload processed images and results to the database via a web services client application that can be downloaded from the database. Conclusions We developed ClearedLeavesDB, a database focusing on cleared leaf images that combines interactions between users and data via an intuitive web interface. The web interface allows storage of large collections and integrates with leaf image analysis applications via an open application programming interface (API). The open API allows uploading of processed images and other trait data to the database, further enabling distribution and documentation of analyzed data within the community. The initial database is seeded with nearly 19,000 cleared leaf images representing over 40 GB of image data. Extensible storage and growth of the database is ensured by using the data storage resources of the iPlant Discovery Environment. ClearedLeavesDB can be accessed at http://clearedleavesdb.org. PMID:24678985

ClearedLeavesDB: an online database of cleared plant leaf images.

PubMed

Das, Abhiram; Bucksch, Alexander; Price, Charles A; Weitz, Joshua S

2014-03-28

Leaf vein networks are critical to both the structure and function of leaves. A growing body of recent work has linked leaf vein network structure to the physiology, ecology and evolution of land plants. In the process, multiple institutions and individual researchers have assembled collections of cleared leaf specimens in which vascular bundles (veins) are rendered visible. In an effort to facilitate analysis and digitally preserve these specimens, high-resolution images are usually created, either of entire leaves or of magnified leaf subsections. In a few cases, collections of digital images of cleared leaves are available for use online. However, these collections do not share a common platform nor is there a means to digitally archive cleared leaf images held by individual researchers (in addition to those held by institutions). Hence, there is a growing need for a digital archive that enables online viewing, sharing and disseminating of cleared leaf image collections held by both institutions and individual researchers. The Cleared Leaf Image Database (ClearedLeavesDB), is an online web-based resource for a community of researchers to contribute, access and share cleared leaf images. ClearedLeavesDB leverages resources of large-scale, curated collections while enabling the aggregation of small-scale collections within the same online platform. ClearedLeavesDB is built on Drupal, an open source content management platform. It allows plant biologists to store leaf images online with corresponding meta-data, share image collections with a user community and discuss images and collections via a common forum. We provide tools to upload processed images and results to the database via a web services client application that can be downloaded from the database. We developed ClearedLeavesDB, a database focusing on cleared leaf images that combines interactions between users and data via an intuitive web interface. The web interface allows storage of large collections and integrates with leaf image analysis applications via an open application programming interface (API). The open API allows uploading of processed images and other trait data to the database, further enabling distribution and documentation of analyzed data within the community. The initial database is seeded with nearly 19,000 cleared leaf images representing over 40 GB of image data. Extensible storage and growth of the database is ensured by using the data storage resources of the iPlant Discovery Environment. ClearedLeavesDB can be accessed at http://clearedleavesdb.org.

A high-level 3D visualization API for Java and ImageJ.

PubMed

Schmid, Benjamin; Schindelin, Johannes; Cardona, Albert; Longair, Mark; Heisenberg, Martin

2010-05-21

Current imaging methods such as Magnetic Resonance Imaging (MRI), Confocal microscopy, Electron Microscopy (EM) or Selective Plane Illumination Microscopy (SPIM) yield three-dimensional (3D) data sets in need of appropriate computational methods for their analysis. The reconstruction, segmentation and registration are best approached from the 3D representation of the data set. Here we present a platform-independent framework based on Java and Java 3D for accelerated rendering of biological images. Our framework is seamlessly integrated into ImageJ, a free image processing package with a vast collection of community-developed biological image analysis tools. Our framework enriches the ImageJ software libraries with methods that greatly reduce the complexity of developing image analysis tools in an interactive 3D visualization environment. In particular, we provide high-level access to volume rendering, volume editing, surface extraction, and image annotation. The ability to rely on a library that removes the low-level details enables concentrating software development efforts on the algorithm implementation parts. Our framework enables biomedical image software development to be built with 3D visualization capabilities with very little effort. We offer the source code and convenient binary packages along with extensive documentation at http://3dviewer.neurofly.de.

Incorporating the whole-mount prostate histology reconstruction program Histostitcher into the extensible imaging platform (XIP) framework

NASA Astrophysics Data System (ADS)

Toth, Robert; Chappelow, Jonathan; Vetter, Christoph; Kutter, Oliver; Russ, Christoph; Feldman, Michael; Tomaszewski, John; Shih, Natalie; Madabhushi, Anant

2012-03-01

There is a need for identifying quantitative imaging (e.g. MRI) signatures for prostate cancer (CaP), so that computer-aided diagnostic methods can be trained to detect disease extent in vivo. Determining CaP extent on in vivo MRI is difficult to do; however, with the availability of ex vivo surgical whole mount histological sections (WMHS) for CaP patients undergoing radical prostatectomy, co-registration methods can be applied to align and map disease extent onto pre-operative MR imaging from the post-operative histology. Yet obtaining digitized images of WHMS for co-registration with the pre-operative MRI is cumbersome since (a) most digital slide scanners are unable to accommodate the entire section, and (b) significant technical expertise is required for whole mount slide preparation. Consequently, most centers opt to construct quartered sections of each histology slice. Prior to co-registration with MRI, however, these quartered sections need to be digitally stitched together to reconstitute a digital, pseudo WMHS. Histostitcheris an interactive software program that uses semi-automatic registration tools to digitally stitch quartered sections into pseudo WMHS. Histostitcherwas originally developed using the GUI tools provided by the Matlab programming interface, but the clinical use was limited due to the inefficiency of the interface. The limitations of the Matlab based GUI include (a) an inability to edit the fiducials, (b) the rendering being extremely slow, and (c) lack of interactive and rapid visualization tools. In this work, Histostitcherhas been integrated into the eXtensible Imaging Platform (XIP TM ) framework (a set of libraries containing functionalities for analyzing and visualizing medical image data). XIP TM lends the stitching tool much greater flexibility and functionality by (a) allowing interactive and seamless navigation through the full resolution histology images, (b) the ability to easily add, edit, or remove fiducials and annotations in order to register the quadrants and map the disease extent. In this work, we showcase examples of digital stitching of quartered histological sections into pseudo-WHMS using Histostitcher via the new XIP TM interface. This tool will be particularly useful in clinical trials and large cohort studies where a quick, interactive way of digitally reconstructing pseudo WMHS is required.

VA's Integrated Imaging System on three platforms.

PubMed

Dayhoff, R E; Maloney, D L; Majurski, W J

1992-01-01

The DHCP Integrated Imaging System provides users with integrated patient data including text, image and graphics data. This system has been transferred from its original two screen DOS-based MUMPS platform to an X window workstation and a Microsoft Windows-based workstation. There are differences between these various platforms that impact on software design and on software development strategy. Data structures and conventions were used to isolate hardware, operating system, imaging software, and user-interface differences between platforms in the implementation of functionality for text and image display and interaction. The use of an object-oriented approach greatly increased system portability.

VA's Integrated Imaging System on three platforms.

PubMed Central

Dayhoff, R. E.; Maloney, D. L.; Majurski, W. J.

1992-01-01

The DHCP Integrated Imaging System provides users with integrated patient data including text, image and graphics data. This system has been transferred from its original two screen DOS-based MUMPS platform to an X window workstation and a Microsoft Windows-based workstation. There are differences between these various platforms that impact on software design and on software development strategy. Data structures and conventions were used to isolate hardware, operating system, imaging software, and user-interface differences between platforms in the implementation of functionality for text and image display and interaction. The use of an object-oriented approach greatly increased system portability. PMID:1482983

Fast multi-core based multimodal registration of 2D cross-sections and 3D datasets

PubMed Central

2010-01-01

Background Solving bioinformatics tasks often requires extensive computational power. Recent trends in processor architecture combine multiple cores into a single chip to improve overall performance. The Cell Broadband Engine (CBE), a heterogeneous multi-core processor, provides power-efficient and cost-effective high-performance computing. One application area is image analysis and visualisation, in particular registration of 2D cross-sections into 3D image datasets. Such techniques can be used to put different image modalities into spatial correspondence, for example, 2D images of histological cuts into morphological 3D frameworks. Results We evaluate the CBE-driven PlayStation 3 as a high performance, cost-effective computing platform by adapting a multimodal alignment procedure to several characteristic hardware properties. The optimisations are based on partitioning, vectorisation, branch reducing and loop unrolling techniques with special attention to 32-bit multiplies and limited local storage on the computing units. We show how a typical image analysis and visualisation problem, the multimodal registration of 2D cross-sections and 3D datasets, benefits from the multi-core based implementation of the alignment algorithm. We discuss several CBE-based optimisation methods and compare our results to standard solutions. More information and the source code are available from http://cbe.ipk-gatersleben.de. Conclusions The results demonstrate that the CBE processor in a PlayStation 3 accelerates computational intensive multimodal registration, which is of great importance in biological/medical image processing. The PlayStation 3 as a low cost CBE-based platform offers an efficient option to conventional hardware to solve computational problems in image processing and bioinformatics. PMID:20064262

Holistic approach to design and implementation of a medical teleconsultation workspace.

PubMed

Czekierda, Łukasz; Malawski, Filip; Wyszkowski, Przemysław

2015-10-01

While there are many state-of-the-art approaches to introducing telemedical services in the area of medical imaging, it is hard to point to studies which would address all relevant aspects in a complete and comprehensive manner. In this paper we describe our approach to design and implementation of a universal platform for imaging medicine which is based on our longstanding experience in this area. We claim it is holistic, because, contrary to most of the available studies it addresses all aspects related to creation and utilization of a medical teleconsultation workspace. We present an extensive analysis of requirements, including possible usage scenarios, user needs, organizational and security issues and infrastructure components. We enumerate and analyze multiple usage scenarios related to medical imaging data in treatment, research and educational applications - with typical teleconsultations treated as just one of many possible options. Certain phases common to all these scenarios have been identified, with the resulting classification distinguishing several modes of operation (local vs. remote, collaborative vs. non-interactive etc.). On this basis we propose a system architecture which addresses all of the identified requirements, applying two key concepts: Service Oriented Architecture (SOA) and Virtual Organizations (VO). The SOA paradigm allows us to decompose the functionality of the system into several distinct building blocks, ensuring flexibility and reliability. The VO paradigm defines the cooperation model for all participating healthcare institutions. Our approach is validated by an ICT platform called TeleDICOM II which implements the proposed architecture. All of its main elements are described in detail and cross-checked against the listed requirements. A case study presents the role and usage of the platform in a specific scenario. Finally, our platform is compared with similar systems described into-date studies and available on the market. Copyright © 2015. Published by Elsevier Inc.

Measurement of time-varying displacement fields in cell culture for traction force optical coherence microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Mulligan, Jeffrey A.; Adie, Steven G.

2017-02-01

Mechanobiology is an emerging field which seeks to link mechanical forces and properties to the behaviors of cells and tissues in cancer, stem cell growth, and other processes. Traction force microscopy (TFM) is an imaging technique that enables the study of traction forces exerted by cells on their environment to migrate as well as sense and manipulate their surroundings. To date, TFM research has been performed using incoherent imaging modalities and, until recently, has been largely confined to the study of cell-induced tractions within two-dimensions using highly artificial and controlled environments. As the field of mechanobiology advances, and demand grows for research in physiologically relevant 3D culture and in vivo models, TFM will require imaging modalities that support such settings. Optical coherence microscopy (OCM) is an interferometric imaging modality which enables 3D cellular resolution imaging in highly scattering environments. Moreover, optical coherence elastography (OCE) enables the measurement of tissue mechanical properties. OCE relies on the principle of measuring material deformations in response to artificially applied stress. By extension, similar techniques can enable the measurement of cell-induced deformations, imaged with OCM. We propose traction force optical coherence microscopy (TF-OCM) as a natural extension and partner to existing OCM and OCE methods. We report the first use of OCM data and digital image correlation to track temporally varying displacement fields exhibited within a 3D culture setting. These results mark the first steps toward the realization of TF-OCM in 2D and 3D settings, bolstering OCM as a platform for advancing research in mechanobiology.

General consumer communication tools for improved image management and communication in medicine.

PubMed

Rosset, Chantal; Rosset, Antoine; Ratib, Osman

2005-12-01

We elected to explore new technologies emerging on the general consumer market that can improve and facilitate image and data communication in medical and clinical environment. These new technologies developed for communication and storage of data can improve the user convenience and facilitate the communication and transport of images and related data beyond the usual limits and restrictions of a traditional picture archiving and communication systems (PACS) network. We specifically tested and implemented three new technologies provided on Apple computer platforms. (1) We adopted the iPod, a MP3 portable player with a hard disk storage, to easily and quickly move large number of DICOM images. (2) We adopted iChat, a videoconference and instant-messaging software, to transmit DICOM images in real time to a distant computer for conferencing teleradiology. (3) Finally, we developed a direct secure interface to use the iDisk service, a file-sharing service based on the WebDAV technology, to send and share DICOM files between distant computers. These three technologies were integrated in a new open-source image navigation and display software called OsiriX allowing for manipulation and communication of multimodality and multidimensional DICOM image data sets. This software is freely available as an open-source project at http://homepage.mac.com/rossetantoine/OsiriX. Our experience showed that the implementation of these technologies allowed us to significantly enhance the existing PACS with valuable new features without any additional investment or the need for complex extensions of our infrastructure. The added features such as teleradiology, secure and convenient image and data communication, and the use of external data storage services open the gate to a much broader extension of our imaging infrastructure to the outside world.

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.

A Multimodal Search Engine for Medical Imaging Studies.

PubMed

Pinho, Eduardo; Godinho, Tiago; Valente, Frederico; Costa, Carlos

2017-02-01

The use of digital medical imaging systems in healthcare institutions has increased significantly, and the large amounts of data in these systems have led to the conception of powerful support tools: recent studies on content-based image retrieval (CBIR) and multimodal information retrieval in the field hold great potential in decision support, as well as for addressing multiple challenges in healthcare systems, such as computer-aided diagnosis (CAD). However, the subject is still under heavy research, and very few solutions have become part of Picture Archiving and Communication Systems (PACS) in hospitals and clinics. This paper proposes an extensible platform for multimodal medical image retrieval, integrated in an open-source PACS software with profile-based CBIR capabilities. In this article, we detail a technical approach to the problem by describing its main architecture and each sub-component, as well as the available web interfaces and the multimodal query techniques applied. Finally, we assess our implementation of the engine with computational performance benchmarks.

Multimedia explorer: image database, image proxy-server and search-engine.

PubMed Central

Frankewitsch, T.; Prokosch, U.

1999-01-01

Multimedia plays a major role in medicine. Databases containing images, movies or other types of multimedia objects are increasing in number, especially on the WWW. However, no good retrieval mechanism or search engine currently exists to efficiently track down such multimedia sources in the vast of information provided by the WWW. Secondly, the tools for searching databases are usually not adapted to the properties of images. HTML pages do not allow complex searches. Therefore establishing a more comfortable retrieval involves the use of a higher programming level like JAVA. With this platform independent language it is possible to create extensions to commonly used web browsers. These applets offer a graphical user interface for high level navigation. We implemented a database using JAVA objects as the primary storage container which are then stored by a JAVA controlled ORACLE8 database. Navigation depends on a structured vocabulary enhanced by a semantic network. With this approach multimedia objects can be encapsulated within a logical module for quick data retrieval. PMID:10566463

Multimedia explorer: image database, image proxy-server and search-engine.

PubMed

Frankewitsch, T; Prokosch, U

1999-01-01

Multimedia plays a major role in medicine. Databases containing images, movies or other types of multimedia objects are increasing in number, especially on the WWW. However, no good retrieval mechanism or search engine currently exists to efficiently track down such multimedia sources in the vast of information provided by the WWW. Secondly, the tools for searching databases are usually not adapted to the properties of images. HTML pages do not allow complex searches. Therefore establishing a more comfortable retrieval involves the use of a higher programming level like JAVA. With this platform independent language it is possible to create extensions to commonly used web browsers. These applets offer a graphical user interface for high level navigation. We implemented a database using JAVA objects as the primary storage container which are then stored by a JAVA controlled ORACLE8 database. Navigation depends on a structured vocabulary enhanced by a semantic network. With this approach multimedia objects can be encapsulated within a logical module for quick data retrieval.

Integrated Optics for Planar imaging and Optical Signal Processing

NASA Astrophysics Data System (ADS)

Song, Qi

Silicon photonics is a subject of growing interest with the potential of delivering planar electro-optical devices with chip scale integration. Silicon-on-insulator (SOI) technology has provided a marvelous platform for photonics industry because of its advantages in integration capability in CMOS circuit and countless nonlinearity applications in optical signal processing. This thesis is focused on the investigation of planar imaging techniques on SOI platform and potential applications in ultra-fast optical signal processing. In the first part, a general review and background introduction about integrated photonics circuit and planar imaging technique are provided. In chapter 2, planar imaging platform is realized by a silicon photodiode on SOI chip. Silicon photodiode on waveguide provides a high numerical aperture for an imaging transceiver pixel. An erbium doped Y2O3 particle is excited by 1550nm Laser and the fluorescent image is obtained with assistance of the scanning system. Fluorescence image is reconstructed by using image de-convolution technique. Under photovoltaic mode, we use an on-chip photodiode and an external PIN photodiode to realize similar resolution as 5μm. In chapter 3, a time stretching technique is developed to a spatial domain to realize a 2D imaging system as an ultrafast imaging tool. The system is evaluated based on theoretical calculation. The experimental results are shown for a verification of system capability to imaging a micron size particle or a finger print. Meanwhile, dynamic information for a moving object is also achieved by correlation algorithm. In chapter 4, the optical leaky wave antenna based on SOI waveguide has been utilized for imaging applications and extensive numerical studied has been conducted. and the theoretical explanation is supported by leaky wave theory. The highly directive radiation has been obtained from the broadside with 15.7 dB directivity and a 3dB beam width of ΔØ 3dB ≈ 1.65° in free space environment when β -1 = 2.409 × 105/m, α=4.576 ×103/m. At the end, electronics beam-steering principle has been studied and the comprehensive model has been built to explain carrier transformation behavior in a PIN junction as individual silicon perturbation. Results show that 1019/cm3 is possible obtained with electron injection mechanism. Although the radiation modulation based on carrier injection of 1019/cm3 gives 0.5dB variation, resonant structure, such as Fabry Perrot Cavity, can be integrated with LOWAs to enhance modulation effect.

Polymer nanoassemblies with solvato- and halo-fluorochromism for drug release monitoring and metastasis imaging

PubMed Central

Reichel, Derek; Rychahou, Piotr; Bae, Younsoo

2015-01-01

Background: Theranostics, an emerging technique that combines therapeutic and diagnostic modalities for various diseases, holds promise to detect cancer in early stages, eradicate metastatic tumors and ultimately reduce cancer mortality. Methods & results: This study reports unique polymer nanoassemblies that increase fluorescence intensity upon addition of hydrophobic drugs and either increase or decrease fluorescence intensity in acidic environments, depending on nanoparticle core environment properties. Extensive spectroscopic analyses were performed to determine optimal excitation and emission wavelengths, which enabled real time measurement of drugs releasing from the nanoassemblies and ex vivo imaging of acidic liver metastatic tumors from mice. Conclusion: Polymer nanoassemblies with solvato- and halo-fluorochromic properties are promising platforms to develop novel theranostic tools for the detection and treatment of metastatic tumors. PMID:26446432

The COMET Sleep Research Platform.

PubMed

Nichols, Deborah A; DeSalvo, Steven; Miller, Richard A; Jónsson, Darrell; Griffin, Kara S; Hyde, Pamela R; Walsh, James K; Kushida, Clete A

2014-01-01

The Comparative Outcomes Management with Electronic Data Technology (COMET) platform is extensible and designed for facilitating multicenter electronic clinical research. Our research goals were the following: (1) to conduct a comparative effectiveness trial (CET) for two obstructive sleep apnea treatments-positive airway pressure versus oral appliance therapy; and (2) to establish a new electronic network infrastructure that would support this study and other clinical research studies. The COMET platform was created to satisfy the needs of CET with a focus on creating a platform that provides comprehensive toolsets, multisite collaboration, and end-to-end data management. The platform also provides medical researchers the ability to visualize and interpret data using business intelligence (BI) tools. COMET is a research platform that is scalable and extensible, and which, in a future version, can accommodate big data sets and enable efficient and effective research across multiple studies and medical specialties. The COMET platform components were designed for an eventual move to a cloud computing infrastructure that enhances sustainability, overall cost effectiveness, and return on investment.

The COMET Sleep Research Platform

PubMed Central

Nichols, Deborah A.; DeSalvo, Steven; Miller, Richard A.; Jónsson, Darrell; Griffin, Kara S.; Hyde, Pamela R.; Walsh, James K.; Kushida, Clete A.

2014-01-01

Introduction: The Comparative Outcomes Management with Electronic Data Technology (COMET) platform is extensible and designed for facilitating multicenter electronic clinical research. Background: Our research goals were the following: (1) to conduct a comparative effectiveness trial (CET) for two obstructive sleep apnea treatments—positive airway pressure versus oral appliance therapy; and (2) to establish a new electronic network infrastructure that would support this study and other clinical research studies. Discussion: The COMET platform was created to satisfy the needs of CET with a focus on creating a platform that provides comprehensive toolsets, multisite collaboration, and end-to-end data management. The platform also provides medical researchers the ability to visualize and interpret data using business intelligence (BI) tools. Conclusion: COMET is a research platform that is scalable and extensible, and which, in a future version, can accommodate big data sets and enable efficient and effective research across multiple studies and medical specialties. The COMET platform components were designed for an eventual move to a cloud computing infrastructure that enhances sustainability, overall cost effectiveness, and return on investment. PMID:25848590

Preparation, Surface Properties, and Therapeutic Applications of Gold Nanoparticles in Biomedicine.

PubMed

Panahi, Yunes; Mohammadhosseini, Majid; Nejati-Koshki, Kazem; Abadi, Azam Jafari Najaf; Moafi, Hadi Fallah; Akbarzadeh, Abolfazl; Farshbaf, Masoud

2017-02-01

Gold nanoparticles (AuNPs) due to their unique properties and manifold surface functionalities have been applied in bio-nanotechnology. The application of GNPs in recent medical and biological research is very extensive. Especially it involves applications such as detection and photothermalysis of microorganisms and cancer stem cells, biosensors; optical bio-imaging and observing of cells and these nanostructures also serve as practical platforms for therapeutic agents. In this review we studied all therapeutic applications of gold nanoparticles in biomedicine, synthesis methods, and surface properties. © Georg Thieme Verlag KG Stuttgart · New York.

A picture tells a thousand words: A content analysis of concussion-related images online.

PubMed

Ahmed, Osman H; Lee, Hopin; Struik, Laura L

2016-09-01

Recently image-sharing social media platforms have become a popular medium for sharing health-related images and associated information. However within the field of sports medicine, and more specifically sports related concussion, the content of images and meta-data shared through these popular platforms have not been investigated. The aim of this study was to analyse the content of concussion-related images and its accompanying meta-data on image-sharing social media platforms. We retrieved 300 images from Pinterest, Instagram and Flickr by using a standardised search strategy. All images were screened and duplicate images were removed. We excluded images if they were: non-static images; illustrations; animations; or screenshots. The content and characteristics of each image was evaluated using a customised coding scheme to determine major content themes, and images were referenced to the current international concussion management guidelines. From 300 potentially relevant images, 176 images were included for analysis; 70 from Pinterest, 63 from Flickr, and 43 from Instagram. Most images were of another person or a scene (64%), with the primary content depicting injured individuals (39%). The primary purposes of the images were to share a concussion-related incident (33%) and to dispense education (19%). For those images where it could be evaluated, the majority (91%) were found to reflect the Sports Concussion Assessment Tool 3 (SCAT3) guidelines. The ability to rapidly disseminate rich information though photos, images, and infographics to a wide-reaching audience suggests that image-sharing social media platforms could be used as an effective communication tool for sports concussion. Public health strategies could direct educative content to targeted populations via the use of image-sharing platforms. Further research is required to understand how image-sharing platforms can be used to effectively relay evidence-based information to patients and sports medicine clinicians. Copyright © 2016 Elsevier Ltd. All rights reserved.

Simulation analysis of space remote sensing image quality degradation induced by satellite platform vibration

NASA Astrophysics Data System (ADS)

Yang, Feng; Zhang, Xiaofang; Huang, Yu; Hao, Weiwei; Guo, Baiwei

2012-11-01

Satellite platform vibration causes the image quality to be degraded, it is necessary to study its influence on image quality. The forms of Satellite platform vibration consist of linear vibration, sinusoidal vibration and random vibration. Based on Matlab & Zemax, the simulation system has been developed for simulating impact caused by satellite platform vibration on image quality. Dynamic Data Exchange is used for the communication between Matlab and Zemax. The data of sinusoidal vibration are produced by sinusoidal curve with specific amplitude and frequency. The data of random vibration are obtained by combining sinusoidal signals with 10Hz, 100Hz and 200Hz's frequency, 100, 12, 1.9's amplitude and white noise with zero mean value. Satellite platform vibration data which produced by Matlab are added to the optical system, and its point spread function can be obtained by Zemax. Blurred image can be gained by making the convolution of PSF and the original image. The definition of the original image and the blurred image are evaluated by using average gradient values of image gray. The impact caused by the sine and random vibration of six DOFs on the image quality are respectively simulated. The simulation result reveal that the decenter of X-, Y-, Z- direction and the tilt of Z-direction have a little effect on image quality, while the tilt of X-, Y- direction make image quality seriously degraded. Thus, it can be concluded that correcting the error of satellite platform vibration by FSM is a viable and effective way.

The Design and Development of Test Platform for Wheat Precision Seeding Based on Image Processing Techniques

NASA Astrophysics Data System (ADS)

Li, Qing; Lin, Haibo; Xiu, Yu-Feng; Wang, Ruixue; Yi, Chuijie

The test platform of wheat precision seeding based on image processing techniques is designed to develop the wheat precision seed metering device with high efficiency and precision. Using image processing techniques, this platform gathers images of seeds (wheat) on the conveyer belt which are falling from seed metering device. Then these data are processed and analyzed to calculate the qualified rate, reseeding rate and leakage sowing rate, etc. This paper introduces the whole structure, design parameters of the platform and hardware & software of the image acquisition system were introduced, as well as the method of seed identification and seed-space measurement using image's threshold and counting the seed's center. By analyzing the experimental result, the measurement error is less than ± 1mm.

Design of e-Science platform for biomedical imaging research cross multiple academic institutions and hospitals

NASA Astrophysics Data System (ADS)

Zhang, Jianguo; Zhang, Kai; Yang, Yuanyuan; Ling, Tonghui; Wang, Tusheng; Wang, Mingqing; Hu, Haibo; Xu, Xuemin

2012-02-01

More and more image informatics researchers and engineers are considering to re-construct imaging and informatics infrastructure or to build new framework to enable multiple disciplines of medical researchers, clinical physicians and biomedical engineers working together in a secured, efficient, and transparent cooperative environment. In this presentation, we show an outline and our preliminary design work of building an e-Science platform for biomedical imaging and informatics research and application in Shanghai. We will present our consideration and strategy on designing this platform, and preliminary results. We also will discuss some challenges and solutions in building this platform.

TrackMate: An open and extensible platform for single-particle tracking.

PubMed

Tinevez, Jean-Yves; Perry, Nick; Schindelin, Johannes; Hoopes, Genevieve M; Reynolds, Gregory D; Laplantine, Emmanuel; Bednarek, Sebastian Y; Shorte, Spencer L; Eliceiri, Kevin W

2017-02-15

We present TrackMate, an open source Fiji plugin for the automated, semi-automated, and manual tracking of single-particles. It offers a versatile and modular solution that works out of the box for end users, through a simple and intuitive user interface. It is also easily scriptable and adaptable, operating equally well on 1D over time, 2D over time, 3D over time, or other single and multi-channel image variants. TrackMate provides several visualization and analysis tools that aid in assessing the relevance of results. The utility of TrackMate is further enhanced through its ability to be readily customized to meet specific tracking problems. TrackMate is an extensible platform where developers can easily write their own detection, particle linking, visualization or analysis algorithms within the TrackMate environment. This evolving framework provides researchers with the opportunity to quickly develop and optimize new algorithms based on existing TrackMate modules without the need of having to write de novo user interfaces, including visualization, analysis and exporting tools. The current capabilities of TrackMate are presented in the context of three different biological problems. First, we perform Caenorhabditis-elegans lineage analysis to assess how light-induced damage during imaging impairs its early development. Our TrackMate-based lineage analysis indicates the lack of a cell-specific light-sensitive mechanism. Second, we investigate the recruitment of NEMO (NF-κB essential modulator) clusters in fibroblasts after stimulation by the cytokine IL-1 and show that photodamage can generate artifacts in the shape of TrackMate characterized movements that confuse motility analysis. Finally, we validate the use of TrackMate for quantitative lifetime analysis of clathrin-mediated endocytosis in plant cells. Copyright © 2016 The Author(s). Published by Elsevier Inc. All rights reserved.

Calibration of Viking imaging system pointing, image extraction, and optical navigation measure

NASA Technical Reports Server (NTRS)

Breckenridge, W. G.; Fowler, J. W.; Morgan, E. M.

1977-01-01

Pointing control and knowledge accuracy of Viking Orbiter science instruments is controlled by the scan platform. Calibration of the scan platform and the imaging system was accomplished through mathematical models. The calibration procedure and results obtained for the two Viking spacecraft are described. Included are both ground and in-flight scan platform calibrations, and the additional calibrations unique to optical navigation.

Phenotiki: an open software and hardware platform for affordable and easy image-based phenotyping of rosette-shaped plants.

PubMed

Minervini, Massimo; Giuffrida, Mario V; Perata, Pierdomenico; Tsaftaris, Sotirios A

2017-04-01

Phenotyping is important to understand plant biology, but current solutions are costly, not versatile or are difficult to deploy. To solve this problem, we present Phenotiki, an affordable system for plant phenotyping that, relying on off-the-shelf parts, provides an easy to install and maintain platform, offering an out-of-box experience for a well-established phenotyping need: imaging rosette-shaped plants. The accompanying software (with available source code) processes data originating from our device seamlessly and automatically. Our software relies on machine learning to devise robust algorithms, and includes an automated leaf count obtained from 2D images without the need of depth (3D). Our affordable device (~€200) can be deployed in growth chambers or greenhouse to acquire optical 2D images of approximately up to 60 adult Arabidopsis rosettes concurrently. Data from the device are processed remotely on a workstation or via a cloud application (based on CyVerse). In this paper, we present a proof-of-concept validation experiment on top-view images of 24 Arabidopsis plants in a combination of genotypes that has not been compared previously. Phenotypic analysis with respect to morphology, growth, color and leaf count has not been performed comprehensively before now. We confirm the findings of others on some of the extracted traits, showing that we can phenotype at reduced cost. We also perform extensive validations with external measurements and with higher fidelity equipment, and find no loss in statistical accuracy when we use the affordable setting that we propose. Device set-up instructions and analysis software are publicly available ( http://phenotiki.com). © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

Gold nanoparticles for cancer theranostics — A brief update

DOE PAGES

Zhao, Ning; Pan, Yongxu; Cheng, Zhen; ...

2016-03-04

Gold nanoparticles (AuNPs) exhibit superior optical and physical properties for more effective treatment of cancer through incorporating both diagnostic and therapeutic functions into one single platform. The ability to passively accumulate on tumor cells provides AuNPs the opportunity to become an attractive contrast agent for X-ray based computed tomography (CT) imaging in vivo. Because of facile surface modification, various size and shape of AuNPs have been extensively functionalized and applied as active nanoprobes and drug carriers for cancer targeted theranostics. Moreover, their capabilities on producing photoacoustic (PA) signals and photothermal effects have been used to image and treat tumor progression,more » respectively. Furthermore, we review the developments of AuNPs as cancer diagnostics and chemotherapeutic drug vector, summarizing strategies for tumor targeting and their applications in vitro and in vivo.« less

Mobile service for open data visualization on geo-based images

NASA Astrophysics Data System (ADS)

Lee, Kiwon; Kim, Kwangseob; Kang, Sanggoo

2015-12-01

Since the early 2010s, governments in most countries have adopted and promoted open data policy and open data platform. Korea are in the same situation, and government and public organizations have operated the public-accessible open data portal systems since 2011. The number of open data and data type have been increasing every year. These trends are more expandable or extensible on mobile environments. The purpose of this study is to design and implement a mobile application service to visualize various typed or formatted public open data with geo-based images on the mobile web. Open data cover downloadable data sets or open-accessible data application programming interface API. Geo-based images mean multi-sensor satellite imageries which are referred in geo-coordinates and matched with digital map sets. System components for mobile service are fully based on open sources and open development environments without any commercialized tools: PostgreSQL for database management system, OTB for remote sensing image processing, GDAL for data conversion, GeoServer for application server, OpenLayers for mobile web mapping, R for data analysis and D3.js for web-based data graphic processing. Mobile application in client side was implemented by using HTML5 for cross browser and cross platform. The result shows many advantageous points such as linking open data and geo-based data, integrating open data and open source, and demonstrating mobile applications with open data. It is expected that this approach is cost effective and process efficient implementation strategy for intelligent earth observing data.

Deformable image registration with a featurelet algorithm: implementation as a 3D-slicer extension and validation

NASA Astrophysics Data System (ADS)

Renner, A.; Furtado, H.; Seppenwoolde, Y.; Birkfellner, W.; Georg, D.

2016-03-01

A radiotherapy (RT) treatment can last for several weeks. In that time organ motion and shape changes introduce uncertainty in dose application. Monitoring and quantifying the change can yield a more precise irradiation margin definition and thereby reduce dose delivery to healthy tissue and adjust tumor targeting. Deformable image registration (DIR) has the potential to fulfill this task by calculating a deformation field (DF) between a planning CT and a repeated CT of the altered anatomy. Application of the DF on the original contours yields new contours that can be used for an adapted treatment plan. DIR is a challenging method and therefore needs careful user interaction. Without a proper graphical user interface (GUI) a misregistration cannot be easily detected by visual inspection and the results cannot be fine-tuned by changing registration parameters. To provide a DIR algorithm with such a GUI available for everyone, we created the extension Featurelet-Registration for the open source software platform 3D Slicer. The registration logic is an upgrade of an in-house-developed DIR method, which is a featurelet-based piecewise rigid registration. The so called "featurelets" are equally sized rectangular subvolumes of the moving image which are rigidly registered to rectangular search regions on the fixed image. The output is a deformed image and a deformation field. Both can be visualized directly in 3D Slicer facilitating the interpretation and quantification of the results. For validation of the registration accuracy two deformable phantoms were used. The performance was benchmarked against a demons algorithm with comparable results.

Hybrid-modality high-resolution imaging: for diagnostic biomedical imaging and sensing for disease diagnosis

NASA Astrophysics Data System (ADS)

Murukeshan, Vadakke M.; Hoong Ta, Lim

2014-11-01

Medical diagnostics in the recent past has seen the challenging trend to come up with dual and multi-modality imaging for implementing better diagnostic procedures. The changes in tissues in the early disease stages are often subtle and can occur beneath the tissue surface. In most of these cases, conventional types of medical imaging using optics may not be able to detect these changes easily due to its penetration depth of the orders of 1 mm. Each imaging modality has its own advantages and limitations, and the use of a single modality is not suitable for every diagnostic applications. Therefore the need for multi or hybrid-modality imaging arises. Combining more than one imaging modalities overcomes the limitation of individual imaging method and integrates the respective advantages into a single setting. In this context, this paper will be focusing on the research and development of two multi-modality imaging platforms. The first platform combines ultrasound and photoacoustic imaging for diagnostic applications in the eye. The second platform consists of optical hyperspectral and photoacoustic imaging for diagnostic applications in the colon. Photoacoustic imaging is used as one of the modalities in both platforms as it can offer deeper penetration depth compared to optical imaging. The optical engineering and research challenges in developing the dual/multi-modality platforms will be discussed, followed by initial results validating the proposed scheme. The proposed schemes offer high spatial and spectral resolution imaging and sensing, and is expected to offer potential biomedical imaging solutions in the near future.

Novel Cs-Based Upconversion Nanoparticles as Dual-Modal CT and UCL Imaging Agents for Chemo-Photothermal Synergistic Therapy.

PubMed

Liu, Yuxin; Li, Luoyuan; Guo, Quanwei; Wang, Lu; Liu, Dongdong; Wei, Ziwei; Zhou, Jing

2016-01-01

Lanthanide-based contrast agents have attracted increasing attention for their unique properties and potential applications in cancer theranostics. To date, many of these agents have been studied extensively in cells and small animal models. However, performance of these theranostic nanoparticles requires further improvement. In this study, a novel CsLu2F7:Yb,Er,Tm-based visual therapeutic platform was developed for imaging-guided synergistic cancer therapy. Due to the presence of the heavy alkali metal Cesium (Cs) in host lattice, the nanoplatform can provide a higher resolution X-ray CT imaging than many other reported lanthanide-based CT contrast agents. Furthermore, by using the targeted RGD motif, chemotherapy drug alpha-tocopheryl succinate (α-TOS), and photothermal coupling agent ICG, this nanoplatform simultaneously provides multifunctional imaging and targeted synergistic therapy. To demonstrate the theranostic performance of this novel nanoplatform in vivo, visual diagnosis in the small animal model was realized by UCL/CT imaging which was further integrated with targeted chemo-photothermal synergistic therapy. These results provided evidence for the successful construction of a novel lanthanide-based nanoplatform coupled with multimodal imaging diagnosis and potential application in synergistic cancer theranostics.

Open-source software platform for medical image segmentation applications

NASA Astrophysics Data System (ADS)

Namías, R.; D'Amato, J. P.; del Fresno, M.

2017-11-01

Segmenting 2D and 3D images is a crucial and challenging problem in medical image analysis. Although several image segmentation algorithms have been proposed for different applications, no universal method currently exists. Moreover, their use is usually limited when detection of complex and multiple adjacent objects of interest is needed. In addition, the continually increasing volumes of medical imaging scans require more efficient segmentation software design and highly usable applications. In this context, we present an extension of our previous segmentation framework which allows the combination of existing explicit deformable models in an efficient and transparent way, handling simultaneously different segmentation strategies and interacting with a graphic user interface (GUI). We present the object-oriented design and the general architecture which consist of two layers: the GUI at the top layer, and the processing core filters at the bottom layer. We apply the framework for segmenting different real-case medical image scenarios on public available datasets including bladder and prostate segmentation from 2D MRI, and heart segmentation in 3D CT. Our experiments on these concrete problems show that this framework facilitates complex and multi-object segmentation goals while providing a fast prototyping open-source segmentation tool.

SPEKTROP DPU: optoelectronic platform for fast multispectral imaging

NASA Astrophysics Data System (ADS)

Graczyk, Rafal; Sitek, Piotr; Stolarski, Marcin

2010-09-01

In recent years it easy to spot and increasing need of high-quality Earth imaging in airborne and space applications. This is due fact that government and local authorities urge for up to date topological data for administrative purposes. On the other hand, interest in environmental sciences, push for ecological approach, efficient agriculture and forests management are also heavily supported by Earth images in various resolutions and spectral ranges. "SPEKTROP DPU: Opto-electronic platform for fast multi-spectral imaging" paper describes architectural datails of data processing unit, part of universal and modular platform that provides high quality imaging functionality in aerospace applications.

Open source pipeline for ESPaDOnS reduction and analysis

NASA Astrophysics Data System (ADS)

Martioli, Eder; Teeple, Doug; Manset, Nadine; Devost, Daniel; Withington, Kanoa; Venne, Andre; Tannock, Megan

2012-09-01

OPERA is a Canada-France-Hawaii Telescope (CFHT) open source collaborative software project currently under development for an ESPaDOnS echelle spectro-polarimetric image reduction pipeline. OPERA is designed to be fully automated, performing calibrations and reduction, producing one-dimensional intensity and polarimetric spectra. The calibrations are performed on two-dimensional images. Spectra are extracted using an optimal extraction algorithm. While primarily designed for CFHT ESPaDOnS data, the pipeline is being written to be extensible to other echelle spectrographs. A primary design goal is to make use of fast, modern object-oriented technologies. Processing is controlled by a harness, which manages a set of processing modules, that make use of a collection of native OPERA software libraries and standard external software libraries. The harness and modules are completely parametrized by site configuration and instrument parameters. The software is open- ended, permitting users of OPERA to extend the pipeline capabilities. All these features have been designed to provide a portable infrastructure that facilitates collaborative development, code re-usability and extensibility. OPERA is free software with support for both GNU/Linux and MacOSX platforms. The pipeline is hosted on SourceForge under the name "opera-pipeline".

A hybrid approach to device integration on a genetic analysis platform

NASA Astrophysics Data System (ADS)

Brennan, Des; Jary, Dorothee; Kurg, Ants; Berik, Evgeny; Justice, John; Aherne, Margaret; Macek, Milan; Galvin, Paul

2012-10-01

Point-of-care (POC) systems require significant component integration to implement biochemical protocols associated with molecular diagnostic assays. Hybrid platforms where discrete components are combined in a single platform are a suitable approach to integration, where combining multiple device fabrication steps on a single substrate is not possible due to incompatible or costly fabrication steps. We integrate three devices each with a specific system functionality: (i) a silicon electro-wetting-on-dielectric (EWOD) device to move and mix sample and reagent droplets in an oil phase, (ii) a polymer microfluidic chip containing channels and reservoirs and (iii) an aqueous phase glass microarray for fluorescence microarray hybridization detection. The EWOD device offers the possibility of fully integrating on-chip sample preparation using nanolitre sample and reagent volumes. A key challenge is sample transfer from the oil phase EWOD device to the aqueous phase microarray for hybridization detection. The EWOD device, waveguide performance and functionality are maintained during the integration process. An on-chip biochemical protocol for arrayed primer extension (APEX) was implemented for single nucleotide polymorphism (SNiP) analysis. The prepared sample is aspirated from the EWOD oil phase to the aqueous phase microarray for hybridization. A bench-top instrumentation system was also developed around the integrated platform to drive the EWOD electrodes, implement APEX sample heating and image the microarray after hybridization.

Developmental Testing of Electric Thrust Vector Control Systems for Manned Launch Vehicle Applications

NASA Technical Reports Server (NTRS)

Bates, Lisa B.; Young, David T.

2012-01-01

This paper describes recent developmental testing to verify the integration of a developmental electromechanical actuator (EMA) with high rate lithium ion batteries and a cross platform extensible controller. Testing was performed at the Thrust Vector Control Research, Development and Qualification Laboratory at the NASA George C. Marshall Space Flight Center. Electric Thrust Vector Control (ETVC) systems like the EMA may significantly reduce recurring launch costs and complexity compared to heritage systems. Electric actuator mechanisms and control requirements across dissimilar platforms are also discussed with a focus on the similarities leveraged and differences overcome by the cross platform extensible common controller architecture.

RadMAP: The Radiological Multi-sensor Analysis Platform

NASA Astrophysics Data System (ADS)

Bandstra, Mark S.; Aucott, Timothy J.; Brubaker, Erik; Chivers, Daniel H.; Cooper, Reynold J.; Curtis, Joseph C.; Davis, John R.; Joshi, Tenzing H.; Kua, John; Meyer, Ross; Negut, Victor; Quinlan, Michael; Quiter, Brian J.; Srinivasan, Shreyas; Zakhor, Avideh; Zhang, Richard; Vetter, Kai

2016-12-01

The variability of gamma-ray and neutron background during the operation of a mobile detector system greatly limits the ability of the system to detect weak radiological and nuclear threats. The natural radiation background measured by a mobile detector system is the result of many factors, including the radioactivity of nearby materials, the geometric configuration of those materials and the system, the presence of absorbing materials, and atmospheric conditions. Background variations tend to be highly non-Poissonian, making it difficult to set robust detection thresholds using knowledge of the mean background rate alone. The Radiological Multi-sensor Analysis Platform (RadMAP) system is designed to allow the systematic study of natural radiological background variations and to serve as a development platform for emerging concepts in mobile radiation detection and imaging. To do this, RadMAP has been used to acquire extensive, systematic background measurements and correlated contextual data that can be used to test algorithms and detector modalities at low false alarm rates. By combining gamma-ray and neutron detector systems with data from contextual sensors, the system enables the fusion of data from multiple sensors into novel data products. The data are curated in a common format that allows for rapid querying across all sensors, creating detailed multi-sensor datasets that are used to study correlations between radiological and contextual data, and develop and test novel techniques in mobile detection and imaging. In this paper we will describe the instruments that comprise the RadMAP system, the effort to curate and provide access to multi-sensor data, and some initial results on the fusion of contextual and radiological data.

Applications of Sentinel-2 data for agriculture and forest monitoring using the absolute difference (ZABUD) index derived from the AgroEye software (ESA)

NASA Astrophysics Data System (ADS)

de Kok, R.; WeŻyk, P.; PapieŻ, M.; Migo, L.

2017-10-01

To convince new users of the advantages of the Sentinel_2 sensor, a simplification of classic remote sensing tools allows to create a platform of communication among domain specialists of agricultural analysis, visual image interpreters and remote sensing programmers. An index value, known in the remote sensing user domain as "Zabud" was selected to represent, in color, the essentials of a time series analysis. The color index used in a color atlas offers a working platform for an agricultural field control. This creates a database of test and training areas that enables rapid anomaly detection in the agricultural domain. The use cases and simplifications now function as an introduction to Sentinel_2 based remote sensing, in an area that before relies on VHR imagery and aerial data, to serve mainly the visual interpretation. The database extension with detected anomalies allows developers of open source software to design solutions for further agricultural control with remote sensing.

[Study of sharing platform of web-based enhanced extracorporeal counterpulsation hemodynamic waveform data].

PubMed

Huang, Mingbo; Hu, Ding; Yu, Donglan; Zheng, Zhensheng; Wang, Kuijian

2011-12-01

Enhanced extracorporeal counterpulsation (EECP) information consists of both text and hemodynamic waveform data. At present EECP text information has been successfully managed through Web browser, while the management and sharing of hemodynamic waveform data through Internet has not been solved yet. In order to manage EECP information completely, based on the in-depth analysis of EECP hemodynamic waveform file of digital imaging and communications in medicine (DICOM) format and its disadvantages in Internet sharing, we proposed the use of the extensible markup language (XML), which is currently the Internet popular data exchange standard, as the storage specification for the sharing of EECP waveform data. Then we designed a web-based sharing system of EECP hemodynamic waveform data via ASP. NET 2.0 platform. Meanwhile, we specifically introduced the four main system function modules and their implement methods, including DICOM to XML conversion module, EECP waveform data management module, retrieval and display of EECP waveform module and the security mechanism of the system.

Quantum cascade lasers for defense and security

NASA Astrophysics Data System (ADS)

Day, Timothy; Pushkarsky, Michael; Caffey, Dave; Cecchetti, Kristen; Arp, Ron; Whitmore, Alex; Henson, Michael; Takeuchi, Eric B.

2013-10-01

Quantum cascade laser (QCL) systems are mature and at the vanguard of a new generation of products that support military applications such as Infrared Countermeasures (IRCM) and targeting. The demanding product requirements for aircraft platforms that include reduced size, weight, power consumption and cost (SWaP-C) extends to portable, battery powered handheld products. QCL technology operates throughout the mid-wave (MWIR) and long-wave (LWIR) infrared to provide new capabilities that leverage existing thermal imaging cameras. In addition to their suitability for aircraft platforms, QCL products are a natural fit to meet operator demands for small, lightweight pointer and beacon capabilities. Field-testing of high power, lightweight, battery operated devices has demonstrated their utility across a range of air and ground applications. This talk will present an overview of QCL technology and the Defense and Security products and capabilities that are enabled by it. This talk will also provide an overview of the extensive environmental and performance testing associated with products based on QCL technology.

Xi-cam: a versatile interface for data visualization and analysis

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

Pandolfi, Ronald J.; Allan, Daniel B.; Arenholz, Elke

Xi-cam is an extensible platform for data management, analysis and visualization.Xi-camaims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core ofXi-camis an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. WithXi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data.Xi-cam's plugin-based architecture targetsmore » cross-facility and cross-technique collaborative development, in support of multi-modal analysis.Xi-camis open-source and cross-platform, and available for download on GitHub.« less

Xi-cam: a versatile interface for data visualization and analysis

DOE PAGES

Pandolfi, Ronald J.; Allan, Daniel B.; Arenholz, Elke; ...

2018-05-31

Xi-cam is an extensible platform for data management, analysis and visualization.Xi-camaims to provide a flexible and extensible approach to synchrotron data treatment as a solution to rising demands for high-volume/high-throughput processing pipelines. The core ofXi-camis an extensible plugin-based graphical user interface platform which provides users with an interactive interface to processing algorithms. Plugins are available for SAXS/WAXS/GISAXS/GIWAXS, tomography and NEXAFS data. WithXi-cam's `advanced' mode, data processing steps are designed as a graph-based workflow, which can be executed live, locally or remotely. Remote execution utilizes high-performance computing or de-localized resources, allowing for the effective reduction of high-throughput data.Xi-cam's plugin-based architecture targetsmore » cross-facility and cross-technique collaborative development, in support of multi-modal analysis.Xi-camis open-source and cross-platform, and available for download on GitHub.« less

A Strategic Plan for Introducing, Implementing, Managing, and Monitoring an Urban Extension Platform

ERIC Educational Resources Information Center

Warner, Laura A.; Vavrina, Charlie S.; Campbell, Mary L.; Elliott, Monica L.; Northrop, Robert J.; Place, Nick T.

2017-01-01

Florida's Strategic Plan for Extension in Metropolitan Regions reflects an adaptive management approach to the state's urban Extension mission within the context of establishing essential elements, performance indicators, key outcomes, and suggested alternatives for action. Extension leadership has adopted the strategic plan, and implementation…

SU-D-BRD-02: A Web-Based Image Processing and Plan Evaluation Platform (WIPPEP) for Future Cloud-Based Radiotherapy

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

Chai, X; Liu, L; Xing, L

Purpose: Visualization and processing of medical images and radiation treatment plan evaluation have traditionally been constrained to local workstations with limited computation power and ability of data sharing and software update. We present a web-based image processing and planning evaluation platform (WIPPEP) for radiotherapy applications with high efficiency, ubiquitous web access, and real-time data sharing. Methods: This software platform consists of three parts: web server, image server and computation server. Each independent server communicates with each other through HTTP requests. The web server is the key component that provides visualizations and user interface through front-end web browsers and relay informationmore » to the backend to process user requests. The image server serves as a PACS system. The computation server performs the actual image processing and dose calculation. The web server backend is developed using Java Servlets and the frontend is developed using HTML5, Javascript, and jQuery. The image server is based on open source DCME4CHEE PACS system. The computation server can be written in any programming language as long as it can send/receive HTTP requests. Our computation server was implemented in Delphi, Python and PHP, which can process data directly or via a C++ program DLL. Results: This software platform is running on a 32-core CPU server virtually hosting the web server, image server, and computation servers separately. Users can visit our internal website with Chrome browser, select a specific patient, visualize image and RT structures belonging to this patient and perform image segmentation running Delphi computation server and Monte Carlo dose calculation on Python or PHP computation server. Conclusion: We have developed a webbased image processing and plan evaluation platform prototype for radiotherapy. This system has clearly demonstrated the feasibility of performing image processing and plan evaluation platform through a web browser and exhibited potential for future cloud based radiotherapy.« less

The content of social media's shared images about Ebola: a retrospective study.

PubMed

Seltzer, E K; Jean, N S; Kramer-Golinkoff, E; Asch, D A; Merchant, R M

2015-09-01

Social media have strongly influenced awareness and perceptions of public health emergencies, but a considerable amount of social media content is now carried through images, rather than just text. This study's objective is to explore how image-sharing platforms are used for information dissemination in public health emergencies. Retrospective review of images posted on two popular image-sharing platforms to characterize public discourse about Ebola. Using the keyword '#ebola' we identified a 1% sample of images posted on Instagram and Flickr across two sequential weeks in November 2014. Images from both platforms were independently coded by two reviewers and characterized by themes. We reviewed 1217 images posted on Instagram and Flickr and identified themes. Nine distinct themes were identified. These included: images of health care workers and professionals [308 (25%)], West Africa [75 (6%)], the Ebola virus [59 (5%)], and artistic renderings of Ebola [64 (5%)]. Also identified were images with accompanying embedded text related to Ebola and associated: facts [68 (6%)], fears [40 (3%)], politics [46 (4%)], and jokes [284 (23%)]. Several [273 (22%)] images were unrelated to Ebola or its sequelae. Instagram images were primarily coded as jokes [255 (42%)] or unrelated [219 (36%)], while Flickr images primarily depicted health care workers and other professionals [281 (46%)] providing care or other services for prevention or treatment. Image sharing platforms are being used for information exchange about public health crises, like Ebola. Use differs by platform and discerning these differences can help inform future uses for health care professionals and researchers seeking to assess public fears and misinformation or provide targeted education/awareness interventions. Copyright © 2015 The Royal Institute of Public Health. All rights reserved.

Open source software projects of the caBIG In Vivo Imaging Workspace Software special interest group.

PubMed

Prior, Fred W; Erickson, Bradley J; Tarbox, Lawrence

2007-11-01

The Cancer Bioinformatics Grid (caBIG) program was created by the National Cancer Institute to facilitate sharing of IT infrastructure, data, and applications among the National Cancer Institute-sponsored cancer research centers. The program was launched in February 2004 and now links more than 50 cancer centers. In April 2005, the In Vivo Imaging Workspace was added to promote the use of imaging in cancer clinical trials. At the inaugural meeting, four special interest groups (SIGs) were established. The Software SIG was charged with identifying projects that focus on open-source software for image visualization and analysis. To date, two projects have been defined by the Software SIG. The eXtensible Imaging Platform project has produced a rapid application development environment that researchers may use to create targeted workflows customized for specific research projects. The Algorithm Validation Tools project will provide a set of tools and data structures that will be used to capture measurement information and associated needed to allow a gold standard to be defined for the given database against which change analysis algorithms can be tested. Through these and future efforts, the caBIG In Vivo Imaging Workspace Software SIG endeavors to advance imaging informatics and provide new open-source software tools to advance cancer research.

Portable fiber-optic taper coupled optical microscopy platform

NASA Astrophysics Data System (ADS)

Wang, Weiming; Yu, Yan; Huang, Hui; Ou, Jinping

2017-04-01

The optical fiber taper coupled with CMOS has advantages of high sensitivity, compact structure and low distortion in the imaging platform. So it is widely used in low light, high speed and X-ray imaging systems. In the meanwhile, the peculiarity of the coupled structure can meet the needs of the demand in microscopy imaging. Toward this end, we developed a microscopic imaging platform based on the coupling of cellphone camera module and fiber optic taper for the measurement of the human blood samples and ascaris lumbricoides. The platform, weighing 70 grams, is based on the existing camera module of the smartphone and a fiber-optic array which providing a magnification factor of 6x.The top facet of the taper, on which samples are placed, serves as an irregular sampling grid for contact imaging. The magnified images of the sample, located on the bottom facet of the fiber, are then projected onto the CMOS sensor. This paper introduces the portable medical imaging system based on the optical fiber coupling with CMOS, and theoretically analyzes the feasibility of the system. The image data and process results either can be stored on the memory or transmitted to the remote medical institutions for the telemedicine. We validate the performance of this cell-phone based microscopy platform using human blood samples and test target, achieving comparable results to a standard bench-top microscope.

Real-time label-free quantitative fluorescence microscopy-based detection of ATP using a tunable fluorescent nano-aptasensor platform

NASA Astrophysics Data System (ADS)

Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung

2015-11-01

Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr05839b

User Oriented Platform for Data Analytics in Medical Imaging Repositories.

PubMed

Valerio, Miguel; Godinho, Tiago Marques; Costa, Carlos

2016-01-01

The production of medical imaging studies and associated data has been growing in the last decades. Their primary use is to support medical diagnosis and treatment processes. However, the secondary use of the tremendous amount of stored data is generally more limited. Nowadays, medical imaging repositories have turned into rich databanks holding not only the images themselves, but also a wide range of metadata related to the medical practice. Exploring these repositories through data analysis and business intelligence techniques has the potential of increasing the efficiency and quality of the medical practice. Nevertheless, the continuous production of tremendous amounts of data makes their analysis difficult by conventional approaches. This article proposes a novel automated methodology to derive knowledge from medical imaging repositories that does not disrupt the regular medical practice. Our method is able to apply statistical analysis and business intelligence techniques directly on top of live institutional repositories. It is a Web-based solution that provides extensive dashboard capabilities, including complete charting and reporting options, combined with data mining components. Moreover, it enables the operator to set a wide multitude of query parameters and operators through the use of an intuitive graphical interface.

An actuator extension transformation for a motion simulator and an inverse transformation applying Newton-Raphson's method

NASA Technical Reports Server (NTRS)

Dieudonne, J. E.

1972-01-01

A set of equations which transform position and angular orientation of the centroid of the payload platform of a six-degree-of-freedom motion simulator into extensions of the simulator's actuators has been derived and is based on a geometrical representation of the system. An iterative scheme, Newton-Raphson's method, has been successfully used in a real time environment in the calculation of the position and angular orientation of the centroid of the payload platform when the magnitude of the actuator extensions is known. Sufficient accuracy is obtained by using only one Newton-Raphson iteration per integration step of the real time environment.

Friendly Extensible Transfer Tool Beta Version

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

Collins, William P.; Gutierrez, Kenneth M.; McRee, Susan R.

2016-04-15

Often data transfer software is designed to meet specific requirements or apply to specific environments. Frequently, this requires source code integration for added functionality. An extensible data transfer framework is needed to more easily incorporate new capabilities, in modular fashion. Using FrETT framework, functionality may be incorporated (in many cases without need of source code) to handle new platform capabilities: I/O methods (e.g., platform specific data access), network transport methods, data processing (e.g., data compression.).

Engineering and algorithm design for an image processing Api: a technical report on ITK--the Insight Toolkit.

PubMed

Yoo, Terry S; Ackerman, Michael J; Lorensen, William E; Schroeder, Will; Chalana, Vikram; Aylward, Stephen; Metaxas, Dimitris; Whitaker, Ross

2002-01-01

We present the detailed planning and execution of the Insight Toolkit (ITK), an application programmers interface (API) for the segmentation and registration of medical image data. This public resource has been developed through the NLM Visible Human Project, and is in beta test as an open-source software offering under cost-free licensing. The toolkit concentrates on 3D medical data segmentation and registration algorithms, multimodal and multiresolution capabilities, and portable platform independent support for Windows, Linux/Unix systems. This toolkit was built using current practices in software engineering. Specifically, we embraced the concept of generic programming during the development of these tools, working extensively with C++ templates and the freedom and flexibility they allow. Software development tools for distributed consortium-based code development have been created and are also publicly available. We discuss our assumptions, design decisions, and some lessons learned.

Extension Online: Utilizing Technology to Enhance Educational Outreach

ERIC Educational Resources Information Center

Green, Stephen

2012-01-01

Extension Online is an Internet-based online course platform that enables the Texas AgriLife Extension Service's Family Development and Resource Management (FDRM) unit to reach tens of thousands of users across the U.S. annually with research-based information. This article introduces readers to Extension Online by describing the history of its…

Floating production platforms and their applications in the development of oil and gas fields in the South China Sea

NASA Astrophysics Data System (ADS)

Zhang, Dagang; Chen, Yongjun; Zhang, Tianyu

2014-03-01

This paper studies the current available options for floating production platforms in developing deepwater oil fields and the potential development models of future oil and gas exploration in the South China Sea. A detailed review of current deepwater platforms worldwide was performed through the examples of industry projects, and the pros and cons of each platform are discussed. Four types of platforms are currently used for the deepwater development: tension leg platform, Spar, semi-submersible platform, and the floating production system offloading. Among these, the TLP and Spar can be used for dry tree applications, and have gained popularity in recent years. The dry tree application enables the extension of the drilling application for fixed platforms into floating systems, and greatly reduces the cost and complexity of the subsea operation. Newly built wet tree semi-submersible production platforms for ultra deepwater are also getting their application, mainly due to the much needed payload for deepwater making the conversion of the old drilling semi-submersible platforms impossible. These platforms have been used in different fields around the world for different environments; each has its own advantages and disadvantages. There are many challenges with the successful use of these floating platforms. A lot of lessons have been learned and extensive experience accumulated through the many project applications. Key technologies are being reviewed for the successful use of floating platforms for field development, and potential future development needs are being discussed. Some of the technologies and experience of platform applications can be well used for the development of the South China Sea oil and gas field.

Platform-independent method for computer aided schematic drawings

DOEpatents

Vell, Jeffrey L [Slingerlands, NY; Siganporia, Darius M [Clifton Park, NY; Levy, Arthur J [Fort Lauderdale, FL

2012-02-14

A CAD/CAM method is disclosed for a computer system to capture and interchange schematic drawing and associated design information. The schematic drawing and design information are stored in an extensible, platform-independent format.

Initial experience with a handheld device digital imaging and communications in medicine viewer: OsiriX mobile on the iPhone.

PubMed

Choudhri, Asim F; Radvany, Martin G

2011-04-01

Medical imaging is commonly used to diagnose many emergent conditions, as well as plan treatment. Digital images can be reviewed on almost any computing platform. Modern mobile phones and handheld devices are portable computing platforms with robust software programming interfaces, powerful processors, and high-resolution displays. OsiriX mobile, a new Digital Imaging and Communications in Medicine viewing program, is available for the iPhone/iPod touch platform. This raises the possibility of mobile review of diagnostic medical images to expedite diagnosis and treatment planning using a commercial off the shelf solution, facilitating communication among radiologists and referring clinicians.

e-Science platform for translational biomedical imaging research: running, statistics, and analysis

NASA Astrophysics Data System (ADS)

Wang, Tusheng; Yang, Yuanyuan; Zhang, Kai; Wang, Mingqing; Zhao, Jun; Xu, Lisa; Zhang, Jianguo

2015-03-01

In order to enable multiple disciplines of medical researchers, clinical physicians and biomedical engineers working together in a secured, efficient, and transparent cooperative environment, we had designed an e-Science platform for biomedical imaging research and application cross multiple academic institutions and hospitals in Shanghai and presented this work in SPIE Medical Imaging conference held in San Diego in 2012. In past the two-years, we implemented a biomedical image chain including communication, storage, cooperation and computing based on this e-Science platform. In this presentation, we presented the operating status of this system in supporting biomedical imaging research, analyzed and discussed results of this system in supporting multi-disciplines collaboration cross-multiple institutions.

Improvement in the clinical practicability of roentgen stereophotogrammetric analysis (RSA): free from the use of the dual X-ray equipment.

PubMed

Shih, Kao-Shang; Lee, Chian-Her; Syu, Ci-Bin; Lai, Jiing-Yih; Chen, Kuo-Jen; Lin, Shang-Chih

2012-10-01

After total knee replacement, the monitoring of the prosthetic performance is often done by roentgenographic examination. However, the two-dimensional (2D) roentgen images only provide information about the projection onto the anteroposterior (AP) and mediolateral (ML) planes. Historically, the model-based roentgen stereophotogrammetric analysis (RSA) technique has been developed to predict the spatial relationship between prostheses by iteratively comparing the projective data for the prosthetic models and the roentgen images. During examination, the prosthetic poses should be stationary. This should be ensured, either by the use of dual synchronized X-ray equipment or by the use of a specific posture. In practice, these methods are uncommon or technically inconvenient during follow-up examination. This study aims to develop a rotation platform to improve the clinical applicability of the model-based RSA technique. The rotation platform allows the patient to assume a weight-bearing posture, while being steadily rotated so that both AP and ML knee images can be obtained. This study uses X-ray equipment with a single source and flat panel detectors (FPDs). Four tests are conducted to evaluate the quality of the FPD images, steadiness of the rotation platform, and accuracy of the RSA results. The results show that the distortion-induced error of the FPD image is quite minor, and the prosthetic size can be cautiously calibrated by means of the scale ball(s). The rotation platform should be placed closer to the FPD and orthogonal to the projection axis of the X-ray source. Image overlap of the prostheses can be avoided by adjusting both X-ray source and knee posture. The device-induced problems associated with the rotation platform include the steadiness of the platform operation and the balance of the rotated subject. Sawbone tests demonstrate that the outline error, due to the platform, is of the order of the image resolution (= 0.145 mm). In conclusion, the rotation platform with steady rotation, a knee support, and a handle can serve as an alternative method to take prosthetic images, without the loss in accuracy associated with the RSA method.

COSBID-M3: a platform for multimodal monitoring, data collection, and research in neurocritical care.

PubMed

Wilson, J Adam; Shutter, Lori A; Hartings, Jed A

2013-01-01

Neuromonitoring in patients with severe brain trauma and stroke is often limited to intracranial pressure (ICP); advanced neuroscience intensive care units may also monitor brain oxygenation (partial pressure of brain tissue oxygen, P(bt)O(2)), electroencephalogram (EEG), cerebral blood flow (CBF), or neurochemistry. For example, cortical spreading depolarizations (CSDs) recorded by electrocorticography (ECoG) are associated with delayed cerebral ischemia after subarachnoid hemorrhage and are an attractive target for novel therapeutic approaches. However, to better understand pathophysiologic relations and realize the potential of multimodal monitoring, a common platform for data collection and integration is needed. We have developed a multimodal system that integrates clinical, research, and imaging data into a single research and development (R&D) platform. Our system is adapted from the widely used BCI2000, a brain-computer interface tool which is written in the C++ language and supports over 20 data acquisition systems. It is optimized for real-time analysis of multimodal data using advanced time and frequency domain analyses and is extensible for research development using a combination of C++, MATLAB, and Python languages. Continuous streams of raw and processed data, including BP (blood pressure), ICP, PtiO2, CBF, ECoG, EEG, and patient video are stored in an open binary data format. Selected events identified in raw (e.g., ICP) or processed (e.g., CSD) measures are displayed graphically, can trigger alarms, or can be sent to researchers or clinicians via text message. For instance, algorithms for automated detection of CSD have been incorporated, and processed ECoG signals are projected onto three-dimensional (3D) brain models based on patient magnetic resonance imaging (MRI) and computed tomographic (CT) scans, allowing real-time correlation of pathoanatomy and cortical function. This platform will provide clinicians and researchers with an advanced tool to investigate pathophysiologic relationships and novel measures of cerebral status, as well as implement treatment algorithms based on such multimodal measures.

OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging

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

Rubel, Oliver; Greiner, Annette; Cholia, Shreyas

Mass spectrometry imaging (MSI) enables researchers to directly probe endogenous molecules directly within the architecture of the biological matrix. Unfortunately, efficient access, management, and analysis of the data generated by MSI approaches remain major challenges to this rapidly developing field. Despite the availability of numerous dedicated file formats and software packages, it is a widely held viewpoint that the biggest challenge is simply opening, sharing, and analyzing a file without loss of information. Here we present OpenMSI, a software framework and platform that addresses these challenges via an advanced, high-performance, extensible file format and Web API for remote data accessmore » (http://openmsi.nersc.gov). The OpenMSI file format supports storage of raw MSI data, metadata, and derived analyses in a single, self-describing format based on HDF5 and is supported by a large range of analysis software (e.g., Matlab and R) and programming languages (e.g., C++, Fortran, and Python). Careful optimization of the storage layout of MSI data sets using chunking, compression, and data replication accelerates common, selective data access operations while minimizing data storage requirements and are critical enablers of rapid data I/O. The OpenMSI file format has shown to provide >2000-fold improvement for image access operations, enabling spectrum and image retrieval in less than 0.3 s across the Internet even for 50 GB MSI data sets. To make remote high-performance compute resources accessible for analysis and to facilitate data sharing and collaboration, we describe an easy-to-use yet powerful Web API, enabling fast and convenient access to MSI data, metadata, and derived analysis results stored remotely to facilitate high-performance data analysis and enable implementation of Web based data sharing, visualization, and analysis.« less

Multiattribute selection of acute stroke imaging software platform for Extending the Time for Thrombolysis in Emergency Neurological Deficits (EXTEND) clinical trial.

PubMed

Churilov, Leonid; Liu, Daniel; Ma, Henry; Christensen, Soren; Nagakane, Yoshinari; Campbell, Bruce; Parsons, Mark W; Levi, Christopher R; Davis, Stephen M; Donnan, Geoffrey A

2013-04-01

The appropriateness of a software platform for rapid MRI assessment of the amount of salvageable brain tissue after stroke is critical for both the validity of the Extending the Time for Thrombolysis in Emergency Neurological Deficits (EXTEND) Clinical Trial of stroke thrombolysis beyond 4.5 hours and for stroke patient care outcomes. The objective of this research is to develop and implement a methodology for selecting the acute stroke imaging software platform most appropriate for the setting of a multi-centre clinical trial. A multi-disciplinary decision making panel formulated the set of preferentially independent evaluation attributes. Alternative Multi-Attribute Value Measurement methods were used to identify the best imaging software platform followed by sensitivity analysis to ensure the validity and robustness of the proposed solution. Four alternative imaging software platforms were identified. RApid processing of PerfusIon and Diffusion (RAPID) software was selected as the most appropriate for the needs of the EXTEND trial. A theoretically grounded generic multi-attribute selection methodology for imaging software was developed and implemented. The developed methodology assured both a high quality decision outcome and a rational and transparent decision process. This development contributes to stroke literature in the area of comprehensive evaluation of MRI clinical software. At the time of evaluation, RAPID software presented the most appropriate imaging software platform for use in the EXTEND clinical trial. The proposed multi-attribute imaging software evaluation methodology is based on sound theoretical foundations of multiple criteria decision analysis and can be successfully used for choosing the most appropriate imaging software while ensuring both robust decision process and outcomes. © 2012 The Authors. International Journal of Stroke © 2012 World Stroke Organization.

Validation of tablet-based evaluation of color fundus images

PubMed Central

Christopher, Mark; Moga, Daniela C.; Russell, Stephen R.; Folk, James C.; Scheetz, Todd; Abràmoff, Michael D.

2012-01-01

Purpose To compare diabetic retinopathy (DR) referral recommendations made by viewing fundus images using a tablet computer to recommendations made using a standard desktop display. Methods A tablet computer (iPad) and a desktop PC with a high-definition color display were compared. For each platform, two retinal specialists independently rated 1200 color fundus images from patients at risk for DR using an annotation program, Truthseeker. The specialists determined whether each image had referable DR, and also how urgently each patient should be referred for medical examination. Graders viewed and rated the randomly presented images independently and were masked to their ratings on the alternative platform. Tablet- and desktop display-based referral ratings were compared using cross-platform, intra-observer kappa as the primary outcome measure. Additionally, inter-observer kappa, sensitivity, specificity, and area under ROC (AUC) were determined. Results A high level of cross-platform, intra-observer agreement was found for the DR referral ratings between the platforms (κ=0.778), and for the two graders, (κ=0.812). Inter-observer agreement was similar for the two platforms (κ=0.544 and κ=0.625 for tablet and desktop, respectively). The tablet-based ratings achieved a sensitivity of 0.848, a specificity of 0.987, and an AUC of 0.950 compared to desktop display-based ratings. Conclusions In this pilot study, tablet-based rating of color fundus images for subjects at risk for DR was consistent with desktop display-based rating. These results indicate that tablet computers can be reliably used for clinical evaluation of fundus images for DR. PMID:22495326

A Software Platform for Post-Processing Waveform-Based NDE

NASA Technical Reports Server (NTRS)

Roth, Donald J.; Martin, Richard E.; Seebo, Jeff P.; Trinh, Long B.; Walker, James L.; Winfree, William P.

2007-01-01

Ultrasonic, microwave, and terahertz nondestructive evaluation imaging systems generally require the acquisition of waveforms at each scan point to form an image. For such systems, signal and image processing methods are commonly needed to extract information from the waves and improve resolution of, and highlight, defects in the image. Since some similarity exists for all waveform-based NDE methods, it would seem a common software platform containing multiple signal and image processing techniques to process the waveforms and images makes sense where multiple techniques, scientists, engineers, and organizations are involved. This presentation describes NASA Glenn Research Center's approach in developing a common software platform for processing waveform-based NDE signals and images. This platform is currently in use at NASA Glenn and at Lockheed Martin Michoud Assembly Facility for processing of pulsed terahertz and ultrasonic data. Highlights of the software operation will be given. A case study will be shown for use with terahertz data. The authors also request scientists and engineers who are interested in sharing customized signal and image processing algorithms to contribute to this effort by letting the authors code up and include these algorithms in future releases.

An integrated compact airborne multispectral imaging system using embedded computer

NASA Astrophysics Data System (ADS)

Zhang, Yuedong; Wang, Li; Zhang, Xuguo

2015-08-01

An integrated compact airborne multispectral imaging system using embedded computer based control system was developed for small aircraft multispectral imaging application. The multispectral imaging system integrates CMOS camera, filter wheel with eight filters, two-axis stabilized platform, miniature POS (position and orientation system) and embedded computer. The embedded computer has excellent universality and expansibility, and has advantages in volume and weight for airborne platform, so it can meet the requirements of control system of the integrated airborne multispectral imaging system. The embedded computer controls the camera parameters setting, filter wheel and stabilized platform working, image and POS data acquisition, and stores the image and data. The airborne multispectral imaging system can connect peripheral device use the ports of the embedded computer, so the system operation and the stored image data management are easy. This airborne multispectral imaging system has advantages of small volume, multi-function, and good expansibility. The imaging experiment results show that this system has potential for multispectral remote sensing in applications such as resource investigation and environmental monitoring.

Hybrid Geometric Calibration Method for Multi-Platform Spaceborne SAR Image with Sparse Gcps

NASA Astrophysics Data System (ADS)

Lv, G.; Tang, X.; Ai, B.; Li, T.; Chen, Q.

2018-04-01

Geometric calibration is able to provide high-accuracy geometric coordinates of spaceborne SAR image through accurate geometric parameters in the Range-Doppler model by ground control points (GCPs). However, it is very difficult to obtain GCPs that covering large-scale areas, especially in the mountainous regions. In addition, the traditional calibration method is only used for single platform SAR images and can't support the hybrid geometric calibration for multi-platform images. To solve the above problems, a hybrid geometric calibration method for multi-platform spaceborne SAR images with sparse GCPs is proposed in this paper. First, we calibrate the master image that contains GCPs. Secondly, the point tracking algorithm is used to obtain the tie points (TPs) between the master and slave images. Finally, we calibrate the slave images using TPs as the GCPs. We take the Beijing-Tianjin- Hebei region as an example to study SAR image hybrid geometric calibration method using 3 TerraSAR-X images, 3 TanDEM-X images and 5 GF-3 images covering more than 235 kilometers in the north-south direction. Geometric calibration of all images is completed using only 5 GCPs. The GPS data extracted from GNSS receiver are used to assess the plane accuracy after calibration. The results after geometric calibration with sparse GCPs show that the geometric positioning accuracy is 3 m for TSX/TDX images and 7.5 m for GF-3 images.

Cloud-based image sharing network for collaborative imaging diagnosis and consultation

NASA Astrophysics Data System (ADS)

Yang, Yuanyuan; Gu, Yiping; Wang, Mingqing; Sun, Jianyong; Li, Ming; Zhang, Weiqiang; Zhang, Jianguo

2018-03-01

In this presentation, we presented a new approach to design cloud-based image sharing network for collaborative imaging diagnosis and consultation through Internet, which can enable radiologists, specialists and physicians locating in different sites collaboratively and interactively to do imaging diagnosis or consultation for difficult or emergency cases. The designed network combined a regional RIS, grid-based image distribution management, an integrated video conferencing system and multi-platform interactive image display devices together with secured messaging and data communication. There are three kinds of components in the network: edge server, grid-based imaging documents registry and repository, and multi-platform display devices. This network has been deployed in a public cloud platform of Alibaba through Internet since March 2017 and used for small lung nodule or early staging lung cancer diagnosis services between Radiology departments of Huadong hospital in Shanghai and the First Hospital of Jiaxing in Zhejiang Province.

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.

Modification to the Joint Platform Allocation Tool (JPAT) to Include Additional Warfighting Functions. Aerial R&S Future

DTIC Science & Technology

2013-07-01

example, System 2 is four P2 platforms with four SN2 and four SN3 items of available equipment to build configura- tions. Image from [10...System 2 is four P2 platforms with four SN2 and four SN3 items of available equipment to build configurations. Image from [10]. UNCLASSIFIED 3

Performing data analytics on information obtained from various sensors on an OSUS compliant system

NASA Astrophysics Data System (ADS)

Cashion, Kelly; Landoll, Darian; Klawon, Kevin; Powar, Nilesh

2017-05-01

The Open Standard for Unattended Sensors (OSUS) was developed by DIA and ARL to provide a plug-n-play platform for sensor interoperability. Our objective is to use the standardized data produced by OSUS in performing data analytics on information obtained from various sensors. Data analytics can be integrated in one of three ways: within an asset itself; as an independent plug-in designed for one type of asset (i.e. camera or seismic sensor); or as an independent plug-in designed to incorporate data from multiple assets. As a proof-of-concept, we develop a model that can be used in the second of these types - an independent component for camera images. The dataset used was collected as part of a demonstration and test of OSUS capabilities. The image data includes images of empty outdoor scenes and scenes with human or vehicle activity. We design, test, and train a convolution neural network (CNN) to analyze these images and assess the presence of activity in the image. The resulting classifier labels input images as empty or activity with 86.93% accuracy, demonstrating the promising opportunities for deep learning, machine learning, and predictive analytics as an extension of OSUS's already robust suite of capabilities.

Informatics in radiology (infoRAD): free DICOM image viewing and processing software for the Macintosh computer: what's available and what it can do for you.

PubMed

Escott, Edward J; Rubinstein, David

2004-01-01

It is often necessary for radiologists to use digital images in presentations and conferences. Most imaging modalities produce images in the Digital Imaging and Communications in Medicine (DICOM) format. The image files tend to be large and thus cannot be directly imported into most presentation software, such as Microsoft PowerPoint; the large files also consume storage space. There are many free programs that allow viewing and processing of these files on a personal computer, including conversion to more common file formats such as the Joint Photographic Experts Group (JPEG) format. Free DICOM image viewing and processing software for computers running on the Microsoft Windows operating system has already been evaluated. However, many people use the Macintosh (Apple Computer) platform, and a number of programs are available for these users. The World Wide Web was searched for free DICOM image viewing or processing software that was designed for the Macintosh platform or is written in Java and is therefore platform independent. The features of these programs and their usability were evaluated. There are many free programs for the Macintosh platform that enable viewing and processing of DICOM images. (c) RSNA, 2004.

Lensless on-chip imaging of cells provides a new tool for high-throughput cell-biology and medical diagnostics.

PubMed

Mudanyali, Onur; Erlinger, Anthony; Seo, Sungkyu; Su, Ting-Wei; Tseng, Derek; Ozcan, Aydogan

2009-12-14

Conventional optical microscopes image cells by use of objective lenses that work together with other lenses and optical components. While quite effective, this classical approach has certain limitations for miniaturization of the imaging platform to make it compatible with the advanced state of the art in microfluidics. In this report, we introduce experimental details of a lensless on-chip imaging concept termed LUCAS (Lensless Ultra-wide field-of-view Cell monitoring Array platform based on Shadow imaging) that does not require any microscope objectives or other bulky optical components to image a heterogeneous cell solution over an ultra-wide field of view that can span as large as approximately 18 cm(2). Moreover, unlike conventional microscopes, LUCAS can image a heterogeneous cell solution of interest over a depth-of-field of approximately 5 mm without the need for refocusing which corresponds to up to approximately 9 mL sample volume. This imaging platform records the shadows (i.e., lensless digital holograms) of each cell of interest within its field of view, and automated digital processing of these cell shadows can determine the type, the count and the relative positions of cells within the solution. Because it does not require any bulky optical components or mechanical scanning stages it offers a significantly miniaturized platform that at the same time reduces the cost, which is quite important for especially point of care diagnostic tools. Furthermore, the imaging throughput of this platform is orders of magnitude better than conventional optical microscopes, which could be exceedingly valuable for high-throughput cell-biology experiments.

Lensless On-chip Imaging of Cells Provides a New Tool for High-throughput Cell-Biology and Medical Diagnostics

PubMed Central

Mudanyali, Onur; Erlinger, Anthony; Seo, Sungkyu; Su, Ting-Wei; Tseng, Derek; Ozcan, Aydogan

2009-01-01

Conventional optical microscopes image cells by use of objective lenses that work together with other lenses and optical components. While quite effective, this classical approach has certain limitations for miniaturization of the imaging platform to make it compatible with the advanced state of the art in microfluidics. In this report, we introduce experimental details of a lensless on-chip imaging concept termed LUCAS (Lensless Ultra-wide field-of-view Cell monitoring Array platform based on Shadow imaging) that does not require any microscope objectives or other bulky optical components to image a heterogeneous cell solution over an ultra-wide field of view that can span as large as ~18 cm2. Moreover, unlike conventional microscopes, LUCAS can image a heterogeneous cell solution of interest over a depth-of-field of ~5 mm without the need for refocusing which corresponds to up to ~9 mL sample volume. This imaging platform records the shadows (i.e., lensless digital holograms) of each cell of interest within its field of view, and automated digital processing of these cell shadows can determine the type, the count and the relative positions of cells within the solution. Because it does not require any bulky optical components or mechanical scanning stages it offers a significantly miniaturized platform that at the same time reduces the cost, which is quite important for especially point of care diagnostic tools. Furthermore, the imaging throughput of this platform is orders of magnitude better than conventional optical microscopes, which could be exceedingly valuable for high-throughput cell-biology experiments. PMID:20010542

Hyperspectral imaging to monitor simultaneously multiple protein subtypes and live track their spatial dynamics: a new platform to screen drugs for CNS diseases

NASA Astrophysics Data System (ADS)

Labrecque, S.; Sylvestre, J.-P.; Marcet, S.; Mangiarini, F.; Verhaegen, M.; De Koninck, P.; Blais-Ouellette, S.

2015-03-01

In the past decade, the efficacy of existing therapies and the discovery of innovative treatments for Central Nervous System (CNS) diseases have been limited by the lack of appropriate methods to investigate complex molecular processes at the synaptic level. In order to better understand the fundamental mechanisms that regulate diseases of the CNS, a fast fluorescence hyperspectral imaging platform was designed to track simultaneously various neurotransmitter receptors trafficking in and out of synapses. With this hyperspectral imaging platform, it was possible to image simultaneously five different synaptic proteins, including subtypes of glutamate receptors (mGluR, NMDAR, AMPAR), postsynaptic density proteins, and signaling proteins. This new imaging platform allows fast simultaneous acquisitions of at least five fluorescent markers in living neurons with a high spatial resolution. This technique provides an effective method to observe several synaptic proteins at the same time, thus study how drugs for CNS impact the spatial dynamics of these proteins.

[Image processing system of visual prostheses based on digital signal processor DM642].

PubMed

Xie, Chengcheng; Lu, Yanyu; Gu, Yun; Wang, Jing; Chai, Xinyu

2011-09-01

This paper employed a DSP platform to create the real-time and portable image processing system, and introduced a series of commonly used algorithms for visual prostheses. The results of performance evaluation revealed that this platform could afford image processing algorithms to be executed in real time.

Topographical and Chemical Imaging of a Phase Separated Polymer Using a Combined Atomic Force Microscopy/Infrared Spectroscopy/Mass Spectrometry Platform

DOE PAGES

Tai, Tamin; Karácsony, Orsolya; Bocharova, Vera; ...

2016-02-18

This article describes how the use of a hybrid atomic force microscopy/infrared spectroscopy/mass spectrometry imaging platform was demonstrated for the acquisition and correlation of nanoscale sample surface topography and chemical images based on infrared spectroscopy and mass spectrometry.

Gamma-Ray imaging for nuclear security and safety: Towards 3-D gamma-ray vision

NASA Astrophysics Data System (ADS)

Vetter, Kai; Barnowksi, Ross; Haefner, Andrew; Joshi, Tenzing H. Y.; Pavlovsky, Ryan; Quiter, Brian J.

2018-01-01

The development of portable gamma-ray imaging instruments in combination with the recent advances in sensor and related computer vision technologies enable unprecedented capabilities in the detection, localization, and mapping of radiological and nuclear materials in complex environments relevant for nuclear security and safety. Though multi-modal imaging has been established in medicine and biomedical imaging for some time, the potential of multi-modal data fusion for radiological localization and mapping problems in complex indoor and outdoor environments remains to be explored in detail. In contrast to the well-defined settings in medical or biological imaging associated with small field-of-view and well-constrained extension of the radiation field, in many radiological search and mapping scenarios, the radiation fields are not constrained and objects and sources are not necessarily known prior to the measurement. The ability to fuse radiological with contextual or scene data in three dimensions, in analog to radiological and functional imaging with anatomical fusion in medicine, provides new capabilities enhancing image clarity, context, quantitative estimates, and visualization of the data products. We have developed new means to register and fuse gamma-ray imaging with contextual data from portable or moving platforms. These developments enhance detection and mapping capabilities as well as provide unprecedented visualization of complex radiation fields, moving us one step closer to the realization of gamma-ray vision in three dimensions.

Handling Different Spatial Resolutions in Image Fusion by Multivariate Curve Resolution-Alternating Least Squares for Incomplete Image Multisets.

PubMed

Piqueras, Sara; Bedia, Carmen; Beleites, Claudia; Krafft, Christoph; Popp, Jürgen; Maeder, Marcel; Tauler, Romà; de Juan, Anna

2018-06-05

Data fusion of different imaging techniques allows a comprehensive description of chemical and biological systems. Yet, joining images acquired with different spectroscopic platforms is complex because of the different sample orientation and image spatial resolution. Whereas matching sample orientation is often solved by performing suitable affine transformations of rotation, translation, and scaling among images, the main difficulty in image fusion is preserving the spatial detail of the highest spatial resolution image during multitechnique image analysis. In this work, a special variant of the unmixing algorithm Multivariate Curve Resolution Alternating Least Squares (MCR-ALS) for incomplete multisets is proposed to provide a solution for this kind of problem. This algorithm allows analyzing simultaneously images collected with different spectroscopic platforms without losing spatial resolution and ensuring spatial coherence among the images treated. The incomplete multiset structure concatenates images of the two platforms at the lowest spatial resolution with the image acquired with the highest spatial resolution. As a result, the constituents of the sample analyzed are defined by a single set of distribution maps, common to all platforms used and with the highest spatial resolution, and their related extended spectral signatures, covering the signals provided by each of the fused techniques. We demonstrate the potential of the new variant of MCR-ALS for multitechnique analysis on three case studies: (i) a model example of MIR and Raman images of pharmaceutical mixture, (ii) FT-IR and Raman images of palatine tonsil tissue, and (iii) mass spectrometry and Raman images of bean tissue.

VO-Dance an IVOA tools to easy publish data into VO and it's extension on planetology request

NASA Astrophysics Data System (ADS)

Smareglia, R.; Capria, M. T.; Molinaro, M.

2012-09-01

Data publishing through the self standing portals can be joined to VO resource publishing, i.e. astronomical resources deployed through VO compliant services. Since the IVOA (International Virtual Observatory Alliance) provides many protocols and standards for the various data flavors (images, spectra, catalogues … ), and since the data center has as a goal to grow up in number of hosted archives and services providing, the idea arose to find a way to easily deploy and maintain VO resources. VO-Dance is a java web application developed at IA2 that addresses this idea creating, in a dynamical way, VO resources out of database tables or views. It is structured to be potentially DBMS and platform independent and consists of 3 main tokens, an internal DB to store resources description and model metadata information, a restful web application to deploy the resources to the VO community. It's extension to planetology request is under study to best effort INAF software development and archive efficiency.

The CAOS camera platform: ushering in a paradigm change in extreme dynamic range imager design

NASA Astrophysics Data System (ADS)

Riza, Nabeel A.

2017-02-01

Multi-pixel imaging devices such as CCD, CMOS and Focal Plane Array (FPA) photo-sensors dominate the imaging world. These Photo-Detector Array (PDA) devices certainly have their merits including increasingly high pixel counts and shrinking pixel sizes, nevertheless, they are also being hampered by limitations in instantaneous dynamic range, inter-pixel crosstalk, quantum full well capacity, signal-to-noise ratio, sensitivity, spectral flexibility, and in some cases, imager response time. Recently invented is the Coded Access Optical Sensor (CAOS) Camera platform that works in unison with current Photo-Detector Array (PDA) technology to counter fundamental limitations of PDA-based imagers while providing high enough imaging spatial resolution and pixel counts. Using for example the Texas Instruments (TI) Digital Micromirror Device (DMD) to engineer the CAOS camera platform, ushered in is a paradigm change in advanced imager design, particularly for extreme dynamic range applications.

High-speed laser photoacoustic imaging system combined with a digital ultrasonic imaging platform

NASA Astrophysics Data System (ADS)

Zeng, Lvming; Liu, Guodong; Ji, Xuanrong; Ren, Zhong; Huang, Zhen

2009-07-01

As a new field of combined ultrasound/photoacoustic imaging in biomedical photonics research, we present and demonstrate a high-speed laser photoacoustic imaging system combined with digital ultrasound imaging platform. In the prototype system, a new B-mode digital ultrasonic imaging system is modified as the hardware platform with 384 vertical transducer elements. The centre resonance frequency of the piezoelectric transducer is 5.0 MHz with greater than 70% pulse-echo -6dB fractional bandwidth. The modular instrument of PCI-6541 is used as the hardware control centre of the testing system, which features 32 high-speed channels to build low-skew and multi-channel system. The digital photoacoustic data is transported into computer for subsequent reconstruction at 25 MHz clock frequency. Meantime, the software system for controlling and analyzing is correspondingly explored with LabVIEW language on virtual instrument platform. In the breast tissue experiment, the reconstructed image agrees well with the original sample, and the spatial resolution of the system can reach 0.2 mm with multi-element synthetic aperture focusing technique. Therefore, the system and method may have a significant value in improving early detecting level of cancer in the breast and other organs.

Web surveillance system using platform-based design

NASA Astrophysics Data System (ADS)

Lin, Shin-Yo; Tsai, Tsung-Han

2004-04-01

A revolutionary methodology of SOPC platform-based design environment for multimedia communications will be developed. We embed a softcore processor to perform the image compression in FPGA. Then, we plug-in an Ethernet daughter board in the SOPC development platform system. Afterward, a web surveillance platform system is presented. The web surveillance system consists of three parts: image capture, web server and JPEG compression. In this architecture, user can control the surveillance system by remote. By the IP address configures to Ethernet daughter board, the user can access the surveillance system via browser. When user access the surveillance system, the CMOS sensor presently capture the remote image. After that, it will feed the captured image with the embedded processor. The embedded processor immediately performs the JPEG compression. Afterward, the user receives the compressed data via Ethernet. To sum up of the above mentioned, the all system will be implemented on APEX20K200E484-2X device.

Recent Progress in Optical Biosensors Based on Smartphone Platforms

PubMed Central

Geng, Zhaoxin; Zhang, Xiong; Fan, Zhiyuan; Lv, Xiaoqing; Su, Yue; Chen, Hongda

2017-01-01

With a rapid improvement of smartphone hardware and software, especially complementary metal oxide semiconductor (CMOS) cameras, many optical biosensors based on smartphone platforms have been presented, which have pushed the development of the point-of-care testing (POCT). Imaging-based and spectrometry-based detection techniques have been widely explored via different approaches. Combined with the smartphone, imaging-based and spectrometry-based methods are currently used to investigate a wide range of molecular properties in chemical and biological science for biosensing and diagnostics. Imaging techniques based on smartphone-based microscopes are utilized to capture microscale analysts, while spectrometry-based techniques are used to probe reactions or changes of molecules. Here, we critically review the most recent progress in imaging-based and spectrometry-based smartphone-integrated platforms that have been developed for chemical experiments and biological diagnosis. We focus on the analytical performance and the complexity for implementation of the platforms. PMID:29068375

Recent Progress in Optical Biosensors Based on Smartphone Platforms.

PubMed

Geng, Zhaoxin; Zhang, Xiong; Fan, Zhiyuan; Lv, Xiaoqing; Su, Yue; Chen, Hongda

2017-10-25

With a rapid improvement of smartphone hardware and software, especially complementary metal oxide semiconductor (CMOS) cameras, many optical biosensors based on smartphone platforms have been presented, which have pushed the development of the point-of-care testing (POCT). Imaging-based and spectrometry-based detection techniques have been widely explored via different approaches. Combined with the smartphone, imaging-based and spectrometry-based methods are currently used to investigate a wide range of molecular properties in chemical and biological science for biosensing and diagnostics. Imaging techniques based on smartphone-based microscopes are utilized to capture microscale analysts, while spectrometry-based techniques are used to probe reactions or changes of molecules. Here, we critically review the most recent progress in imaging-based and spectrometry-based smartphone-integrated platforms that have been developed for chemical experiments and biological diagnosis. We focus on the analytical performance and the complexity for implementation of the platforms.

Real-time label-free quantitative fluorescence microscopy-based detection of ATP using a tunable fluorescent nano-aptasensor platform.

PubMed

Shrivastava, Sajal; Sohn, Il-Yung; Son, Young-Min; Lee, Won-Il; Lee, Nae-Eung

2015-12-14

Although real-time label-free fluorescent aptasensors based on nanomaterials are increasingly recognized as a useful strategy for the detection of target biomolecules with high fidelity, the lack of an imaging-based quantitative measurement platform limits their implementation with biological samples. Here we introduce an ensemble strategy for a real-time label-free fluorescent graphene (Gr) aptasensor platform. This platform employs aptamer length-dependent tunability, thus enabling the reagentless quantitative detection of biomolecules through computational processing coupled with real-time fluorescence imaging data. We demonstrate that this strategy effectively delivers dose-dependent quantitative readouts of adenosine triphosphate (ATP) concentration on chemical vapor deposited (CVD) Gr and reduced graphene oxide (rGO) surfaces, thereby providing cytotoxicity assessment. Compared with conventional fluorescence spectrometry methods, our highly efficient, universally applicable, and rational approach will facilitate broader implementation of imaging-based biosensing platforms for the quantitative evaluation of a range of target molecules.

Multimodal Microchannel and Nanowell-Based Microfluidic Platforms for Bioimaging

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

Geng, Tao; Smallwood, Chuck R.; Zhu, Ying

2017-03-30

Modern live-cell imaging approaches permit real-time visualization of biological processes. However, limitations for unicellular organism trapping, culturing and long-term imaging can preclude complete understanding of how such microorganisms respond to perturbations in their local environment or linking single-cell variability to whole population dynamics. We have developed microfluidic platforms to overcome prior technical bottlenecks to allow both chemostat and compartmentalized cellular growth conditions using the same device. Additionally, a nanowell-based platform enables a high throughput approach to scale up compartmentalized imaging optimized within the microfluidic device. These channel and nanowell platforms are complementary, and both provide fine control over the localmore » environment as well as the ability to add/replace media components at any experimental time point.« less

A Parallel Point Matching Algorithm for Landmark Based Image Registration Using Multicore Platform

PubMed Central

Yang, Lin; Gong, Leiguang; Zhang, Hong; Nosher, John L.; Foran, David J.

2013-01-01

Point matching is crucial for many computer vision applications. Establishing the correspondence between a large number of data points is a computationally intensive process. Some point matching related applications, such as medical image registration, require real time or near real time performance if applied to critical clinical applications like image assisted surgery. In this paper, we report a new multicore platform based parallel algorithm for fast point matching in the context of landmark based medical image registration. We introduced a non-regular data partition algorithm which utilizes the K-means clustering algorithm to group the landmarks based on the number of available processing cores, which optimize the memory usage and data transfer. We have tested our method using the IBM Cell Broadband Engine (Cell/B.E.) platform. The results demonstrated a significant speed up over its sequential implementation. The proposed data partition and parallelization algorithm, though tested only on one multicore platform, is generic by its design. Therefore the parallel algorithm can be extended to other computing platforms, as well as other point matching related applications. PMID:24308014

Carbonate Platform Development and Stromatolite Morphogenesis: Constraints on Environmental and Biological Evolution

NASA Technical Reports Server (NTRS)

Grotzinger, John P.

2003-01-01

Work has been completed on the digital mapping of a terminal Proterozoic reef complex in Namibia. This complex formed an isolated carbonate platform developed downdip on a carbonate ramp of the Nama Group. The stratigraphic evolution of the platform was digitally reconstructed from an extensive dataset that was compiled by using digital surveying technologies. The platform comprises three accommodation cycles in which each subsequent cycle experienced progressively greater influence of a long-term accommodation increase. Aggradation and progradation during the first cycle resulted in a flat, uniform, sheet-like platform. The coarsening and shallowing-upward sequence representing the first cycle is dominated by columnar stromatolitic thrombolites and massive dolostones with interbedded mudstone-grainstone at the base of the sequence grading into cross-bedded dolostones. The second cycle features aggradation, formation of a distinct margin containing thrombolite mounds and domes, and the development of a bucket geometry. Columnar stromatolitic thrombolites dominate the platform interior. The final stage of platform development shows a deepening trend with initial aggradation and formation of well-bedded, thin deposits in the interior and mound development at the margins. While the interior drowned, the platform margin kept up with rising sea level and a complex pinnacle reef formed containing fused and coalesced thrombolite mounds flanked by bioclastic grainstones (containing Cloudina and Namacalathus fossils) and collapse breccias. A set of isolated large thrombolite mounds flanked by shales indicate the final stage of the carbonate platform. During a progressive increase in accommodation, a flat-topped isolated carbonate platform becomes aerially less extensive by either backstepping or formation of smaller pinnacles or a combination of both. The overall geometric evolution of the studied platform from flat-topped to bucket with elevated margins is recorded in many Proterozoic and Phanerozoic isolated carbonate platforms with similar dimensions. The terminal Proterozoic, microbial-dominated, isolated carbonate platform of this study clearly illustrates that the answer to accommodation changes was already familiar among carbonate platforms before the dawn of metazoan-dominated platforms.

Determination of a potential quantitative measure of the state of the lung using lung ultrasound spectroscopy.

PubMed

Demi, Libertario; van Hoeve, Wim; van Sloun, Ruud J G; Soldati, Gino; Demi, Marcello

2017-10-06

B-lines are ultrasound-imaging artifacts, which correlate with several lung-pathologies. However, their understanding and characterization is still largely incomplete. To further study B-lines, lung-phantoms were developed by trapping a layer of microbubbles in tissue-mimicking gel. To simulate the alveolar size reduction typical of various pathologies, 170 and 80 µm bubbles were used for phantom-type 1 and 2, respectively. A normal alveolar diameter is approximately 280 µm. A LA332 linear-array connected to the ULA-OP platform was used for imaging. Standard ultrasound (US) imaging at 4.5 MHz was performed. Subsequently, a multi-frequency approach was used where images were sequentially generated using orthogonal sub-bands centered at different frequencies (3, 4, 5, and 6 MHz). Results show that B-lines appear predominantly with phantom-type 2. Moreover, the multi-frequency approach revealed that the B-lines originate from a specific portion of the US spectrum. These results can give rise to significant clinical applications since, if further confirmed by extensive in-vivo studies, the native frequency of B-lines could provide a quantitative-measure of the state of the lung.

Functional imaging of photovoltaic materials

NASA Astrophysics Data System (ADS)

Leite, Marina

For the past two decades, extensive efforts have been made to increase the short-circuit current (Jsc) of non-epitaxial solar cells to achieve higher efficiency devices. Yet, improvements in the overall device performance are still limited by the open-circuit voltage (Voc). We address this critical limiting factor of all promising materials for photovoltaics by realizing a novel nanoscale imaging platform with unprecedented spatial resolution (<100 nm), based on a variant of Kelvin-probe force microscopy. We mapped the local Voc of a variety of inorganic materials, and measured local changes >150 mV in CIGS, not resolved by conventional electrical measurements. To identify the origin of the instability frequently observed in perovskite solar cells, we leveraged our recently developed method to scan one frame in 16 seconds to spatially and temporally resolve their photo-voltage. Surprisingly, we observed local and reversible changes in the Voc of the devices upon post-illumination treatments. Our innovative functional imaging is non destructive and can be applied to other optoelectronic devices, such as LEDs and photodetectors. The author acknowledge APS and NSF (Award # 16-10833) for funding.

Fluorinated porphyrinoids as efficient platforms for new photonic materials, sensors, and therapeutics.

PubMed

Bhupathiraju, N V S Dinesh K; Rizvi, Waqar; Batteas, James D; Drain, Charles Michael

2016-01-14

Porphyrinoids are robust heterocyclic dyes studied extensively for their applications in medicine and as photonic materials because of their tunable photophysical properties, diverse means of modifying the periphery, and the ability to chelate most transition metals. Commercial applications include their use as phthalocyanine dyes in optical discs, porphyrins in photodynamic therapy, and as oxygen sensors. Most applications of these dyes require exocyclic moieties to improve solubility, target diseases, modulate photophysical properties, or direct the self-organization into architectures with desired photonic properties. The synthesis of the porphyrinoid depends on the desired application, but the de novo synthesis often involves several steps, is time consuming, and results in low isolated yields. Thus, the application of core porphyrinoid platforms that can be rapidly and efficiently modified to evaluate new molecular architectures allows researchers to focus on the design concepts rather than the synthesis methods, and opens porphyrinoid chemistry to a broader scientific community. We have focused on several widely available, commercially viable porphyrinoids as platforms: meso-perfluorophenylporphyrin, perfluorophthalocyanine, and meso-perfluorophenylcorrole. The perfluorophenylporphyrin is readily converted to the chlorin, bacteriochlorin, and isobacteriochlorin. Derivatives of all six of these core platforms can be efficiently and controllably made via mild nucleophilic aromatic substitution reactions using primary S, N, and O nucleophiles bearing a wide variety of functional groups. The remaining fluoro groups enhance the photo and oxidative stability of the dyes and can serve as spectroscopic signatures to characterize the compounds or in imaging applications using (19)F NMR. This review provides an overview of the chemistry of fluorinated porphyrinoids that are being used as a platform to create libraries of photo-active compounds for applications in medicine and materials.

Fiji: an open-source platform for biological-image analysis.

PubMed

Schindelin, Johannes; Arganda-Carreras, Ignacio; Frise, Erwin; Kaynig, Verena; Longair, Mark; Pietzsch, Tobias; Preibisch, Stephan; Rueden, Curtis; Saalfeld, Stephan; Schmid, Benjamin; Tinevez, Jean-Yves; White, Daniel James; Hartenstein, Volker; Eliceiri, Kevin; Tomancak, Pavel; Cardona, Albert

2012-06-28

Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.

ROS-IGTL-Bridge: an open network interface for image-guided therapy using the ROS environment.

PubMed

Frank, Tobias; Krieger, Axel; Leonard, Simon; Patel, Niravkumar A; Tokuda, Junichi

2017-08-01

With the growing interest in advanced image-guidance for surgical robot systems, rapid integration and testing of robotic devices and medical image computing software are becoming essential in the research and development. Maximizing the use of existing engineering resources built on widely accepted platforms in different fields, such as robot operating system (ROS) in robotics and 3D Slicer in medical image computing could simplify these tasks. We propose a new open network bridge interface integrated in ROS to ensure seamless cross-platform data sharing. A ROS node named ROS-IGTL-Bridge was implemented. It establishes a TCP/IP network connection between the ROS environment and external medical image computing software using the OpenIGTLink protocol. The node exports ROS messages to the external software over the network and vice versa simultaneously, allowing seamless and transparent data sharing between the ROS-based devices and the medical image computing platforms. Performance tests demonstrated that the bridge could stream transforms, strings, points, and images at 30 fps in both directions successfully. The data transfer latency was <1.2 ms for transforms, strings and points, and 25.2 ms for color VGA images. A separate test also demonstrated that the bridge could achieve 900 fps for transforms. Additionally, the bridge was demonstrated in two representative systems: a mock image-guided surgical robot setup consisting of 3D slicer, and Lego Mindstorms with ROS as a prototyping and educational platform for IGT research; and the smart tissue autonomous robot surgical setup with 3D Slicer. The study demonstrated that the bridge enabled cross-platform data sharing between ROS and medical image computing software. This will allow rapid and seamless integration of advanced image-based planning/navigation offered by the medical image computing software such as 3D Slicer into ROS-based surgical robot systems.

apART: system for the acquisition, processing, archiving, and retrieval of digital images in an open, distributed imaging environment

NASA Astrophysics Data System (ADS)

Schneider, Uwe; Strack, Ruediger

1992-04-01

apART reflects the structure of an open, distributed environment. According to the general trend in the area of imaging, network-capable, general purpose workstations with capabilities of open system image communication and image input are used. Several heterogeneous components like CCD cameras, slide scanners, and image archives can be accessed. The system is driven by an object-oriented user interface where devices (image sources and destinations), operators (derived from a commercial image processing library), and images (of different data types) are managed and presented uniformly to the user. Browsing mechanisms are used to traverse devices, operators, and images. An audit trail mechanism is offered to record interactive operations on low-resolution image derivatives. These operations are processed off-line on the original image. Thus, the processing of extremely high-resolution raster images is possible, and the performance of resolution dependent operations is enhanced significantly during interaction. An object-oriented database system (APRIL), which can be browsed, is integrated into the system. Attribute retrieval is supported by the user interface. Other essential features of the system include: implementation on top of the X Window System (X11R4) and the OSF/Motif widget set; a SUN4 general purpose workstation, inclusive ethernet, magneto optical disc, etc., as the hardware platform for the user interface; complete graphical-interactive parametrization of all operators; support of different image interchange formats (GIF, TIFF, IIF, etc.); consideration of current IPI standard activities within ISO/IEC for further refinement and extensions.

Campus Energy Model for Control and Performance Validation

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

2014-09-19

The core of the modeling platform is an extensible block library for the MATLAB/Simulink software suite. The platform enables true co-simulation (interaction at each simulation time step) with NREL's state-of-the-art modeling tools and other energy modeling software.

Securing a web-based teleradiology platform according to German law and "best practices".

PubMed

Spitzer, Michael; Ullrich, Tobias; Ueckert, Frank

2009-01-01

The Medical Data and Picture Exchange platform (MDPE), as a teleradiology system, facilitates the exchange of digital medical imaging data among authorized users. It features extensive support of the DICOM standard including networking functions. Since MDPE is designed as a web service, security and confidentiality of data and communication pose an outstanding challenge. To comply with demands of German laws and authorities, a generic data security concept considered as "best practice" in German health telematics was adapted to the specific demands of MDPE. The concept features strict logical and physical separation of diagnostic and identity data and thus an all-encompassing pseudonymization throughout the system. Hence, data may only be merged at authorized clients. MDPE's solution of merging data from separate sources within a web browser avoids technically questionable techniques such as deliberate cross-site scripting. Instead, data is merged dynamically by JavaScriptlets running in the user's browser. These scriptlets are provided by one server, while content and method calls are generated by another server. Additionally, MDPE uses encrypted temporary IDs for communication and merging of data.

Automated Long-Term Monitoring of Parallel Microfluidic Operations Applying a Machine Vision-Assisted Positioning Method

PubMed Central

Yip, Hon Ming; Li, John C. S.; Cui, Xin; Gao, Qiannan; Leung, Chi Chiu

2014-01-01

As microfluidics has been applied extensively in many cell and biochemical applications, monitoring the related processes is an important requirement. In this work, we design and fabricate a high-throughput microfluidic device which contains 32 microchambers to perform automated parallel microfluidic operations and monitoring on an automated stage of a microscope. Images are captured at multiple spots on the device during the operations for monitoring samples in microchambers in parallel; yet the device positions may vary at different time points throughout operations as the device moves back and forth on a motorized microscopic stage. Here, we report an image-based positioning strategy to realign the chamber position before every recording of microscopic image. We fabricate alignment marks at defined locations next to the chambers in the microfluidic device as reference positions. We also develop image processing algorithms to recognize the chamber positions in real-time, followed by realigning the chambers to their preset positions in the captured images. We perform experiments to validate and characterize the device functionality and the automated realignment operation. Together, this microfluidic realignment strategy can be a platform technology to achieve precise positioning of multiple chambers for general microfluidic applications requiring long-term parallel monitoring of cell and biochemical activities. PMID:25133248

Effectiveness of an e-Learning Platform for Image Interpretation Education of Medical Staff and Students.

PubMed

Ogura, Akio; Hayashi, Norio; Negishi, Tohru; Watanabe, Haruyuki

2018-05-09

Medical staff must be able to perform accurate initial interpretations of radiography to prevent diagnostic errors. Education in medical image interpretation is an ongoing need that is addressed by text-based and e-learning platforms. The effectiveness of these methods has been previously reported. Here, we describe the effectiveness of an e-learning platform used for medical image interpretation education. Ten third-year medical students without previous experience in chest radiography interpretation were provided with e-learning instructions. Accuracy of diagnosis using chest radiography was provided before and after e-learning education. We measured detection accuracy for two image groups: nodular shadow and ground-glass shadow. We also distributed the e-learning system to the two groups and analyzed the effectiveness of education for both types of image shadow. The mean correct answer rate after the 2-week e-learning period increased from 34.5 to 72.7%. Diagnosis of the ground glass shadow improved significantly more than that of the mass shadow. Education using the e-leaning platform is effective for interpretation of chest radiography results. E-learning is particularly effective for the interpretation of chest radiography images containing ground glass shadow.

Space Radar Image of Oil Slicks

NASA Technical Reports Server (NTRS)

1994-01-01

This is a radar image of an offshore drilling field about 150 km (93 miles) west of Bombay, India, in the Arabian Sea. The dark streaks are extensive oil slicks surrounding many of the drilling platforms, which appear as bright white spots. Radar images are useful for detecting and measuring the extent of oil seepages on the ocean surface, from both natural and industrial sources. The long, thin streaks extending from many of the platforms are spreading across the sea surface, pushed by local winds. The larger dark patches are dispersed slicks that were likely discharged earlier than the longer streaks, when the winds were probably from a different direction. The dispersed oil will eventually spread out over the more dense water and become a layer which is a single molecule thick. Many forms of oil, both from biological and from petroleum sources, smooth out the ocean surface, causing the area to appear dark in radar images. There are also two forms of ocean waves shown in this image. The dominant group of large waves (upper center) are called internal waves. These waves are formed below the ocean surface at the boundary between layers of warm and cold water and they appear in the radar image because of the way they change the ocean surface. Ocean swells, which are waves generated by winds, are shown throughout the image but are most distinct in the blue area adjacent to the internal waves. Identification of waves provide oceanographers with information about the smaller scale dynamic processes of the ocean. This image was acquired by the Spaceborne Imaging Radar-C/X-Band Synthetic Aperture Radar (SIR-C/X-SAR) aboard the space shuttle Endeavour on October 9, 1994. The colors are assigned to different frequencies and polarizations of the radar as follows: Red is L-band vertically transmitted, vertically received; green is the average of L-band vertically transmitted, vertically received and C-band vertically transmitted, vertically received; blue is C-band vertically transmitted, vertically received. The image is located at 19.25 degrees north latitude and 71.34 degrees east longitude and covers an area 20 km by 45 km (12.4 miles by 27.9 miles). SIR-C/X-SAR, a joint mission of the German, Italian and United States space agencies, is part of NASA's Mission to Planet Earth.

Analysis of scalability of high-performance 3D image processing platform for virtual colonoscopy

NASA Astrophysics Data System (ADS)

Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli

2014-03-01

One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. For this purpose, we previously developed a software platform for high-performance 3D medical image processing, called HPC 3D-MIP platform, which employs increasingly available and affordable commodity computing systems such as the multicore, cluster, and cloud computing systems. To achieve scalable high-performance computing, the platform employed size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D-MIP algorithms, supported task scheduling for efficient load distribution and balancing, and consisted of a layered parallel software libraries that allow image processing applications to share the common functionalities. We evaluated the performance of the HPC 3D-MIP platform by applying it to computationally intensive processes in virtual colonoscopy. Experimental results showed a 12-fold performance improvement on a workstation with 12-core CPUs over the original sequential implementation of the processes, indicating the efficiency of the platform. Analysis of performance scalability based on the Amdahl's law for symmetric multicore chips showed the potential of a high performance scalability of the HPC 3DMIP platform when a larger number of cores is available.

NiftyPET: a High-throughput Software Platform for High Quantitative Accuracy and Precision PET Imaging and Analysis.

PubMed

Markiewicz, Pawel J; Ehrhardt, Matthias J; Erlandsson, Kjell; Noonan, Philip J; Barnes, Anna; Schott, Jonathan M; Atkinson, David; Arridge, Simon R; Hutton, Brian F; Ourselin, Sebastien

2018-01-01

We present a standalone, scalable and high-throughput software platform for PET image reconstruction and analysis. We focus on high fidelity modelling of the acquisition processes to provide high accuracy and precision quantitative imaging, especially for large axial field of view scanners. All the core routines are implemented using parallel computing available from within the Python package NiftyPET, enabling easy access, manipulation and visualisation of data at any processing stage. The pipeline of the platform starts from MR and raw PET input data and is divided into the following processing stages: (1) list-mode data processing; (2) accurate attenuation coefficient map generation; (3) detector normalisation; (4) exact forward and back projection between sinogram and image space; (5) estimation of reduced-variance random events; (6) high accuracy fully 3D estimation of scatter events; (7) voxel-based partial volume correction; (8) region- and voxel-level image analysis. We demonstrate the advantages of this platform using an amyloid brain scan where all the processing is executed from a single and uniform computational environment in Python. The high accuracy acquisition modelling is achieved through span-1 (no axial compression) ray tracing for true, random and scatter events. Furthermore, the platform offers uncertainty estimation of any image derived statistic to facilitate robust tracking of subtle physiological changes in longitudinal studies. The platform also supports the development of new reconstruction and analysis algorithms through restricting the axial field of view to any set of rings covering a region of interest and thus performing fully 3D reconstruction and corrections using real data significantly faster. All the software is available as open source with the accompanying wiki-page and test data.

Lensless transport-of-intensity phase microscopy and tomography with a color LED matrix

NASA Astrophysics Data System (ADS)

Zuo, Chao; Sun, Jiasong; Zhang, Jialin; Hu, Yan; Chen, Qian

2015-07-01

We demonstrate lens-less quantitative phase microscopy and diffraction tomography based on a compact on-chip platform, using only a CMOS image sensor and a programmable color LED array. Based on multi-wavelength transport-of- intensity phase retrieval and multi-angle illumination diffraction tomography, this platform offers high quality, depth resolved images with a lateral resolution of ˜3.7μm and an axial resolution of ˜5μm, over wide large imaging FOV of 24mm2. The resolution and FOV can be further improved by using a larger image sensors with small pixels straightforwardly. This compact, low-cost, robust, portable platform with a decent imaging performance may offer a cost-effective tool for telemedicine needs, or for reducing health care costs for point-of-care diagnostics in resource-limited environments.

Non-invasive, Contrast-enhanced Spectral Imaging of Breast Cancer Signatures in Preclinical Animal Models In vivo

PubMed Central

Ramanujan, V Krishnan; Ren, Songyang; Park, Sangyong; Farkas, Daniel L

2011-01-01

We report here a non-invasive multispectral imaging platform for monitoring spectral reflectance and fluorescence images from primary breast carcinoma and metastatic lymph nodes in preclinical rat model in vivo. The system is built around a monochromator light source and an acousto-optic tunable filter (AOTF) for spectral selection. Quantitative analysis of the measured reflectance profiles in the presence of a widely-used lymphazurin dye clearly demonstrates the capability of the proposed imaging platform to detect tumor-associated spectral signatures in the primary tumors as well as metastatic lymphatics. Tumor-associated changes in vascular oxygenation and interstitial fluid pressure are reasoned to be the physiological sources of the measured reflectance profiles. We also discuss the translational potential of our imaging platform in intra-operative clinical setting. PMID:21572915

Open-source platforms for navigated image-guided interventions.

PubMed

Ungi, Tamas; Lasso, Andras; Fichtinger, Gabor

2016-10-01

Navigation technology is changing the clinical standards in medical interventions by making existing procedures more accurate, and new procedures possible. Navigation is based on preoperative or intraoperative imaging combined with 3-dimensional position tracking of interventional tools registered to the images. Research of navigation technology in medical interventions requires significant engineering efforts. The difficulty of developing such complex systems has been limiting the clinical translation of new methods and ideas. A key to the future success of this field is to provide researchers with platforms that allow rapid implementation of applications with minimal resources spent on reimplementing existing system features. A number of platforms have been already developed that can share data in real time through standard interfaces. Complete navigation systems can be built using these platforms using a layered software architecture. In this paper, we review the most popular platforms, and show an effective way to take advantage of them through an example surgical navigation application. Copyright © 2016 Elsevier B.V. All rights reserved.

Volumetric neuroimage analysis extensions for the MIPAV software package.

PubMed

Bazin, Pierre-Louis; Cuzzocreo, Jennifer L; Yassa, Michael A; Gandler, William; McAuliffe, Matthew J; Bassett, Susan S; Pham, Dzung L

2007-09-15

We describe a new collection of publicly available software tools for performing quantitative neuroimage analysis. The tools perform semi-automatic brain extraction, tissue classification, Talairach alignment, and atlas-based measurements within a user-friendly graphical environment. They are implemented as plug-ins for MIPAV, a freely available medical image processing software package from the National Institutes of Health. Because the plug-ins and MIPAV are implemented in Java, both can be utilized on nearly any operating system platform. In addition to the software plug-ins, we have also released a digital version of the Talairach atlas that can be used to perform regional volumetric analyses. Several studies are conducted applying the new tools to simulated and real neuroimaging data sets.

A comparative analysis of dynamic grids vs. virtual grids using the A3pviGrid framework.

PubMed

Shankaranarayanan, Avinas; Amaldas, Christine

2010-11-01

With the proliferation of Quad/Multi-core micro-processors in mainstream platforms such as desktops and workstations; a large number of unused CPU cycles can be utilized for running virtual machines (VMs) as dynamic nodes in distributed environments. Grid services and its service oriented business broker now termed cloud computing could deploy image based virtualization platforms enabling agent based resource management and dynamic fault management. In this paper we present an efficient way of utilizing heterogeneous virtual machines on idle desktops as an environment for consumption of high performance grid services. Spurious and exponential increases in the size of the datasets are constant concerns in medical and pharmaceutical industries due to the constant discovery and publication of large sequence databases. Traditional algorithms are not modeled at handing large data sizes under sudden and dynamic changes in the execution environment as previously discussed. This research was undertaken to compare our previous results with running the same test dataset with that of a virtual Grid platform using virtual machines (Virtualization). The implemented architecture, A3pviGrid utilizes game theoretic optimization and agent based team formation (Coalition) algorithms to improve upon scalability with respect to team formation. Due to the dynamic nature of distributed systems (as discussed in our previous work) all interactions were made local within a team transparently. This paper is a proof of concept of an experimental mini-Grid test-bed compared to running the platform on local virtual machines on a local test cluster. This was done to give every agent its own execution platform enabling anonymity and better control of the dynamic environmental parameters. We also analyze performance and scalability of Blast in a multiple virtual node setup and present our findings. This paper is an extension of our previous research on improving the BLAST application framework using dynamic Grids on virtualization platforms such as the virtual box.

A Cross-Platform Infrastructure for Scalable Runtime Application Performance Analysis

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

Jack Dongarra; Shirley Moore; Bart Miller, Jeffrey Hollingsworth

2005-03-15

The purpose of this project was to build an extensible cross-platform infrastructure to facilitate the development of accurate and portable performance analysis tools for current and future high performance computing (HPC) architectures. Major accomplishments include tools and techniques for multidimensional performance analysis, as well as improved support for dynamic performance monitoring of multithreaded and multiprocess applications. Previous performance tool development has been limited by the burden of having to re-write a platform-dependent low-level substrate for each architecture/operating system pair in order to obtain the necessary performance data from the system. Manual interpretation of performance data is not scalable for large-scalemore » long-running applications. The infrastructure developed by this project provides a foundation for building portable and scalable performance analysis tools, with the end goal being to provide application developers with the information they need to analyze, understand, and tune the performance of terascale applications on HPC architectures. The backend portion of the infrastructure provides runtime instrumentation capability and access to hardware performance counters, with thread-safety for shared memory environments and a communication substrate to support instrumentation of multiprocess and distributed programs. Front end interfaces provides tool developers with a well-defined, platform-independent set of calls for requesting performance data. End-user tools have been developed that demonstrate runtime data collection, on-line and off-line analysis of performance data, and multidimensional performance analysis. The infrastructure is based on two underlying performance instrumentation technologies. These technologies are the PAPI cross-platform library interface to hardware performance counters and the cross-platform Dyninst library interface for runtime modification of executable images. The Paradyn and KOJAK projects have made use of this infrastructure to build performance measurement and analysis tools that scale to long-running programs on large parallel and distributed systems and that automate much of the search for performance bottlenecks.« less

Multiple wavelength silicon photonic 200 mm R+D platform for 25Gb/s and above applications

NASA Astrophysics Data System (ADS)

Szelag, B.; Blampey, B.; Ferrotti, T.; Reboud, V.; Hassan, K.; Malhouitre, S.; Grand, G.; Fowler, D.; Brision, S.; Bria, T.; Rabillé, G.; Brianceau, P.; Hartmann, J. M.; Hugues, V.; Myko, A.; Elleboode, F.; Gays, F.; Fédéli, J. M.; Kopp, C.

2016-05-01

A silicon photonics platform that uses a CMOS foundry line is described. Fabrication process is following a modular integration scheme which leads to a flexible platform, allowing different device combinations. A complete device library is demonstrated for 1310 nm applications with state of the art performances. A PDK which includes specific photonic features and which is compatible with commercial EDA tools has been developed allowing an MPW shuttle service. Finally platform evolutions such as device offer extension to 1550 nm or new process modules introduction are presented.

NiftyNet: a deep-learning platform for medical imaging.

PubMed

Gibson, Eli; Li, Wenqi; Sudre, Carole; Fidon, Lucas; Shakir, Dzhoshkun I; Wang, Guotai; Eaton-Rosen, Zach; Gray, Robert; Doel, Tom; Hu, Yipeng; Whyntie, Tom; Nachev, Parashkev; Modat, Marc; Barratt, Dean C; Ourselin, Sébastien; Cardoso, M Jorge; Vercauteren, Tom

2018-05-01

Medical image analysis and computer-assisted intervention problems are increasingly being addressed with deep-learning-based solutions. Established deep-learning platforms are flexible but do not provide specific functionality for medical image analysis and adapting them for this domain of application requires substantial implementation effort. Consequently, there has been substantial duplication of effort and incompatible infrastructure developed across many research groups. This work presents the open-source NiftyNet platform for deep learning in medical imaging. The ambition of NiftyNet is to accelerate and simplify the development of these solutions, and to provide a common mechanism for disseminating research outputs for the community to use, adapt and build upon. The NiftyNet infrastructure provides a modular deep-learning pipeline for a range of medical imaging applications including segmentation, regression, image generation and representation learning applications. Components of the NiftyNet pipeline including data loading, data augmentation, network architectures, loss functions and evaluation metrics are tailored to, and take advantage of, the idiosyncracies of medical image analysis and computer-assisted intervention. NiftyNet is built on the TensorFlow framework and supports features such as TensorBoard visualization of 2D and 3D images and computational graphs by default. We present three illustrative medical image analysis applications built using NiftyNet infrastructure: (1) segmentation of multiple abdominal organs from computed tomography; (2) image regression to predict computed tomography attenuation maps from brain magnetic resonance images; and (3) generation of simulated ultrasound images for specified anatomical poses. The NiftyNet infrastructure enables researchers to rapidly develop and distribute deep learning solutions for segmentation, regression, image generation and representation learning applications, or extend the platform to new applications. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Implementing a Data Quality Strategy to Simplify Access to Data

NASA Astrophysics Data System (ADS)

Druken, K. A.; Trenham, C. E.; Evans, B. J. K.; Richards, C. J.; Wang, J.; Wyborn, L. A.

2016-12-01

To ensure seamless programmatic access for data analysis (including machine learning), standardization of both data and services is vital. At the Australian National Computational Infrastructure (NCI) we have developed a Data Quality Strategy (DQS) that currently provides processes for: (1) the consistency of data structures in the underlying High Performance Data (HPD) platform; (2) quality control through compliance with recognized community standards; and (3) data quality assurance through demonstrated functionality across common platforms, tools and services. NCI hosts one of Australia's largest repositories (10+ PBytes) of research data collections spanning datasets from climate, coasts, oceans and geophysics through to astronomy, bioinformatics and the social sciences. A key challenge is the application of community-agreed data standards to the broad set of Earth systems and environmental data that are being used. Within these disciplines, data span a wide range of gridded, ungridded (i.e., line surveys, point clouds), and raster image types, as well as diverse coordinate reference projections and resolutions. By implementing our DQS we have seen progressive improvement in the quality of the datasets across the different subject domains, and through this, the ease by which the users can programmatically access the data, either in situ or via web services. As part of its quality control procedures, NCI has developed a compliance checker based upon existing domain standards. The DQS also includes extensive Functionality Testing which include readability by commonly used libraries (e.g., netCDF, HDF, GDAL, etc.); accessibility by data servers (e.g., THREDDS, Hyrax, GeoServer), validation against scientific analysis and programming platforms (e.g., Python, Matlab, QGIS); and visualization tools (e.g., ParaView, NASA Web World Wind). These tests ensure smooth interoperability between products and services as well as exposing unforeseen requirements and dependencies. The results provide an important component of quality control within the DQS as well as clarifying the requirement for any extensions to the relevant standards that help support the uptake of data by broader international communities.

Simulation of transmission electron microscope images of biological specimens.

PubMed

Rullgård, H; Ofverstedt, L-G; Masich, S; Daneholt, B; Oktem, O

2011-09-01

We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrödinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated. © 2011 The Authors Journal of Microscopy © 2011 Royal Microscopical Society.

A review of novel optical imaging strategies of the stroke pathology and stem cell therapy in stroke

PubMed Central

Aswendt, Markus; Adamczak, Joanna; Tennstaedt, Annette

2014-01-01

Transplanted stem cells can induce and enhance functional recovery in experimental stroke. Invasive analysis has been extensively used to provide detailed cellular and molecular characterization of the stroke pathology and engrafted stem cells. But post mortem analysis is not appropriate to reveal the time scale of the dynamic interplay between the cell graft, the ischemic lesion and the endogenous repair mechanisms. This review describes non-invasive imaging techniques which have been developed to provide complementary in vivo information. Recent advances were made in analyzing simultaneously different aspects of the cell graft (e.g., number of cells, viability state, and cell fate), the ischemic lesion (e.g., blood–brain-barrier consistency, hypoxic, and necrotic areas) and the neuronal and vascular network. We focus on optical methods, which permit simple animal preparation, repetitive experimental conditions, relatively medium-cost instrumentation and are performed under mild anesthesia, thus nearly under physiological conditions. A selection of recent examples of optical intrinsic imaging, fluorescence imaging and bioluminescence imaging to characterize the stroke pathology and engrafted stem cells are discussed. Special attention is paid to novel optimal reporter genes/probes for genetic labeling and tracking of stem cells and appropriate transgenic animal models. Requirements, advantages and limitations of these imaging platforms are critically discussed and placed into the context of other non-invasive techniques, e.g., magnetic resonance imaging and positron emission tomography, which can be joined with optical imaging in multimodal approaches. PMID:25177269

A service protocol for post-processing of medical images on the mobile device

NASA Astrophysics Data System (ADS)

He, Longjun; Ming, Xing; Xu, Lang; Liu, Qian

2014-03-01

With computing capability and display size growing, the mobile device has been used as a tool to help clinicians view patient information and medical images anywhere and anytime. It is uneasy and time-consuming for transferring medical images with large data size from picture archiving and communication system to mobile client, since the wireless network is unstable and limited by bandwidth. Besides, limited by computing capability, memory and power endurance, it is hard to provide a satisfactory quality of experience for radiologists to handle some complex post-processing of medical images on the mobile device, such as real-time direct interactive three-dimensional visualization. In this work, remote rendering technology is employed to implement the post-processing of medical images instead of local rendering, and a service protocol is developed to standardize the communication between the render server and mobile client. In order to make mobile devices with different platforms be able to access post-processing of medical images, the Extensible Markup Language is taken to describe this protocol, which contains four main parts: user authentication, medical image query/ retrieval, 2D post-processing (e.g. window leveling, pixel values obtained) and 3D post-processing (e.g. maximum intensity projection, multi-planar reconstruction, curved planar reformation and direct volume rendering). And then an instance is implemented to verify the protocol. This instance can support the mobile device access post-processing of medical image services on the render server via a client application or on the web page.

Improved detection of soma location and morphology in fluorescence microscopy images of neurons.

PubMed

Kayasandik, Cihan Bilge; Labate, Demetrio

2016-12-01

Automated detection and segmentation of somas in fluorescent images of neurons is a major goal in quantitative studies of neuronal networks, including applications of high-content-screenings where it is required to quantify multiple morphological properties of neurons. Despite recent advances in image processing targeted to neurobiological applications, existing algorithms of soma detection are often unreliable, especially when processing fluorescence image stacks of neuronal cultures. In this paper, we introduce an innovative algorithm for the detection and extraction of somas in fluorescent images of networks of cultured neurons where somas and other structures exist in the same fluorescent channel. Our method relies on a new geometrical descriptor called Directional Ratio and a collection of multiscale orientable filters to quantify the level of local isotropy in an image. To optimize the application of this approach, we introduce a new construction of multiscale anisotropic filters that is implemented by separable convolution. Extensive numerical experiments using 2D and 3D confocal images show that our automated algorithm reliably detects somas, accurately segments them, and separates contiguous ones. We include a detailed comparison with state-of-the-art existing methods to demonstrate that our algorithm is extremely competitive in terms of accuracy, reliability and computational efficiency. Our algorithm will facilitate the development of automated platforms for high content neuron image processing. A Matlab code is released open-source and freely available to the scientific community. Copyright © 2016 Elsevier B.V. All rights reserved.

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

PubMed Central

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-01-01

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com PMID:22543367

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

PubMed

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-06-15

The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

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).

Combining field performance with controlled environment plant imaging to identify the genetic control of growth and transpiration underlying yield response to water-deficit stress in wheat

PubMed Central

Parent, Boris; Shahinnia, Fahimeh; Maphosa, Lance; Berger, Bettina; Rabie, Huwaida; Chalmers, Ken; Kovalchuk, Alex; Langridge, Peter; Fleury, Delphine

2015-01-01

Crop yield in low-rainfall environments is a complex trait under multigenic control that shows significant genotype×environment (G×E) interaction. One way to understand and track this trait is to link physiological studies to genetics by using imaging platforms to phenotype large segregating populations. A wheat population developed from parental lines contrasting in their mechanisms of yield maintenance under water deficit was studied in both an imaging platform and in the field. We combined phenotyping methods in a common analysis pipeline to estimate biomass and leaf area from images and then inferred growth and relative growth rate, transpiration, and water-use efficiency, and applied these to genetic analysis. From the 20 quantitative trait loci (QTLs) found for several traits in the platform, some showed strong effects, accounting for between 26 and 43% of the variation on chromosomes 1A and 1B, indicating that the G×E interaction could be reduced in a controlled environment and by using dynamic variables. Co-location of QTLs identified in the platform and in the field showed a possible common genetic basis at some loci. Co-located QTLs were found for average growth rate, leaf expansion rate, transpiration rate, and water-use efficiency from the platform with yield, spike number, grain weight, grain number, and harvest index in the field. These results demonstrated that imaging platforms are a suitable alternative to field-based screening and may be used to phenotype recombinant lines for positional cloning. PMID:26179580

Building an Open-source Simulation Platform of Acoustic Radiation Force-based Breast Elastography

PubMed Central

Wang, Yu; Peng, Bo; Jiang, Jingfeng

2017-01-01

Ultrasound-based elastography including strain elastography (SE), acoustic radiation force Impulse (ARFI) imaging, point shear wave elastography (pSWE) and supersonic shear imaging (SSI) have been used to differentiate breast tumors among other clinical applications. The objective of this study is to extend a previously published virtual simulation platform built for ultrasound quasi-static breast elastography toward acoustic radiation force-based breast elastography. Consequently, the extended virtual breast elastography simulation platform can be used to validate image pixels with known underlying soft tissue properties (i.e. “ground truth”) in complex, heterogeneous media, enhancing confidence in elastographic image interpretations. The proposed virtual breast elastography system inherited four key components from the previously published virtual simulation platform: an ultrasound simulator (Field II), a mesh generator (Tetgen), a finite element solver (FEBio) and a visualization and data processing package (VTK). Using a simple message passing mechanism, functionalities have now been extended to acoustic radiation force-based elastography simulations. Examples involving three different numerical breast models with increasing complexity – one uniform model, one simple inclusion model and one virtual complex breast model derived from magnetic resonance imaging data, were used to demonstrate capabilities of this extended virtual platform. Overall, simulation results were compared with the published results. In the uniform model, the estimated shear wave speed (SWS) values were within 4% compared to the predetermined SWS values. In the simple inclusion and the complex breast models, SWS values of all hard inclusions in soft backgrounds were slightly underestimated, similar to what has been reported. The elastic contrast values and visual observation show that ARFI images have higher spatial resolution, while SSI images can provide higher inclusion-to-background contrast. In summary, our initial results were consistent with our expectations and what have been reported in the literature. The proposed (open-source) simulation platform can serve as a single gateway to perform many elastographic simulations in a transparent manner, thereby promoting collaborative developments. PMID:28075330

Building an open-source simulation platform of acoustic radiation force-based breast elastography

NASA Astrophysics Data System (ADS)

Wang, Yu; Peng, Bo; Jiang, Jingfeng

2017-03-01

Ultrasound-based elastography including strain elastography, acoustic radiation force impulse (ARFI) imaging, point shear wave elastography and supersonic shear imaging (SSI) have been used to differentiate breast tumors among other clinical applications. The objective of this study is to extend a previously published virtual simulation platform built for ultrasound quasi-static breast elastography toward acoustic radiation force-based breast elastography. Consequently, the extended virtual breast elastography simulation platform can be used to validate image pixels with known underlying soft tissue properties (i.e. ‘ground truth’) in complex, heterogeneous media, enhancing confidence in elastographic image interpretations. The proposed virtual breast elastography system inherited four key components from the previously published virtual simulation platform: an ultrasound simulator (Field II), a mesh generator (Tetgen), a finite element solver (FEBio) and a visualization and data processing package (VTK). Using a simple message passing mechanism, functionalities have now been extended to acoustic radiation force-based elastography simulations. Examples involving three different numerical breast models with increasing complexity—one uniform model, one simple inclusion model and one virtual complex breast model derived from magnetic resonance imaging data, were used to demonstrate capabilities of this extended virtual platform. Overall, simulation results were compared with the published results. In the uniform model, the estimated shear wave speed (SWS) values were within 4% compared to the predetermined SWS values. In the simple inclusion and the complex breast models, SWS values of all hard inclusions in soft backgrounds were slightly underestimated, similar to what has been reported. The elastic contrast values and visual observation show that ARFI images have higher spatial resolution, while SSI images can provide higher inclusion-to-background contrast. In summary, our initial results were consistent with our expectations and what have been reported in the literature. The proposed (open-source) simulation platform can serve as a single gateway to perform many elastographic simulations in a transparent manner, thereby promoting collaborative developments.

Imaging cytometry in a plastic ultra-mobile system

NASA Astrophysics Data System (ADS)

Martínez Vázquez, R.; Trotta, G.; Paturzo, M.; Volpe, A.; Bernava, G.; Basile, V.; Ancona, A.; Ferraro, P.; Fassi, I.; Osellame, R.

2017-03-01

We present a cost-effective and highly-portable plastic prototype that can be interfaced with a cell phone to implement an optofluidic imaging cytometry platform. It is based on a PMMA microfluidic chip that fits inside an opto-mechanical platform fabricated by a 3D printer. The fluorescence excitation and imaging is performed using the LED and the CMOS from the cell phone increasing the compactness of the system. A custom developed application is used to analyze the images and provide a value of particle concentration.

Good clean fun? A content analysis of profanity in video games and its prevalence across game systems and ratings.

PubMed

Ivory, James D; Williams, Dmitri; Martins, Nicole; Consalvo, Mia

2009-08-01

Although violent video game content and its effects have been examined extensively by empirical research, verbal aggression in the form of profanity has received less attention. Building on preliminary findings from previous studies, an extensive content analysis of profanity in video games was conducted using a sample of the 150 top-selling video games across all popular game platforms (including home consoles, portable consoles, and personal computers). The frequency of profanity, both in general and across three profanity categories, was measured and compared to games' ratings, sales, and platforms. Generally, profanity was found in about one in five games and appeared primarily in games rated for teenagers or above. Games containing profanity, however, tended to contain it frequently. Profanity was not found to be related to games' sales or platforms.

TDat: An Efficient Platform for Processing Petabyte-Scale Whole-Brain Volumetric Images.

PubMed

Li, Yuxin; Gong, Hui; Yang, Xiaoquan; Yuan, Jing; Jiang, Tao; Li, Xiangning; Sun, Qingtao; Zhu, Dan; Wang, Zhenyu; Luo, Qingming; Li, Anan

2017-01-01

Three-dimensional imaging of whole mammalian brains at single-neuron resolution has generated terabyte (TB)- and even petabyte (PB)-sized datasets. Due to their size, processing these massive image datasets can be hindered by the computer hardware and software typically found in biological laboratories. To fill this gap, we have developed an efficient platform named TDat, which adopts a novel data reformatting strategy by reading cuboid data and employing parallel computing. In data reformatting, TDat is more efficient than any other software. In data accessing, we adopted parallelization to fully explore the capability for data transmission in computers. We applied TDat in large-volume data rigid registration and neuron tracing in whole-brain data with single-neuron resolution, which has never been demonstrated in other studies. We also showed its compatibility with various computing platforms, image processing software and imaging systems.

Development of an optical inspection platform for surface defect detection in touch panel glass

NASA Astrophysics Data System (ADS)

Chang, Ming; Chen, Bo-Cheng; Gabayno, Jacque Lynn; Chen, Ming-Fu

2016-04-01

An optical inspection platform combining parallel image processing with high resolution opto-mechanical module was developed for defect inspection of touch panel glass. Dark field images were acquired using a 12288-pixel line CCD camera with 3.5 µm per pixel resolution and 12 kHz line rate. Key features of the glass surface were analyzed by parallel image processing on combined CPU and GPU platforms. Defect inspection of touch panel glass, which provided 386 megapixel image data per sample, was completed in roughly 5 seconds. High detection rate of surface scratches on the touch panel glass was realized with minimum defects size of about 10 µm after inspection. The implementation of a custom illumination source significantly improved the scattering efficiency on the surface, therefore enhancing the contrast in the acquired images and overall performance of the inspection system.

Flexible medical image management using service-oriented architecture.

PubMed

Shaham, Oded; Melament, Alex; Barak-Corren, Yuval; Kostirev, Igor; Shmueli, Noam; Peres, Yardena

2012-01-01

Management of medical images increasingly involves the need for integration with a variety of information systems. To address this need, we developed Content Management Offering (CMO), a platform for medical image management supporting interoperability through compliance with standards. CMO is based on the principles of service-oriented architecture, implemented with emphasis on three areas: clarity of business process definition, consolidation of service configuration management, and system scalability. Owing to the flexibility of this platform, a small team is able to accommodate requirements of customers varying in scale and in business needs. We describe two deployments of CMO, highlighting the platform's value to customers. CMO represents a flexible approach to medical image management, which can be applied to a variety of information technology challenges in healthcare and life sciences organizations.

Multiplex immunoassay for persistent organic pollutants in tilapia: Comparison of imaging- and flow cytometry-based platforms using spectrally encoded paramagnetic microspheres

USDA-ARS?s Scientific Manuscript database

Recent developments in spectrally encoded microspheres (SEMs)-based technologies provide high multiplexing possibilities. Most SEMs-based assays required a flow cytometer with sophisticated fluidics and optics. The new imaging superparamagnetic SEMs-based platform transports SEMs with considerably ...

GATE: a simulation toolkit for PET and SPECT.

PubMed

Jan, S; Santin, G; Strul, D; Staelens, S; Assié, K; Autret, D; Avner, S; Barbier, R; Bardiès, M; Bloomfield, P M; Brasse, D; Breton, V; Bruyndonckx, P; Buvat, I; Chatziioannou, A F; Choi, Y; Chung, Y H; Comtat, C; Donnarieix, D; Ferrer, L; Glick, S J; Groiselle, C J; Guez, D; Honore, P F; Kerhoas-Cavata, S; Kirov, A S; Kohli, V; Koole, M; Krieguer, M; van der Laan, D J; Lamare, F; Largeron, G; Lartizien, C; Lazaro, D; Maas, M C; Maigne, L; Mayet, F; Melot, F; Merheb, C; Pennacchio, E; Perez, J; Pietrzyk, U; Rannou, F R; Rey, M; Schaart, D R; Schmidtlein, C R; Simon, L; Song, T Y; Vieira, J M; Visvikis, D; Van de Walle, R; Wieërs, E; Morel, C

2004-10-07

Monte Carlo simulation is an essential tool in emission tomography that can assist in the design of new medical imaging devices, the optimization of acquisition protocols and the development or assessment of image reconstruction algorithms and correction techniques. GATE, the Geant4 Application for Tomographic Emission, encapsulates the Geant4 libraries to achieve a modular, versatile, scripted simulation toolkit adapted to the field of nuclear medicine. In particular, GATE allows the description of time-dependent phenomena such as source or detector movement, and source decay kinetics. This feature makes it possible to simulate time curves under realistic acquisition conditions and to test dynamic reconstruction algorithms. This paper gives a detailed description of the design and development of GATE by the OpenGATE collaboration, whose continuing objective is to improve, document and validate GATE by simulating commercially available imaging systems for PET and SPECT. Large effort is also invested in the ability and the flexibility to model novel detection systems or systems still under design. A public release of GATE licensed under the GNU Lesser General Public License can be downloaded at http:/www-lphe.epfl.ch/GATE/. Two benchmarks developed for PET and SPECT to test the installation of GATE and to serve as a tutorial for the users are presented. Extensive validation of the GATE simulation platform has been started, comparing simulations and measurements on commercially available acquisition systems. References to those results are listed. The future prospects towards the gridification of GATE and its extension to other domains such as dosimetry are also discussed.

GATE - Geant4 Application for Tomographic Emission: a simulation toolkit for PET and SPECT

PubMed Central

Jan, S.; Santin, G.; Strul, D.; Staelens, S.; Assié, K.; Autret, D.; Avner, S.; Barbier, R.; Bardiès, M.; Bloomfield, P. M.; Brasse, D.; Breton, V.; Bruyndonckx, P.; Buvat, I.; Chatziioannou, A. F.; Choi, Y.; Chung, Y. H.; Comtat, C.; Donnarieix, D.; Ferrer, L.; Glick, S. J.; Groiselle, C. J.; Guez, D.; Honore, P.-F.; Kerhoas-Cavata, S.; Kirov, A. S.; Kohli, V.; Koole, M.; Krieguer, M.; van der Laan, D. J.; Lamare, F.; Largeron, G.; Lartizien, C.; Lazaro, D.; Maas, M. C.; Maigne, L.; Mayet, F.; Melot, F.; Merheb, C.; Pennacchio, E.; Perez, J.; Pietrzyk, U.; Rannou, F. R.; Rey, M.; Schaart, D. R.; Schmidtlein, C. R.; Simon, L.; Song, T. Y.; Vieira, J.-M.; Visvikis, D.; Van de Walle, R.; Wieërs, E.; Morel, C.

2012-01-01

Monte Carlo simulation is an essential tool in emission tomography that can assist in the design of new medical imaging devices, the optimization of acquisition protocols, and the development or assessment of image reconstruction algorithms and correction techniques. GATE, the Geant4 Application for Tomographic Emission, encapsulates the Geant4 libraries to achieve a modular, versatile, scripted simulation toolkit adapted to the field of nuclear medicine. In particular, GATE allows the description of time-dependent phenomena such as source or detector movement, and source decay kinetics. This feature makes it possible to simulate time curves under realistic acquisition conditions and to test dynamic reconstruction algorithms. This paper gives a detailed description of the design and development of GATE by the OpenGATE collaboration, whose continuing objective is to improve, document, and validate GATE by simulating commercially available imaging systems for PET and SPECT. Large effort is also invested in the ability and the flexibility to model novel detection systems or systems still under design. A public release of GATE licensed under the GNU Lesser General Public License can be downloaded at the address http://www-lphe.ep.ch/GATE/. Two benchmarks developed for PET and SPECT to test the installation of GATE and to serve as a tutorial for the users are presented. Extensive validation of the GATE simulation platform has been started, comparing simulations and measurements on commercially available acquisition systems. References to those results are listed. The future prospects toward the gridification of GATE and its extension to other domains such as dosimetry are also discussed. PMID:15552416

European research platform IPANEMA at the SOLEIL synchrotron for ancient and historical materials.

PubMed

Bertrand, L; Languille, M-A; Cohen, S X; Robinet, L; Gervais, C; Leroy, S; Bernard, D; Le Pennec, E; Josse, W; Doucet, J; Schöder, S

2011-09-01

IPANEMA, a research platform devoted to ancient and historical materials (archaeology, cultural heritage, palaeontology and past environments), is currently being set up at the synchrotron facility SOLEIL (Saint-Aubin, France; SOLEIL opened to users in January 2008). The new platform is open to French, European and international users. The activities of the platform are centred on two main fields: increased support to synchrotron projects on ancient materials and methodological research. The IPANEMA team currently occupies temporary premises at SOLEIL, but the platform comprises construction of a new building that will comply with conservation and environmental standards and of a hard X-ray imaging beamline today in its conceptual design phase, named PUMA. Since 2008, the team has supported synchrotron works at SOLEIL and at European synchrotron facilities on a range of topics including pigment degradation in paintings, composition of musical instrument varnishes, and provenancing of medieval archaeological ferrous artefacts. Once the platform is fully operational, user support will primarily take place within medium-term research projects for `hosted' scientists, PhDs and post-docs. IPANEMA methodological research is focused on advanced two-dimensional/three-dimensional imaging and spectroscopy and statistical image analysis, both optimized for ancient materials.

The Architecture of an Automatic eHealth Platform With Mobile Client for Cerebrovascular Disease Detection

PubMed Central

Wang, Xingce; Bie, Rongfang; Wu, Zhongke; Zhou, Mingquan; Cao, Rongfei; Xie, Lizhi; Zhang, Dong

2013-01-01

Background In recent years, cerebrovascular disease has been the leading cause of death and adult disability in the world. This study describes an efficient approach to detect cerebrovascular disease. Objective In order to improve cerebrovascular treatment, prevention, and care, an automatic cerebrovascular disease detection eHealth platform is designed and studied. Methods We designed an automatic eHealth platform for cerebrovascular disease detection with a four-level architecture: object control layer, data transmission layer, service supporting layer, and application service layer. The platform has eight main functions: cerebrovascular database management, preprocessing of cerebral image data, image viewing and adjustment model, image cropping compression and measurement, cerebrovascular segmentation, 3-dimensional cerebrovascular reconstruction, cerebrovascular rendering, cerebrovascular virtual endoscope, and automatic detection. Several key technologies were employed for the implementation of the platform. The anisotropic diffusion model was used to reduce the noise. Statistics segmentation with Gaussian-Markov random field model (G-MRF) and Stochastic Estimation Maximization (SEM) parameter estimation method were used to realize the cerebrovascular segmentation. Ball B-Spline curve was proposed to model the cerebral blood vessels. Compute unified device architecture (CUDA) based on ray-casting volume rendering presented by curvature enhancement and boundary enhancement were used to realize the volume rendering model. We implemented the platform with a network client and mobile phone client to fit different users. Results The implemented platform is running on a common personal computer. Experiments on 32 patients’ brain computed tomography data or brain magnetic resonance imaging data stored in the system verified the feasibility and validity of each model we proposed. The platform is partly used in the cranial nerve surgery of the First Hospital Affiliated to the General Hospital of People's Liberation Army and radiology of Beijing Navy General Hospital. At the same time it also gets some applications in medical imaging specialty teaching of Tianjin Medical University. The application results have also been validated by our neurosurgeon and radiologist. Conclusions The platform appears beneficial in diagnosis of the cerebrovascular disease. The long-term benefits and additional applications of this technology warrant further study. The research built a diagnosis and treatment platform of the human tissue with complex geometry and topology such as brain vessel based on the Internet of things. PMID:25098861

FPscope: a field-portable high-resolution microscope using a cellphone lens.

PubMed

Dong, Siyuan; Guo, Kaikai; Nanda, Pariksheet; Shiradkar, Radhika; Zheng, Guoan

2014-10-01

The large consumer market has made cellphone lens modules available at low-cost and in high-quality. In a conventional cellphone camera, the lens module is used to demagnify the scene onto the image plane of the camera, where image sensor is located. In this work, we report a 3D-printed high-resolution Fourier ptychographic microscope, termed FPscope, which uses a cellphone lens in a reverse manner. In our platform, we replace the image sensor with sample specimens, and use the cellphone lens to project the magnified image to the detector. To supersede the diffraction limit of the lens module, we use an LED array to illuminate the sample from different incident angles and synthesize the acquired images using the Fourier ptychographic algorithm. As a demonstration, we use the reported platform to acquire high-resolution images of resolution target and biological specimens, with a maximum synthetic numerical aperture (NA) of 0.5. We also show that, the depth-of-focus of the reported platform is about 0.1 mm, orders of magnitude longer than that of a conventional microscope objective with a similar NA. The reported platform may enable healthcare accesses in low-resource settings. It can also be used to demonstrate the concept of computational optics for educational purposes.

Suppressing the image smear of the vibration modulation transfer function for remote-sensing optical cameras.

PubMed

Li, Jin; Liu, Zilong; Liu, Si

2017-02-20

In on-board photographing processes of satellite cameras, the platform vibration can generate image motion, distortion, and smear, which seriously affect the image quality and image positioning. In this paper, we create a mathematical model of a vibrating modulate transfer function (VMTF) for a remote-sensing camera. The total MTF of a camera is reduced by the VMTF, which means the image quality is degraded. In order to avoid the degeneration of the total MTF caused by vibrations, we use an Mn-20Cu-5Ni-2Fe (M2052) manganese copper alloy material to fabricate a vibration-isolation mechanism (VIM). The VIM can transform platform vibration energy into irreversible thermal energy with its internal twin crystals structure. Our experiment shows the M2052 manganese copper alloy material is good enough to suppress image motion below 125 Hz, which is the vibration frequency of satellite platforms. The camera optical system has a higher MTF after suppressing the vibration of the M2052 material than before.

A user-friendly LabVIEW software platform for grating based X-ray phase-contrast imaging.

PubMed

Wang, Shenghao; Han, Huajie; Gao, Kun; Wang, Zhili; Zhang, Can; Yang, Meng; Wu, Zhao; Wu, Ziyu

2015-01-01

X-ray phase-contrast imaging can provide greatly improved contrast over conventional absorption-based imaging for weakly absorbing samples, such as biological soft tissues and fibre composites. In this study, we introduced an easy and fast way to develop a user-friendly software platform dedicated to the new grating-based X-ray phase-contrast imaging setup at the National Synchrotron Radiation Laboratory of the University of Science and Technology of China. The control of 21 motorized stages, of a piezoelectric stage and of an X-ray tube are achieved with this software, it also covers image acquisition with a flat panel detector for automatic phase stepping scan. Moreover, a data post-processing module for signals retrieval and other custom features are in principle available. With a seamless integration of all the necessary functions in one software package, this platform greatly facilitate users' activities during experimental runs with this grating based X-ray phase contrast imaging setup.

Platform for intraoperative analysis of video streams

NASA Astrophysics Data System (ADS)

Clements, Logan; Galloway, Robert L., Jr.

2004-05-01

Interactive, image-guided surgery (IIGS) has proven to increase the specificity of a variety of surgical procedures. However, current IIGS systems do not compensate for changes that occur intraoperatively and are not reflected in preoperative tomograms. Endoscopes and intraoperative ultrasound, used in minimally invasive surgery, provide real-time (RT) information in a surgical setting. Combining the information from RT imaging modalities with traditional IIGS techniques will further increase surgical specificity by providing enhanced anatomical information. In order to merge these techniques and obtain quantitative data from RT imaging modalities, a platform was developed to allow both the display and processing of video streams in RT. Using a Bandit-II CV frame grabber board (Coreco Imaging, St. Laurent, Quebec) and the associated library API, a dynamic link library was created in Microsoft Visual C++ 6.0 such that the platform could be incorporated into the IIGS system developed at Vanderbilt University. Performance characterization, using two relatively inexpensive host computers, has shown the platform capable of performing simple image processing operations on frames captured from a CCD camera and displaying the processed video data at near RT rates both independent of and while running the IIGS system.

Aerial multi-camera systems: Accuracy and block triangulation issues

NASA Astrophysics Data System (ADS)

Rupnik, Ewelina; Nex, Francesco; Toschi, Isabella; Remondino, Fabio

2015-03-01

Oblique photography has reached its maturity and has now been adopted for several applications. The number and variety of multi-camera oblique platforms available on the market is continuously growing. So far, few attempts have been made to study the influence of the additional cameras on the behaviour of the image block and comprehensive revisions to existing flight patterns are yet to be formulated. This paper looks into the precision and accuracy of 3D points triangulated from diverse multi-camera oblique platforms. Its coverage is divided into simulated and real case studies. Within the simulations, different imaging platform parameters and flight patterns are varied, reflecting both current market offerings and common flight practices. Attention is paid to the aspect of completeness in terms of dense matching algorithms and 3D city modelling - the most promising application of such systems. The experimental part demonstrates the behaviour of two oblique imaging platforms in real-world conditions. A number of Ground Control Point (GCP) configurations are adopted in order to point out the sensitivity of tested imaging networks and arising block deformations. To stress the contribution of slanted views, all scenarios are compared against a scenario in which exclusively nadir images are used for evaluation.

Platforms for hyperspectral imaging, in-situ optical and acoustical imaging in urbanized regions

NASA Astrophysics Data System (ADS)

Bostater, Charles R.; Oney, Taylor

2016-10-01

Hyperspectral measurements of the water surface of urban coastal waters are presented. Oblique bidirectional reflectance factor imagery was acquired made in a turbid coastal sub estuary of the Indian River Lagoon, Florida and along coastal surf zone waters of the nearby Atlantic Ocean. Imagery was also collected using a pushbroom hyperspectral imager mounted on a fixed platform with a calibrated circular mechatronic rotation stage. Oblique imagery of the shoreline and subsurface features clearly shows subsurface bottom features and rip current features within the surf zone water column. In-situ hyperspectral optical signatures were acquired from a vessel as a function of depth to determine the attenuation spectrum in Palm Bay. A unique stationary platform methodology to acquire subsurface acoustic images showing the presence of moving bottom boundary nephelometric layers passing through the acoustic fan beam. The acoustic fan beam imagery indicated the presence of oscillatory subsurface waves in the urbanized coastal estuary. Hyperspectral imaging using the fixed platform techniques are being used to collect hyperspectral bidirectional reflectance factor (BRF) measurements from locations at buildings and bridges in order to provide new opportunities to advance our scientific understanding of aquatic environments in urbanized regions.

Collaborative Visual Seafloor Imaging using a Photographic AUV and a Lagrangian Imaging Float

NASA Astrophysics Data System (ADS)

Friedman, A.; Pizarro, O.; Roman, C.; Toohey, L.; Snyder, W.; Johnson-Roberson, M.; Iscar, E.; Williams, S. B.

2016-02-01

High resolution seafloor imaging from mobile autonomous platforms has become a valuable tool for habitat classification, stock assessment and seafloor exploration. This abstract addresses the concept of joint seafloor survey planning using both navigable and drifting platforms, and presents results from an experiment using a bottom surveying AUV and a drifting Lagrangian camera float. We consider two classes of vehicles; one which is able to self propel and execute structured surveys, and one which is Lagrangian and moves only with the currents. The navigable vehicle is the more capable and the more expensives asset of the two. The Lagrangian platforms is a low cost imaging tool that can actively control its altitude above the seafloor to obtain high quality images but can not otherwise control its trajectory over the bottom. When used together the vehicles offer several scenarios for joint operations. When used in an exploratory manner the Lagrangian float is an inexpensive way to collect images from an unknown area. Depending on the collected images, a follow on structured survey with the navigable AUV can collect additional information if the cost is acceptable given the need and prior data. When used simultaneously the drifting float can guide the AUV trajectory over an area. When both platforms are equipped with acoustic tracking and communications the AUV trajectory can be automatically redirected to follow the Lagrangian float using one of many patterns. This capability allows for surveys that are potentially more representative of the near bottom oceanographic conditions at the desired location. Results will be presented from a cruise to Scott Reef, Australia, where both platforms were used as part of a coral habitat monitoring project.

A Sub-Hertz, Low-Frequency Vibration Isolation Platform

NASA Technical Reports Server (NTRS)

Ortiz, Gerardo, G.; Farr, William H.; Sannibale, Virginio

2011-01-01

One of the major technical problems deep-space optical communication (DSOC) systems need to solve is the isolation of the optical terminal from vibrations produced by the spacecraft navigational control system and by the moving parts of onboard instruments. Even under these vibration perturbations, the DSOC transceivers (telescopes) need to be pointed l000 fs of times more accurately than an RF communication system (parabolic antennas). Mechanical resonators have been extensively used to provide vibration isolation for groundbased, airborne, and spaceborne payloads. The effectiveness of these isolation systems is determined mainly by the ability of designing a mechanical oscillator with the lowest possible resonant frequency. The Low-Frequency Vibration Isolation Platform (LFVIP), developed during this effort, aims to reduce the resonant frequency of the mechanical oscillators into the sub-Hertz region in order to maximize the passive isolation afforded by the 40 dB/decade roll-off response of the resonator. The LFVIP also provides tip/tilt functionality for acquisition and tracking of a beacon signal. An active control system is used for platform positioning and for dampening of the mechanical oscillator. The basic idea in the design of the isolation platform is to use a passive isolation strut with an approximately equal to 100-mHz resonance frequency. This will extend the isolation range to lower frequencies. The harmonic oscillator is a second-order lowpass filter for mechanical disturbances. The resonance quality depends on the dissipation mechanisms, which are mainly hysteretic because of the low resonant frequency and the absence of any viscous medium. The LFVIP system is configured using the well-established Stewart Platform, which consists of a top platform connected to a base with six extensible struts (see figure). The struts are attached to the base and to the platform via universal joints, which permit the extension and contraction of the struts. The struts ends are connected in pairs to the base and to the platform, forming an octahedron. The six struts provide the vibration isolation due to the properties of mechanical oscillators that behave as second-order lowpass filters for frequencies above the resonance. At high frequency, the ideal second-order low-pass filter response is spoiled by the distributed mass and the internal modes of membrane and of the platform with its payload.

A new e-learning platform for radiology education (RadEd).

PubMed

Xiberta, Pau; Boada, Imma

2016-04-01

One of the key elements of e-learning platforms is the content provided to the students. Content creation is a time demanding task that requires teachers to prepare material taking into account that it will be accessed on-line. Moreover, the teacher is restricted by the functionalities provided by the e-learning platforms. In contexts such as radiology where images have a key role, the required functionalities are still more specific and difficult to be provided by these platforms. Our purpose is to create a framework to make teacher's tasks easier, specially when he has to deal with contents where images have a main role. In this paper, we present RadEd, a new web-based teaching framework that integrates a smart editor to create case-based exercises that support image interaction such as changing the window width and the grey scale used to render the image, taking measurements on the image, attaching labels to images and selecting parts of the images, amongst others. It also provides functionalities to prepare courses with different topics, exercises and theory material, and also functionalities to control students' work. Different experts have used RadEd and all of them have considered it a very useful and valuable tool to prepare courses where radiological images are the main component. RadEd provides teachers functionalities to prepare more realistic cases and students the ability to make a more specific diagnosis. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Targeted Nanoparticles for Image-guided Treatment of Triple Negative Breast Cancer: Clinical Significance and Technological Advances

PubMed Central

Miller-Kleinhenz, Jasmine M.; Bozeman, Erica N.

2015-01-01

Effective treatment of triple negative breast cancer (TNBC) with its aggressive tumor biology, highly heterogeneous tumor cells, and poor prognosis requires an integrated therapeutic approach that addresses critical issues in cancer therapy. Multifunctional nanoparticles with the abilities of targeted drug delivery and non-invasive imaging for monitoring drug delivery and responses to therapy, such as theranostic nanoparticles, hold great promise towards the development of novel therapeutic approaches for the treatment of TNBC using a single therapeutic platform. The biological and pathological characteristics of TNBC provide insight into several potential molecular targets for current and future nanoparticle based therapeutics. Extensive tumor stroma, highly proliferative cells, and a high rate of drug-resistance are all barriers that must be appropriately addressed in order for these nanotherapeutic platforms to be effective. Utilization of the enhanced permeability and retention (EPR) effect coupled with active targeting of cell surface receptors expressed by TNBC cells, and tumor associated endothelial cells, stromal fibroblasts and macrophages is likely to overcome such barriers to facilitate more effective drug delivery. An in depth summary of current studies investigating targeted nanoparticles in preclinical TNBC mouse and human xenograft models is presented. This review aims to outline the current status of nanotherapeutic options for TNBC patients, identification of promising molecular targets, challenges associated with the development of targeted nanotherapeutics, the research done by our group as well as others and future perspectives on the nanomedicine field and ways to translate current preclinical studies into the clinic. PMID:25966677

BrainIACS: a system for web-based medical image processing

NASA Astrophysics Data System (ADS)

Kishore, Bhaskar; Bazin, Pierre-Louis; Pham, Dzung L.

2009-02-01

We describe BrainIACS, a web-based medical image processing system that permits and facilitates algorithm developers to quickly create extensible user interfaces for their algorithms. Designed to address the challenges faced by algorithm developers in providing user-friendly graphical interfaces, BrainIACS is completely implemented using freely available, open-source software. The system, which is based on a client-server architecture, utilizes an AJAX front-end written using the Google Web Toolkit (GWT) and Java Servlets running on Apache Tomcat as its back-end. To enable developers to quickly and simply create user interfaces for configuring their algorithms, the interfaces are described using XML and are parsed by our system to create the corresponding user interface elements. Most of the commonly found elements such as check boxes, drop down lists, input boxes, radio buttons, tab panels and group boxes are supported. Some elements such as the input box support input validation. Changes to the user interface such as addition and deletion of elements are performed by editing the XML file or by using the system's user interface creator. In addition to user interface generation, the system also provides its own interfaces for data transfer, previewing of input and output files, and algorithm queuing. As the system is programmed using Java (and finally Java-script after compilation of the front-end code), it is platform independent with the only requirements being that a Servlet implementation be available and that the processing algorithms can execute on the server platform.

Intraoperative visualization and assessment of electromagnetic tracking error

NASA Astrophysics Data System (ADS)

Harish, Vinyas; Ungi, Tamas; Lasso, Andras; MacDonald, Andrew; Nanji, Sulaiman; Fichtinger, Gabor

2015-03-01

Electromagnetic tracking allows for increased flexibility in designing image-guided interventions, however it is well understood that electromagnetic tracking is prone to error. Visualization and assessment of the tracking error should take place in the operating room with minimal interference with the clinical procedure. The goal was to achieve this ideal in an open-source software implementation in a plug and play manner, without requiring programming from the user. We use optical tracking as a ground truth. An electromagnetic sensor and optical markers are mounted onto a stylus device, pivot calibrated for both trackers. Electromagnetic tracking error is defined as difference of tool tip position between electromagnetic and optical readings. Multiple measurements are interpolated into the thin-plate B-spline transform visualized in real time using 3D Slicer. All tracked devices are used in a plug and play manner through the open-source SlicerIGT and PLUS extensions of the 3D Slicer platform. Tracking error was measured multiple times to assess reproducibility of the method, both with and without placing ferromagnetic objects in the workspace. Results from exhaustive grid sampling and freehand sampling were similar, indicating that a quick freehand sampling is sufficient to detect unexpected or excessive field distortion in the operating room. The software is available as a plug-in for the 3D Slicer platforms. Results demonstrate potential for visualizing electromagnetic tracking error in real time for intraoperative environments in feasibility clinical trials in image-guided interventions.

Acquiring experience in pathology predominantly from what you see, not from what you read: the HIPON e-learning platform.

PubMed

Riccioni, Olga; Vrasidas, Charalambos; Brcic, Luka; Armenski, Goce; Seiwerth, Sven; Smeets, Annemieke; van Krieken, J Han Jm; Lazaris, Andreas C

2015-01-01

It is indisputable that nowadays one of the hardest and most important tasks in medicine and especially in medical education, is the conversion of the extensive amount of available data, into medical experience, after a proper analysis. A project under the title "ICT (Information and Communication Technology) eModules on HistoPathology: a useful online tool for students, researchers and professionals - HIPON", co-financed by the Lifelong Learning Program of the Education, Audiovisual and Culture Executive Agency (EACEA), The Commission of the European Union, has been launched at the beginning of 2013. HIPON's purpose is not to provide just another pathology website atlas, but to convey professional experience and thinking in pathology. HIPON has resulted in a well-structured and user-friendly, open resource, multi-language, e-learning platform which, taking advantage of modern image technology, offers medical students, researchers, and professionals a valuable teaching instrument so that they can acquire professional experience in pathology. The mid-term report of HIPON has been favorably evaluated by the EACEA experts who appreciated the potential of our teaching tool in providing the opportunity and the means to acquire medical experience. Through the use of virtual slides, educative videos and microscopic, high resolution, marked images accompanied by relevant questions and answers, HIPON project aims to make end-users able to think as experienced pathologists and become highly efficient in correlating pathologic data with other clinical-laboratory information.

Near-surface, marine seismic-reflection data defines potential hydrogeologic confinement bypass in a tertiary carbonate aquifer, southeastern Florida

USGS Publications Warehouse

Cunningham, Kevin J.; Walker, Cameron; Westcott, Richard L.

2012-01-01

Approximately 210 km of near-surface, high-frequency, marine seismic-reflection data were acquired on the southeastern part of the Florida Platform between 2007 and 2011. Many high-resolution, seismic-reflection profiles, interpretable to a depth of about 730 m, were collected on the shallow-marine shelf of southeastern Florida in water as shallow as 1 m. Landward of the present-day shelf-margin slope, these data image middle Eocene to Pleistocene strata and Paleocene to Pleistocene strata on the Miami Terrace. This high-resolution data set provides an opportunity to evaluate geologic structures that cut across confining units of the Paleocene to Oligocene-age carbonate rocks that form the Floridan aquifer system.Seismic profiles image two structural systems, tectonic faults and karst collapse structures, which breach confining beds in the Floridan aquifer system. Both structural systems may serve as pathways for vertical groundwater flow across relatively low-permeability carbonate strata that separate zones of regionally extensive high-permeability rocks in the Floridan aquifer system. The tectonic faults occur as normal and reverse faults, and collapse-related faults have normal throw. The most common fault occurrence delineated on the reflection profiles is associated with karst collapse structures. These high-frequency seismic data are providing high quality structural analogs to unprecedented depths on the southeastern Florida Platform. The analogs can be used for assessment of confinement of other carbonate aquifers and the sealing potential of deeper carbonate rocks associated with reservoirs around the world.

Overall design of imaging spectrometer on-board light aircraft

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

Zhongqi, H.; Zhengkui, C.; Changhua, C.

1996-11-01

Aerial remote sensing is the earliest remote sensing technical system and has gotten rapid development in recent years. The development of aerial remote sensing was dominated by high to medium altitude platform in the past, and now it is characterized by the diversity platform including planes of high-medium-low flying altitude, helicopter, airship, remotely controlled airplane, glider, and balloon. The widely used and rapidly developed platform recently is light aircraft. Early in the close of 1970s, Beijing Research Institute of Uranium Geology began aerial photography and geophysical survey using light aircraft, and put forward the overall design scheme of light aircraftmore » imaging spectral application system (LAISAS) in 19905. LAISAS is comprised of four subsystem. They are called measuring platform, data acquiring subsystem, ground testing and data processing subsystem respectively. The principal instruments of LAISAS include measuring platform controlled by inertia gyroscope, aerial spectrometer with high spectral resolution, imaging spectrometer, 3-channel scanner, 128-channel imaging spectrometer, GPS, illuminance-meter, and devices for atmospheric parameters measuring, ground testing, data correction and processing. LAISAS has the features of integrity from data acquisition to data processing and to application; of stability which guarantees the image quality and is comprised of measuring, ground testing device, and in-door data correction system; of exemplariness of integrated the technology of GIS, GPS, and Image Processing System; of practicality which embodied LAISAS with flexibility and high ratio of performance to cost. So, it can be used in the fields of fundamental research of Remote Sensing and large-scale mapping for resource exploration, environmental monitoring, calamity prediction, and military purpose.« less

Live Cell in Vitro and in Vivo Imaging Applications: Accelerating Drug Discovery

PubMed Central

Isherwood, Beverley; Timpson, Paul; McGhee, Ewan J; Anderson, Kurt I; Canel, Marta; Serrels, Alan; Brunton, Valerie G; Carragher, Neil O

2011-01-01

Dynamic regulation of specific molecular processes and cellular phenotypes in live cell systems reveal unique insights into cell fate and drug pharmacology that are not gained from traditional fixed endpoint assays. Recent advances in microscopic imaging platform technology combined with the development of novel optical biosensors and sophisticated image analysis solutions have increased the scope of live cell imaging applications in drug discovery. We highlight recent literature examples where live cell imaging has uncovered novel insight into biological mechanism or drug mode-of-action. We survey distinct types of optical biosensors and associated analytical methods for monitoring molecular dynamics, in vitro and in vivo. We describe the recent expansion of live cell imaging into automated target validation and drug screening activities through the development of dedicated brightfield and fluorescence kinetic imaging platforms. We provide specific examples of how temporal profiling of phenotypic response signatures using such kinetic imaging platforms can increase the value of in vitro high-content screening. Finally, we offer a prospective view of how further application and development of live cell imaging technology and reagents can accelerate preclinical lead optimization cycles and enhance the in vitro to in vivo translation of drug candidates. PMID:24310493

SU-E-J-44: Design a Platform and Phantom Model for Photoacoustic Imaging in Combination with CT

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

Sick, J; Alsanea, F; Rancilio, N

2014-06-01

Purpose: Our (long-term) objective is to develop a US manipulator that will provide in situ radiation response and image-guided therapy for bladder cancer based on photoacoustic molecular imaging. Methods: A platform was devised to provide a reproducible positional frame of reference for targeting anatomic structure between MDCT and US scans, in lieu of CBCT, and to fuse photoacoustic molecular imaging. US and photoacoustic scans are taken of a patient while in the CT scanner and IRMT. Through co-registration, based on anatomical positions, we identified a common coordinate system to be used in Eclipse. A bladder phantom was constructed to validatemore » anatomical tracking via US and photoacoustic imaging. We tested the platform using phantom model to demonstrate validity once moved from the CT couch to the linear accelerator couch. Results: This platform interlocks with Varian exact couch index points for reproducibility of positioning. Construction from low Z material and sized appropriately to fit in CT/IMRT gantry. Error in conversion from cylindrical coordinates of the manipulator to X, Y, Z coordinates of the treatment couch was less than 1mm. We measured the bladder size in 3 different directions in both Eclipse from the CT and Acuson from US. The error was less than 2mm in all directions. CT and US images were co-registered in MATLAB. Co-registration of photoacoustic images is still being developed. Conclusion: For Linear Accelerators without on board imaging, MV portal images are not a viable option for the localization of soft tissue anatomy. We believe our manipulator provides an alternative using US imaging, which will be examined in an upcoming clinical trial. We plan to examine the value of hypoxia guided treatment through photoacoustic imaging during this trial.« less

An Integrative Platform for Three-dimensional Quantitative Analysis of Spatially Heterogeneous Metastasis Landscapes

NASA Astrophysics Data System (ADS)

Guldner, Ian H.; Yang, Lin; Cowdrick, Kyle R.; Wang, Qingfei; Alvarez Barrios, Wendy V.; Zellmer, Victoria R.; Zhang, Yizhe; Host, Misha; Liu, Fang; Chen, Danny Z.; Zhang, Siyuan

2016-04-01

Metastatic microenvironments are spatially and compositionally heterogeneous. This seemingly stochastic heterogeneity provides researchers great challenges in elucidating factors that determine metastatic outgrowth. Herein, we develop and implement an integrative platform that will enable researchers to obtain novel insights from intricate metastatic landscapes. Our two-segment platform begins with whole tissue clearing, staining, and imaging to globally delineate metastatic landscape heterogeneity with spatial and molecular resolution. The second segment of our platform applies our custom-developed SMART 3D (Spatial filtering-based background removal and Multi-chAnnel forest classifiers-based 3D ReconsTruction), a multi-faceted image analysis pipeline, permitting quantitative interrogation of functional implications of heterogeneous metastatic landscape constituents, from subcellular features to multicellular structures, within our large three-dimensional (3D) image datasets. Coupling whole tissue imaging of brain metastasis animal models with SMART 3D, we demonstrate the capability of our integrative pipeline to reveal and quantify volumetric and spatial aspects of brain metastasis landscapes, including diverse tumor morphology, heterogeneous proliferative indices, metastasis-associated astrogliosis, and vasculature spatial distribution. Collectively, our study demonstrates the utility of our novel integrative platform to reveal and quantify the global spatial and volumetric characteristics of the 3D metastatic landscape with unparalleled accuracy, opening new opportunities for unbiased investigation of novel biological phenomena in situ.

Anser EMT: the first open-source electromagnetic tracking platform for image-guided interventions.

PubMed

Jaeger, Herman Alexander; Franz, Alfred Michael; O'Donoghue, Kilian; Seitel, Alexander; Trauzettel, Fabian; Maier-Hein, Lena; Cantillon-Murphy, Pádraig

2017-06-01

Electromagnetic tracking is the gold standard for instrument tracking and navigation in the clinical setting without line of sight. Whilst clinical platforms exist for interventional bronchoscopy and neurosurgical navigation, the limited flexibility and high costs of electromagnetic tracking (EMT) systems for research investigations mitigate against a better understanding of the technology's characterisation and limitations. The Anser project provides an open-source implementation for EMT with particular application to image-guided interventions. This work provides implementation schematics for our previously reported EMT system which relies on low-cost acquisition and demodulation techniques using both National Instruments and Arduino hardware alongside MATLAB support code. The system performance is objectively compared to other commercial tracking platforms using the Hummel assessment protocol. Positional accuracy of 1.14 mm and angular rotation accuracy of [Formula: see text] are reported. Like other EMT platforms, Anser is susceptible to tracking errors due to eddy current and ferromagnetic distortion. The system is compatible with commercially available EMT sensors as well as the Open Network Interface for image-guided therapy (OpenIGTLink) for easy communication with visualisation and medical imaging toolkits such as MITK and 3D Slicer. By providing an open-source platform for research investigations, we believe that novel and collaborative approaches can overcome the limitations of current EMT technology.

Automated Formosat Image Processing System for Rapid Response to International Disasters

NASA Astrophysics Data System (ADS)

Cheng, M. C.; Chou, S. C.; Chen, Y. C.; Chen, B.; Liu, C.; Yu, S. J.

2016-06-01

FORMOSAT-2, Taiwan's first remote sensing satellite, was successfully launched in May of 2004 into the Sun-synchronous orbit at 891 kilometers of altitude. With the daily revisit feature, the 2-m panchromatic, 8-m multi-spectral resolution images captured have been used for researches and operations in various societal benefit areas. This paper details the orchestration of various tasks conducted in different institutions in Taiwan in the efforts responding to international disasters. The institutes involved including its space agency-National Space Organization (NSPO), Center for Satellite Remote Sensing Research of National Central University, GIS Center of Feng-Chia University, and the National Center for High-performance Computing. Since each institution has its own mandate, the coordinated tasks ranged from receiving emergency observation requests, scheduling and tasking of satellite operation, downlink to ground stations, images processing including data injection, ortho-rectification, to delivery of image products. With the lessons learned from working with international partners, the FORMOSAT Image Processing System has been extensively automated and streamlined with a goal to shorten the time between request and delivery in an efficient manner. The integrated team has developed an Application Interface to its system platform that provides functions of search in archive catalogue, request of data services, mission planning, inquiry of services status, and image download. This automated system enables timely image acquisition and substantially increases the value of data product. Example outcome of these efforts in recent response to support Sentinel Asia in Nepal Earthquake is demonstrated herein.

Magnetic Resonance Imaging at Ultrahigh Fields

PubMed Central

Uğurbil, Kamil

2014-01-01

Since the introduction of 4 T human systems in three academic laboratories circa 1990, rapid progress in imaging and spectroscopy studies in humans at 4 T and animal model systems at 9.4 T have led to the introduction of 7 T and higher magnetic fields for human investigation at about the turn of the century. Work conducted on these platforms has demonstrated the existence of significant advantages in SNR and biological information content at these ultrahigh fields, as well as the presence of numerous challenges. Primary difference from lower fields is the deviation from the near field regime; at the frequencies corresponding to hydrogen resonance conditions at ultrahigh fields, the RF is characterized by attenuated traveling waves in the human body, which leads to image nonuniformities for a given sample-coil configuration because of interferences. These nonuniformities were considered detrimental to the progress of imaging at high field strengths. However, they are advantageous for parallel imaging for signal reception and parallel transmission, two critical technologies that account, to a large extend, for the success of ultrahigh fields. With these technologies, and improvements in instrumentation and imaging methods, ultra-high fields have provided unprecedented gains in imaging of brain function and anatomy, and started to make inroads into investigation of the human torso and extremities. As extensive as they are, these gains still constitute a prelude to what is to come given the increasingly larger effort committed to ultrahigh field research and development of ever better instrumentation and techniques. PMID:24686229

Spotlight-8 Image Analysis Software

NASA Technical Reports Server (NTRS)

Klimek, Robert; Wright, Ted

2006-01-01

Spotlight is a cross-platform GUI-based software package designed to perform image analysis on sequences of images generated by combustion and fluid physics experiments run in a microgravity environment. Spotlight can perform analysis on a single image in an interactive mode or perform analysis on a sequence of images in an automated fashion. Image processing operations can be employed to enhance the image before various statistics and measurement operations are performed. An arbitrarily large number of objects can be analyzed simultaneously with independent areas of interest. Spotlight saves results in a text file that can be imported into other programs for graphing or further analysis. Spotlight can be run on Microsoft Windows, Linux, and Apple OS X platforms.

Graphene-Plasmonic Hybrid Platform for Label-Free SERS Biomedical Detection

NASA Astrophysics Data System (ADS)

Wang, Pu

Surface Enhanced Raman Scattering (SERS) has attracted explosive interest for the wealth of vibrational information it provides with minimal invasive effects to target analyte. Nanotechnology, especially in the form of noble metal nanoparticles exhibit unique electromagnetic and chemical characteristics that are explored to realize ultra-sensitive SERS detection in chemical and biological analysis. Graphene, atom-thick carbon monolayer, exhibits superior chemical stability and bio-compatibility. A combination of SERS-active metal nanostructures and graphene will create various synergies in SERS. The main objective of this research was to exploit the applications of the graphene-Au tip hybrid platform in SERS. The hybrid platform consists of a periodic Au nano-pyramid substrate to provide reproducible plasmonic enhancement, and the superimposed monolayer graphene sheet, serving as "built-in" Raman marker. Extensive theoretical and experimental studies were conducted to determine the potentials of the hybrid platform as SERS substrate. Results from both Finite-Domain Time-Domain (FDTD) numerical simulation and Raman scattering of graphene suggested that the hybrid platform boosted a high density of hotspots yielding 1000 times SERS enhancement of graphene bands. Ultra-high sensitivity of the hybrid platform was demonstrated by bio-molecules including dye, protein and neurotransmitters. Dopamine and serotonin can be detected and distinguished at 10-9 M concentration in the presence of human body fluid. Single molecule detection was obtained using a bi-analyte technique. Graphene supported a vibration mode dependent SERS chemical enhancement of ˜10 to the analyte. Quantitative evaluation of hotspots was presented using spatially resolved Raman mapping of graphene SERS enhancement. Graphene plays a crucial role in quantifying SERS hotspots and paves the path for defining SERS EF that could be universally applied to various SERS systems. A reproducible and statistically reliable SERS quantification approach using the hybrid platform was proposed. The SERS mapping based approach not only leverages the ultra-sensitivity but also minimizes the spot-to-spot variations. Feasibility of biomedical diagnosis with the hybrid platform was exploited by colon cancer cell sensing and time-dependent SERS of amyloid beta protein monomer. The capabilities of the platform are demonstrated by colon cancer cell detection in simulated body fluid background with cell concentration down to 50 cells /mL. Sensitivity of 95% was evidenced by Principle Components Analysis (PCA). Besides, a noticeable evolution profile of the Abeta SERS peaks was observed and attributed to the Abeta configurational change. Taken together, the results suggested the graphene-plasmonic hybrid platform can potentially deliver a biomedical detection and diagnostic imaging platform with superior sensitivity and resolution.

Combining field performance with controlled environment plant imaging to identify the genetic control of growth and transpiration underlying yield response to water-deficit stress in wheat.

PubMed

Parent, Boris; Shahinnia, Fahimeh; Maphosa, Lance; Berger, Bettina; Rabie, Huwaida; Chalmers, Ken; Kovalchuk, Alex; Langridge, Peter; Fleury, Delphine

2015-09-01

Crop yield in low-rainfall environments is a complex trait under multigenic control that shows significant genotype×environment (G×E) interaction. One way to understand and track this trait is to link physiological studies to genetics by using imaging platforms to phenotype large segregating populations. A wheat population developed from parental lines contrasting in their mechanisms of yield maintenance under water deficit was studied in both an imaging platform and in the field. We combined phenotyping methods in a common analysis pipeline to estimate biomass and leaf area from images and then inferred growth and relative growth rate, transpiration, and water-use efficiency, and applied these to genetic analysis. From the 20 quantitative trait loci (QTLs) found for several traits in the platform, some showed strong effects, accounting for between 26 and 43% of the variation on chromosomes 1A and 1B, indicating that the G×E interaction could be reduced in a controlled environment and by using dynamic variables. Co-location of QTLs identified in the platform and in the field showed a possible common genetic basis at some loci. Co-located QTLs were found for average growth rate, leaf expansion rate, transpiration rate, and water-use efficiency from the platform with yield, spike number, grain weight, grain number, and harvest index in the field. These results demonstrated that imaging platforms are a suitable alternative to field-based screening and may be used to phenotype recombinant lines for positional cloning. © The Author 2015. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Cryo-Imaging and Software Platform for Analysis of Molecular MR Imaging of Micrometastases

PubMed Central

Qutaish, Mohammed Q.; Zhou, Zhuxian; Prabhu, David; Liu, Yiqiao; Busso, Mallory R.; Izadnegahdar, Donna; Gargesha, Madhusudhana; Lu, Hong; Lu, Zheng-Rong

2018-01-01

We created and evaluated a preclinical, multimodality imaging, and software platform to assess molecular imaging of small metastases. This included experimental methods (e.g., GFP-labeled tumor and high resolution multispectral cryo-imaging), nonrigid image registration, and interactive visualization of imaging agent targeting. We describe technological details earlier applied to GFP-labeled metastatic tumor targeting by molecular MR (CREKA-Gd) and red fluorescent (CREKA-Cy5) imaging agents. Optimized nonrigid cryo-MRI registration enabled nonambiguous association of MR signals to GFP tumors. Interactive visualization of out-of-RAM volumetric image data allowed one to zoom to a GFP-labeled micrometastasis, determine its anatomical location from color cryo-images, and establish the presence/absence of targeted CREKA-Gd and CREKA-Cy5. In a mouse with >160 GFP-labeled tumors, we determined that in the MR images every tumor in the lung >0.3 mm2 had visible signal and that some metastases as small as 0.1 mm2 were also visible. More tumors were visible in CREKA-Cy5 than in CREKA-Gd MRI. Tape transfer method and nonrigid registration allowed accurate (<11 μm error) registration of whole mouse histology to corresponding cryo-images. Histology showed inflammation and necrotic regions not labeled by imaging agents. This mouse-to-cells multiscale and multimodality platform should uniquely enable more informative and accurate studies of metastatic cancer imaging and therapy. PMID:29805438

Multipurpose floating platform for hyperspectral imaging, sampling and sensing of surface water sources used in irrigation and recreation

USDA-ARS?s Scientific Manuscript database

The objective of this work was to design, construct, and test the self-propelled aquatic platform for imaging, multi-tier water sampling, water quality sensing, and depth profiling to document microbial content and environmental covariates in the interior of irrigation ponds and reservoirs. The plat...

Line-scan Raman imaging and spectroscopy platform for surface and subsurface evaluation of food safety and quality

USDA-ARS?s Scientific Manuscript database

Both surface and subsurface food inspection is important since interesting safety and quality attributes can be at different sample locations. This paper presents a multipurpose line-scan Raman platform for food safety and quality research, which can be configured for Raman chemical imaging (RCI) mo...

Vibrational imaging of glucose uptake activity in live cells and tissues by stimulated Raman scattering microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Hu, Fanghao; Chen, Zhixing; Zhang, Luyuan; Shen, Yihui; Wei, Lu; Min, Wei

2016-03-01

Glucose is consumed as an energy source by virtually all living organisms, from bacteria to humans. Its uptake activity closely reflects the cellular metabolic status in various pathophysiological transformations, such as diabetes and cancer. Extensive efforts such as positron emission tomography, magnetic resonance imaging and fluorescence microscopy have been made to specifically image glucose uptake activity but all with technical limitations. Here, we report a new platform to visualize glucose uptake activity in live cells and tissues with subcellular resolution and minimal perturbation. A novel glucose analogue with a small alkyne tag (carbon-carbon triple bond) is developed to mimic natural glucose for cellular uptake, which can be imaged with high sensitivity and specificity by targeting the strong and characteristic alkyne vibration on stimulated Raman scattering (SRS) microscope to generate a quantitative three dimensional concentration map. Cancer cells with differing metabolic characteristics can be distinguished. Heterogeneous uptake patterns are observed in tumor xenograft tissues, neuronal culture and mouse brain tissues with clear cell-cell variations. Therefore, by offering the distinct advantage of optical resolution but without the undesirable influence of bulky fluorophores, our method of coupling SRS with alkyne labeled glucose will be an attractive tool to study energy demands of living systems at the single cell level.

Hyperspectral range imaging for transportation systems evaluation

NASA Astrophysics Data System (ADS)

Bridgelall, Raj; Rafert, J. B.; Atwood, Don; Tolliver, Denver D.

2016-04-01

Transportation agencies expend significant resources to inspect critical infrastructure such as roadways, railways, and pipelines. Regular inspections identify important defects and generate data to forecast maintenance needs. However, cost and practical limitations prevent the scaling of current inspection methods beyond relatively small portions of the network. Consequently, existing approaches fail to discover many high-risk defect formations. Remote sensing techniques offer the potential for more rapid and extensive non-destructive evaluations of the multimodal transportation infrastructure. However, optical occlusions and limitations in the spatial resolution of typical airborne and space-borne platforms limit their applicability. This research proposes hyperspectral image classification to isolate transportation infrastructure targets for high-resolution photogrammetric analysis. A plenoptic swarm of unmanned aircraft systems will capture images with centimeter-scale spatial resolution, large swaths, and polarization diversity. The light field solution will incorporate structure-from-motion techniques to reconstruct three-dimensional details of the isolated targets from sequences of two-dimensional images. A comparative analysis of existing low-power wireless communications standards suggests an application dependent tradeoff in selecting the best-suited link to coordinate swarming operations. This study further produced a taxonomy of specific roadway and railway defects, distress symptoms, and other anomalies that the proposed plenoptic swarm sensing system would identify and characterize to estimate risk levels.

Battlefield radar imaging through airborne millimetric wave SAR (Synthetic Aperture Radar)

NASA Astrophysics Data System (ADS)

Carletti, U.; Daddio, E.; Farina, A.; Morabito, C.; Pangrazi, R.; Studer, F. A.

Airborne synthetic aperture radar (SAR), operating in the millimetric-wave (mmw) region, is discussed with reference to a battlefield surveillance application. The SAR system provides high resolution real-time imaging of the battlefield and moving target detection, under adverse environmental conditions (e.g., weather, dust, smoke, obscurants). The most relevant and original aspects of the system are the band of operation (i.e., mmw in lieu of the more traditional microwave region) and the use of an unmanned platform. The former implies reduced weight and size requirements, thus allowing use of small unmanned platforms. The latter enchances the system operational effectiveness by permitting accomplishment of recognition missions in depth beyond the FEBA. An overall system architecture based on the onboard sensor, the platform, the communication equipment, and a mobile ground station is described. The main areas of ongoing investigation are presented: the simulation of the end-to-end system, and the critical technological issues such as mmw antenna, transmitter, signal processor for image formation and platform attitude errors compensation and detection and imaging of moving targets.

Advances in single-cell experimental design made possible by automated imaging platforms with feedback through segmentation.

PubMed

Crick, Alex J; Cammarota, Eugenia; Moulang, Katie; Kotar, Jurij; Cicuta, Pietro

2015-01-01

Live optical microscopy has become an essential tool for studying the dynamical behaviors and variability of single cells, and cell-cell interactions. However, experiments and data analysis in this area are often extremely labor intensive, and it has often not been achievable or practical to perform properly standardized experiments on a statistically viable scale. We have addressed this challenge by developing automated live imaging platforms, to help standardize experiments, increasing throughput, and unlocking previously impossible ones. Our real-time cell tracking programs communicate in feedback with microscope and camera control software, and they are highly customizable, flexible, and efficient. As examples of our current research which utilize these automated platforms, we describe two quite different applications: egress-invasion interactions of malaria parasites and red blood cells, and imaging of immune cells which possess high motility and internal dynamics. The automated imaging platforms are able to track a large number of motile cells simultaneously, over hours or even days at a time, greatly increasing data throughput and opening up new experimental possibilities. Copyright © 2015 Elsevier Inc. All rights reserved.

Unified Framework for Development, Deployment and Robust Testing of Neuroimaging Algorithms

PubMed Central

Joshi, Alark; Scheinost, Dustin; Okuda, Hirohito; Belhachemi, Dominique; Murphy, Isabella; Staib, Lawrence H.; Papademetris, Xenophon

2011-01-01

Developing both graphical and command-line user interfaces for neuroimaging algorithms requires considerable effort. Neuroimaging algorithms can meet their potential only if they can be easily and frequently used by their intended users. Deployment of a large suite of such algorithms on multiple platforms requires consistency of user interface controls, consistent results across various platforms and thorough testing. We present the design and implementation of a novel object-oriented framework that allows for rapid development of complex image analysis algorithms with many reusable components and the ability to easily add graphical user interface controls. Our framework also allows for simplified yet robust nightly testing of the algorithms to ensure stability and cross platform interoperability. All of the functionality is encapsulated into a software object requiring no separate source code for user interfaces, testing or deployment. This formulation makes our framework ideal for developing novel, stable and easy-to-use algorithms for medical image analysis and computer assisted interventions. The framework has been both deployed at Yale and released for public use in the open source multi-platform image analysis software—BioImage Suite (bioimagesuite.org). PMID:21249532

A Web platform for the interactive visualization and analysis of the 3D fractal dimension of MRI data.

PubMed

Jiménez, J; López, A M; Cruz, J; Esteban, F J; Navas, J; Villoslada, P; Ruiz de Miras, J

2014-10-01

This study presents a Web platform (http://3dfd.ujaen.es) for computing and analyzing the 3D fractal dimension (3DFD) from volumetric data in an efficient, visual and interactive way. The Web platform is specially designed for working with magnetic resonance images (MRIs) of the brain. The program estimates the 3DFD by calculating the 3D box-counting of the entire volume of the brain, and also of its 3D skeleton. All of this is done in a graphical, fast and optimized way by using novel technologies like CUDA and WebGL. The usefulness of the Web platform presented is demonstrated by its application in a case study where an analysis and characterization of groups of 3D MR images is performed for three neurodegenerative diseases: Multiple Sclerosis, Intrauterine Growth Restriction and Alzheimer's disease. To the best of our knowledge, this is the first Web platform that allows the users to calculate, visualize, analyze and compare the 3DFD from MRI images in the cloud. Copyright © 2014 Elsevier Inc. All rights reserved.

An intelligent monitoring and management system for cross-enterprise biomedical data sharing platform

NASA Astrophysics Data System (ADS)

Wang, Tusheng; Yang, Yuanyuan; Zhang, Jianguo

2013-03-01

In order to enable multiple disciplines of medical researchers, clinical physicians and biomedical engineers working together in a secured, efficient, and transparent cooperative environment, we had designed an e-Science platform for biomedical imaging research and application cross multiple academic institutions and hospitals in Shanghai by using grid-based or cloud-based distributed architecture and presented this work in SPIE Medical Imaging conference held in San Diego in 2012. However, when the platform integrates more and more nodes over different networks, the first challenge is that how to monitor and maintain all the hosts and services operating cross multiple academic institutions and hospitals in the e-Science platform, such as DICOM and Web based image communication services, messaging services and XDS ITI transaction services. In this presentation, we presented a system design and implementation of intelligent monitoring and management which can collect system resource status of every node in real time, alert when node or service failure occurs, and can finally improve the robustness, reliability and service continuity of this e-Science platform.

Geostationary platform systems concepts definition study. Volume 1: Executive summary

NASA Technical Reports Server (NTRS)

1980-01-01

The results of a geostationary platform concept analysis are summarized. Mission and payloads definition, concept selection, the requirements of an experimental platform, supporting research and technology, and the Space Transportation System interface requirements are addressed. It is concluded that platforms represent a logical extension of current trends toward larger, more complex, multifrequency satellites. Geostationary platforms offer significant cost savings compared to individual satellites, with the majority of these economies being realized with single Shuttle launched platforms. Further cost savings can be realized, however, by having larger platforms. Platforms accommodating communications equipment that operates at multiple frequencies and which provide larger scale frequency reuse through the use of large aperture multibeam antennas and onboard switching maximize the useful capacity of the orbital arc and frequency spectrum. Projections of market demand indicate that such conservation measures are clearly essential if orderly growth is to be provided for. In addition, it is pointed out that a NASA experimental platform is required to demonstrate the technologies necessary for operational geostationary platforms of the 1990's.

The Cyborg Astrobiologist: testing a novelty detection algorithm on two mobile exploration systems at Rivas Vaciamadrid in Spain and at the Mars Desert Research Station in Utah

NASA Astrophysics Data System (ADS)

McGuire, P. C.; Gross, C.; Wendt, L.; Bonnici, A.; Souza-Egipsy, V.; Ormö, J.; Díaz-Martínez, E.; Foing, B. H.; Bose, R.; Walter, S.; Oesker, M.; Ontrup, J.; Haschke, R.; Ritter, H.

2010-01-01

In previous work, a platform was developed for testing computer-vision algorithms for robotic planetary exploration. This platform consisted of a digital video camera connected to a wearable computer for real-time processing of images at geological and astrobiological field sites. The real-time processing included image segmentation and the generation of interest points based upon uncommonness in the segmentation maps. Also in previous work, this platform for testing computer-vision algorithms has been ported to a more ergonomic alternative platform, consisting of a phone camera connected via the Global System for Mobile Communications (GSM) network to a remote-server computer. The wearable-computer platform has been tested at geological and astrobiological field sites in Spain (Rivas Vaciamadrid and Riba de Santiuste), and the phone camera has been tested at a geological field site in Malta. In this work, we (i) apply a Hopfield neural-network algorithm for novelty detection based upon colour, (ii) integrate a field-capable digital microscope on the wearable computer platform, (iii) test this novelty detection with the digital microscope at Rivas Vaciamadrid, (iv) develop a Bluetooth communication mode for the phone-camera platform, in order to allow access to a mobile processing computer at the field sites, and (v) test the novelty detection on the Bluetooth-enabled phone camera connected to a netbook computer at the Mars Desert Research Station in Utah. This systems engineering and field testing have together allowed us to develop a real-time computer-vision system that is capable, for example, of identifying lichens as novel within a series of images acquired in semi-arid desert environments. We acquired sequences of images of geologic outcrops in Utah and Spain consisting of various rock types and colours to test this algorithm. The algorithm robustly recognized previously observed units by their colour, while requiring only a single image or a few images to learn colours as familiar, demonstrating its fast learning capability.

Wound healing revised: A novel reepithelialization mechanism revealed by in vitro and in silico models

PubMed Central

Safferling, Kai; Sütterlin, Thomas; Westphal, Kathi; Ernst, Claudia; Breuhahn, Kai; James, Merlin; Jäger, Dirk; Halama, Niels

2013-01-01

Wound healing is a complex process in which a tissue’s individual cells have to be orchestrated in an efficient and robust way. We integrated multiplex protein analysis, immunohistochemical analysis, and whole-slide imaging into a novel medium-throughput platform for quantitatively capturing proliferation, differentiation, and migration in large numbers of organotypic skin cultures comprising epidermis and dermis. Using fluorescent time-lag staining, we were able to infer source and final destination of keratinocytes in the healing epidermis. This resulted in a novel extending shield reepithelialization mechanism, which we confirmed by computational multicellular modeling and perturbation of tongue extension. This work provides a consistent experimental and theoretical model for epidermal wound closure in 3D, negating the previously proposed concepts of epidermal tongue extension and highlighting the so far underestimated role of the surrounding tissue. Based on our findings, epidermal wound closure is a process in which cell behavior is orchestrated by a higher level of tissue control that 2D monolayer assays are not able to capture. PMID:24385489

Digital imaging of root traits (DIRT): a high-throughput computing and collaboration platform for field-based root phenomics.

PubMed

Das, Abhiram; Schneider, Hannah; Burridge, James; Ascanio, Ana Karine Martinez; Wojciechowski, Tobias; Topp, Christopher N; Lynch, Jonathan P; Weitz, Joshua S; Bucksch, Alexander

2015-01-01

Plant root systems are key drivers of plant function and yield. They are also under-explored targets to meet global food and energy demands. Many new technologies have been developed to characterize crop root system architecture (CRSA). These technologies have the potential to accelerate the progress in understanding the genetic control and environmental response of CRSA. Putting this potential into practice requires new methods and algorithms to analyze CRSA in digital images. Most prior approaches have solely focused on the estimation of root traits from images, yet no integrated platform exists that allows easy and intuitive access to trait extraction and analysis methods from images combined with storage solutions linked to metadata. Automated high-throughput phenotyping methods are increasingly used in laboratory-based efforts to link plant genotype with phenotype, whereas similar field-based studies remain predominantly manual low-throughput. Here, we present an open-source phenomics platform "DIRT", as a means to integrate scalable supercomputing architectures into field experiments and analysis pipelines. DIRT is an online platform that enables researchers to store images of plant roots, measure dicot and monocot root traits under field conditions, and share data and results within collaborative teams and the broader community. The DIRT platform seamlessly connects end-users with large-scale compute "commons" enabling the estimation and analysis of root phenotypes from field experiments of unprecedented size. DIRT is an automated high-throughput computing and collaboration platform for field based crop root phenomics. The platform is accessible at http://www.dirt.iplantcollaborative.org/ and hosted on the iPlant cyber-infrastructure using high-throughput grid computing resources of the Texas Advanced Computing Center (TACC). DIRT is a high volume central depository and high-throughput RSA trait computation platform for plant scientists working on crop roots. It enables scientists to store, manage and share crop root images with metadata and compute RSA traits from thousands of images in parallel. It makes high-throughput RSA trait computation available to the community with just a few button clicks. As such it enables plant scientists to spend more time on science rather than on technology. All stored and computed data is easily accessible to the public and broader scientific community. We hope that easy data accessibility will attract new tool developers and spur creative data usage that may even be applied to other fields of science.

Automatic Extraction of JPF Options and Documentation

NASA Technical Reports Server (NTRS)

Luks, Wojciech; Tkachuk, Oksana; Buschnell, David

2011-01-01

Documenting existing Java PathFinder (JPF) projects or developing new extensions is a challenging task. JPF provides a platform for creating new extensions and relies on key-value properties for their configuration. Keeping track of all possible options and extension mechanisms in JPF can be difficult. This paper presents jpf-autodoc-options, a tool that automatically extracts JPF projects options and other documentation-related information, which can greatly help both JPF users and developers of JPF extensions.

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.

Towards Portable Large-Scale Image Processing with High-Performance Computing.

PubMed

Huo, Yuankai; Blaber, Justin; Damon, Stephen M; Boyd, Brian D; Bao, Shunxing; Parvathaneni, Prasanna; Noguera, Camilo Bermudez; Chaganti, Shikha; Nath, Vishwesh; Greer, Jasmine M; Lyu, Ilwoo; French, William R; Newton, Allen T; Rogers, Baxter P; Landman, Bennett A

2018-05-03

High-throughput, large-scale medical image computing demands tight integration of high-performance computing (HPC) infrastructure for data storage, job distribution, and image processing. The Vanderbilt University Institute for Imaging Science (VUIIS) Center for Computational Imaging (CCI) has constructed a large-scale image storage and processing infrastructure that is composed of (1) a large-scale image database using the eXtensible Neuroimaging Archive Toolkit (XNAT), (2) a content-aware job scheduling platform using the Distributed Automation for XNAT pipeline automation tool (DAX), and (3) a wide variety of encapsulated image processing pipelines called "spiders." The VUIIS CCI medical image data storage and processing infrastructure have housed and processed nearly half-million medical image volumes with Vanderbilt Advanced Computing Center for Research and Education (ACCRE), which is the HPC facility at the Vanderbilt University. The initial deployment was natively deployed (i.e., direct installations on a bare-metal server) within the ACCRE hardware and software environments, which lead to issues of portability and sustainability. First, it could be laborious to deploy the entire VUIIS CCI medical image data storage and processing infrastructure to another HPC center with varying hardware infrastructure, library availability, and software permission policies. Second, the spiders were not developed in an isolated manner, which has led to software dependency issues during system upgrades or remote software installation. To address such issues, herein, we describe recent innovations using containerization techniques with XNAT/DAX which are used to isolate the VUIIS CCI medical image data storage and processing infrastructure from the underlying hardware and software environments. The newly presented XNAT/DAX solution has the following new features: (1) multi-level portability from system level to the application level, (2) flexible and dynamic software development and expansion, and (3) scalable spider deployment compatible with HPC clusters and local workstations.

Lensfree fluorescent on-chip imaging of transgenic Caenorhabditis elegans over an ultra-wide field-of-view.

PubMed

Coskun, Ahmet F; Sencan, Ikbal; Su, Ting-Wei; Ozcan, Aydogan

2011-01-06

We demonstrate lensfree on-chip fluorescent imaging of transgenic Caenorhabditis elegans (C. elegans) over an ultra-wide field-of-view (FOV) of e.g., >2-8 cm(2) with a spatial resolution of ∼10 µm. This is the first time that a lensfree on-chip platform has successfully imaged fluorescent C. elegans samples. In our wide-field lensfree imaging platform, the transgenic samples are excited using a prism interface from the side, where the pump light is rejected through total internal reflection occurring at the bottom facet of the substrate. The emitted fluorescent signal from C. elegans samples is then recorded on a large area opto-electronic sensor-array over an FOV of e.g., >2-8 cm(2), without the use of any lenses, thin-film interference filters or mechanical scanners. Because fluorescent emission rapidly diverges, such lensfree fluorescent images recorded on a chip look blurred due to broad point-spread-function of our platform. To combat this resolution challenge, we use a compressive sampling algorithm to uniquely decode the recorded lensfree fluorescent patterns into higher resolution images, demonstrating ∼10 µm resolution. We tested the efficacy of this compressive decoding approach with different types of opto-electronic sensors to achieve a similar resolution level, independent of the imaging chip. We further demonstrate that this wide FOV lensfree fluorescent imaging platform can also perform sequential bright-field imaging of the same samples using partially-coherent lensfree digital in-line holography that is coupled from the top facet of the same prism used in fluorescent excitation. This unique combination permits ultra-wide field dual-mode imaging of C. elegans on a chip which could especially provide a useful tool for high-throughput screening applications in biomedical research.

Lensfree Fluorescent On-Chip Imaging of Transgenic Caenorhabditis elegans Over an Ultra-Wide Field-of-View

PubMed Central

Ozcan, Aydogan

2011-01-01

We demonstrate lensfree on-chip fluorescent imaging of transgenic Caenorhabditis elegans (C. elegans) over an ultra-wide field-of-view (FOV) of e.g., >2–8 cm2 with a spatial resolution of ∼10µm. This is the first time that a lensfree on-chip platform has successfully imaged fluorescent C. elegans samples. In our wide-field lensfree imaging platform, the transgenic samples are excited using a prism interface from the side, where the pump light is rejected through total internal reflection occurring at the bottom facet of the substrate. The emitted fluorescent signal from C. elegans samples is then recorded on a large area opto-electronic sensor-array over an FOV of e.g., >2–8 cm2, without the use of any lenses, thin-film interference filters or mechanical scanners. Because fluorescent emission rapidly diverges, such lensfree fluorescent images recorded on a chip look blurred due to broad point-spread-function of our platform. To combat this resolution challenge, we use a compressive sampling algorithm to uniquely decode the recorded lensfree fluorescent patterns into higher resolution images, demonstrating ∼10 µm resolution. We tested the efficacy of this compressive decoding approach with different types of opto-electronic sensors to achieve a similar resolution level, independent of the imaging chip. We further demonstrate that this wide FOV lensfree fluorescent imaging platform can also perform sequential bright-field imaging of the same samples using partially-coherent lensfree digital in-line holography that is coupled from the top facet of the same prism used in fluorescent excitation. This unique combination permits ultra-wide field dual-mode imaging of C. elegans on a chip which could especially provide a useful tool for high-throughput screening applications in biomedical research. PMID:21253611

Extensions of algebraic image operators: An approach to model-based vision

NASA Technical Reports Server (NTRS)

Lerner, Bao-Ting; Morelli, Michael V.

1990-01-01

Researchers extend their previous research on a highly structured and compact algebraic representation of grey-level images which can be viewed as fuzzy sets. Addition and multiplication are defined for the set of all grey-level images, which can then be described as polynomials of two variables. Utilizing this new algebraic structure, researchers devised an innovative, efficient edge detection scheme. An accurate method for deriving gradient component information from this edge detector is presented. Based upon this new edge detection system researchers developed a robust method for linear feature extraction by combining the techniques of a Hough transform and a line follower. The major advantage of this feature extractor is its general, object-independent nature. Target attributes, such as line segment lengths, intersections, angles of intersection, and endpoints are derived by the feature extraction algorithm and employed during model matching. The algebraic operators are global operations which are easily reconfigured to operate on any size or shape region. This provides a natural platform from which to pursue dynamic scene analysis. A method for optimizing the linear feature extractor which capitalizes on the spatially reconfiguration nature of the edge detector/gradient component operator is discussed.

The Insight ToolKit image registration framework

PubMed Central

Avants, Brian B.; Tustison, Nicholas J.; Stauffer, Michael; Song, Gang; Wu, Baohua; Gee, James C.

2014-01-01

Publicly available scientific resources help establish evaluation standards, provide a platform for teaching and improve reproducibility. Version 4 of the Insight ToolKit (ITK4) seeks to establish new standards in publicly available image registration methodology. ITK4 makes several advances in comparison to previous versions of ITK. ITK4 supports both multivariate images and objective functions; it also unifies high-dimensional (deformation field) and low-dimensional (affine) transformations with metrics that are reusable across transform types and with composite transforms that allow arbitrary series of geometric mappings to be chained together seamlessly. Metrics and optimizers take advantage of multi-core resources, when available. Furthermore, ITK4 reduces the parameter optimization burden via principled heuristics that automatically set scaling across disparate parameter types (rotations vs. translations). A related approach also constrains steps sizes for gradient-based optimizers. The result is that tuning for different metrics and/or image pairs is rarely necessary allowing the researcher to more easily focus on design/comparison of registration strategies. In total, the ITK4 contribution is intended as a structure to support reproducible research practices, will provide a more extensive foundation against which to evaluate new work in image registration and also enable application level programmers a broad suite of tools on which to build. Finally, we contextualize this work with a reference registration evaluation study with application to pediatric brain labeling.1 PMID:24817849

SMART-OLEV—An orbital life extension vehicle for servicing commercial spacecrafts in GEO

NASA Astrophysics Data System (ADS)

Kaiser, Clemens; Sjöberg, Fredrik; Delcura, Juan Manuel; Eilertsen, Baard

2008-07-01

Orbital Satellite Services Limited (OSSL) is a satellite servicing company that is developing an orbit life extension vehicle (OLEV) to extend the operational lifetime of geostationary satellites. The industrial consortium of SSC (Sweden), Kayser-Threde (Germany) and Sener (Spain) is in charge to develop and industrialize the space and ground segment. It is a fully commercial program with support of several space agencies during the development phase. The business plan is based on life extension for high value commercial satellites while also providing the satellite operators with various fleet management services such as graveyard burns, slot transfers and on orbit protection against replacement satellite or launch failures. The OLEV spacecraft will be able to dock with a geostationary satellite and uses an electrical propulsion system to extend its life by taking over the attitude control and station keeping functions. The OLEV system is building on the SMART-1 platform developed by Swedish Space Corporation. It was developed for ESA as a technology test-bed to demonstrate the use of electrical propulsion for interplanetary orbit transfer manoeuvres. The concept is called SMART-OLEV and takes advantage of the low cost, low mass SMART-1 platform by a maximum use of recurrent platform technology.

Monitoring Forest Regrowth Using a Multi-Platform Time Series

NASA Technical Reports Server (NTRS)

Sabol, Donald E., Jr.; Smith, Milton O.; Adams, John B.; Gillespie, Alan R.; Tucker, Compton J.

1996-01-01

Over the past 50 years, the forests of western Washington and Oregon have been extensively harvested for timber. This has resulted in a heterogeneous mosaic of remaining mature forests, clear-cuts, new plantations, and second-growth stands that now occur in areas that formerly were dominated by extensive old-growth forests and younger forests resulting from fire disturbance. Traditionally, determination of seral stage and stand condition have been made using aerial photography and spot field observations, a methodology that is not only time- and resource-intensive, but falls short of providing current information on a regional scale. These limitations may be solved, in part, through the use of multispectral images which can cover large areas at spatial resolutions in the order of tens of meters. The use of multiple images comprising a time series potentially can be used to monitor land use (e.g. cutting and replanting), and to observe natural processes such as regeneration, maturation and phenologic change. These processes are more likely to be spectrally observed in a time series composed of images taken during different seasons over a long period of time. Therefore, for many areas, it may be necessary to use a variety of images taken with different imaging systems. A common framework for interpretation is needed that reduces topographic, atmospheric, instrumental, effects as well as differences in lighting geometry between images. The present state of remote-sensing technology in general use does not realize the full potential of the multispectral data in areas of high topographic relief. For example, the primary method for analyzing images of forested landscapes in the Northwest has been with statistical classifiers (e.g. parallelepiped, nearest-neighbor, maximum likelihood, etc.), often applied to uncalibrated multispectral data. Although this approach has produced useful information from individual images in some areas, landcover classes defined by these techniques typically are not consistent for the same scene imaged under different illumination conditions, especially in the mountainous regions. In addition, it is difficult to correct for atmospheric and instrumental differences between multiple scenes in a time series. In this paper, we present an approach for monitoring forest cutting/regrowth in a semi-mountainous portion of the southern Gifford Pinchot National Forest using a multisensor-time series composed of MSS, TM, and AVIRIS images.

Research and Development of Target Recognition and Location Crawling Platform based on Binocular Vision

NASA Astrophysics Data System (ADS)

Xu, Weidong; Lei, Zhu; Yuan, Zhang; Gao, Zhenqing

2018-03-01

The application of visual recognition technology in industrial robot crawling and placing operation is one of the key tasks in the field of robot research. In order to improve the efficiency and intelligence of the material sorting in the production line, especially to realize the sorting of the scattered items, the robot target recognition and positioning crawling platform based on binocular vision is researched and developed. The images were collected by binocular camera, and the images were pretreated. Harris operator was used to identify the corners of the images. The Canny operator was used to identify the images. Hough-chain code recognition was used to identify the images. The target image in the image, obtain the coordinates of each vertex of the image, calculate the spatial position and posture of the target item, and determine the information needed to capture the movement and transmit it to the robot control crawling operation. Finally, In this paper, we use this method to experiment the wrapping problem in the express sorting process The experimental results show that the platform can effectively solve the problem of sorting of loose parts, so as to achieve the purpose of efficient and intelligent sorting.

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.

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.

Collegial Activity Learning between Heterogeneous Sensors.

PubMed

Feuz, Kyle D; Cook, Diane J

2017-11-01

Activity recognition algorithms have matured and become more ubiquitous in recent years. However, these algorithms are typically customized for a particular sensor platform. In this paper we introduce PECO, a Personalized activity ECOsystem, that transfers learned activity information seamlessly between sensor platforms in real time so that any available sensor can continue to track activities without requiring its own extensive labeled training data. We introduce a multi-view transfer learning algorithm that facilitates this information handoff between sensor platforms and provide theoretical performance bounds for the algorithm. In addition, we empirically evaluate PECO using datasets that utilize heterogeneous sensor platforms to perform activity recognition. These results indicate that not only can activity recognition algorithms transfer important information to new sensor platforms, but any number of platforms can work together as colleagues to boost performance.

Limited rotation of the mobile-bearing in a rotating platform total knee prosthesis.

PubMed

Garling, E H; Kaptein, B L; Nelissen, R G H H; Valstar, E R

2007-01-01

The hypothesis of this study was that the polyethylene bearing in a rotating platform total knee prosthesis shows axial rotation during a step-up motion, thereby facilitating the theoretical advantages of mobile-bearing knee prostheses. We examined 10 patients with rheumatoid arthritis who had a rotating platform total knee arthroplasty (NexGen LPS mobile, Zimmer Inc. Warsaw, USA). Fluoroscopic data was collected during a step-up motion six months postoperatively. A 3D-2D model fitting technique was used to reconstruct the in vivo 3D kinematics. The femoral component showed more axial rotation than the polyethylene mobile-bearing insert compared to the tibia during extension. In eight knees, the femoral component rotated internally with respect to the tibia during extension. In the other two knees the femoral component rotated externally with respect to the tibia. In all 10 patients, the femur showed more axial rotation than the mobile-bearing insert indicating the femoral component was sliding on the polyethylene of the rotating platform during the step-up motion. Possible explanations are a too limited conformity between femoral component and insert, the anterior located pivot location of the investigated rotating platform design, polyethylene on metal impingement and fibrous tissue formation between the mobile-bearing insert and the tibial plateau.

ASCANS Class of 2013 Tour the O&C with Cabana

NASA Image and Video Library

2014-03-03

CAPE CANAVERAL, Fla. -- In the Operations and Checkout Building of NASA's Kennedy Space Center in Florida, astronaut candidate Andrew Morgan looks over work platforms to gain a look at the Orion spacecraft being prepared for Exploration Flight Test EFT-1. Plans call for the Lockheed Martin-built Orion to launch atop a United Launch Alliance Delta IV Heavy rocket from Cape Canaveral Air Force Station. The astronaut class of 2013 was selected by NASA after an extensive year-and-a-half search. The new group will help the agency push the boundaries of exploration and travel to new destinations in the solar system. To learn more about the astronaut class of 2013, visit: http://www.nasa.gov/astronauts/2013astroclass.html Photo credit: NASA/Kim Shiflett Selected image has been cropped

C-SPECT - a Clinical Cardiac SPECT/Tct Platform: Design Concepts and Performance Potential

PubMed Central

Chang, Wei; Ordonez, Caesar E.; Liang, Haoning; Li, Yusheng; Liu, Jingai

2013-01-01

Because of scarcity of photons emitted from the heart, clinical cardiac SPECT imaging is mainly limited by photon statistics. The sub-optimal detection efficiency of current SPECT systems not only limits the quality of clinical cardiac SPECT imaging but also makes more advanced potential applications difficult to be realized. We propose a high-performance system platform - C-SPECT, which has its sampling geometry optimized for detection of emitted photons in quality and quantity. The C-SPECT has a stationary C-shaped gantry that surrounds the left-front side of a patient’s thorax. The stationary C-shaped collimator and detector systems in the gantry provide effective and efficient detection and sampling of photon emission. For cardiac imaging, the C-SPECT platform could achieve 2 to 4 times the system geometric efficiency of conventional SPECT systems at the same sampling resolution. This platform also includes an integrated transmission CT for attenuation correction. The ability of C-SPECT systems to perform sequential high-quality emission and transmission imaging could bring cost-effective high-performance to clinical imaging. In addition, a C-SPECT system could provide high detection efficiency to accommodate fast acquisition rate for gated and dynamic cardiac imaging. This paper describes the design concepts and performance potential of C-SPECT, and illustrates how these concepts can be implemented in a basic system. PMID:23885129

openECA Platform and Analytics Alpha Test Results

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

Robertson, Russell

The objective of the Open and Extensible Control and Analytics (openECA) Platform for Phasor Data project is to develop an open source software platform that significantly accelerates the production, use, and ongoing development of real-time decision support tools, automated control systems, and off-line planning systems that (1) incorporate high-fidelity synchrophasor data and (2) enhance system reliability while enabling the North American Electric Reliability Corporation (NERC) operating functions of reliability coordinator, transmission operator, and/or balancing authority to be executed more effectively.

openECA Platform and Analytics Beta Demonstration Results

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

Robertson, Russell

The objective of the Open and Extensible Control and Analytics (openECA) Platform for Phasor Data project is to develop an open source software platform that significantly accelerates the production, use, and ongoing development of real-time decision support tools, automated control systems, and off-line planning systems that (1) incorporate high-fidelity synchrophasor data and (2) enhance system reliability while enabling the North American Electric Reliability Corporation (NERC) operating functions of reliability coordinator, transmission operator, and/or balancing authority to be executed more effectively.

Fluorescent Imaging of Single Nanoparticles and Viruses on a Smart Phone

PubMed Central

Wei, Qingshan; Qi, Hangfei; Luo, Wei; Tseng, Derek; Ki, So Jung; Wan, Zhe; Göröcs, Zoltán; Bentolila, Laurent A.; Wu, Ting-Ting; Sun, Ren; Ozcan, Aydogan

2014-01-01

Optical imaging of nanoscale objects, whether it is based on scattering or fluorescence, is a challenging task due to reduced detection signal-to-noise ratio and contrast at subwavelength dimensions. Here, we report a field-portable fluorescence microscopy platform installed on a smart phone for imaging of individual nanoparticles as well as viruses using a lightweight and compact opto-mechanical attachment to the existing camera module of the cell phone. This hand-held fluorescent imaging device utilizes (i) a compact 450 nm laser diode that creates oblique excitation on the sample plane with an incidence angle of ~75°, (ii) a long-pass thin-film interference filter to reject the scattered excitation light, (iii) an external lens creating 2× optical magnification, and (iv) a translation stage for focus adjustment. We tested the imaging performance of this smart-phone-enabled microscopy platform by detecting isolated 100 nm fluorescent particles as well as individual human cytomegaloviruses that are fluorescently labeled. The size of each detected nano-object on the cell phone platform was validated using scanning electron microscopy images of the same samples. This field-portable fluorescence microscopy attachment to the cell phone, weighing only ~186 g, could be used for specific and sensitive imaging of subwavelength objects including various bacteria and viruses and, therefore, could provide a valuable platform for the practice of nanotechnology in field settings and for conducting viral load measurements and other biomedical tests even in remote and resource-limited environments. PMID:24016065

A Novel System for Correction of Relative Angular Displacement between Airborne Platform and UAV in Target Localization

PubMed Central

Liu, Chenglong; Liu, Jinghong; Song, Yueming; Liang, Huaidan

2017-01-01

This paper provides a system and method for correction of relative angular displacements between an Unmanned Aerial Vehicle (UAV) and its onboard strap-down photoelectric platform to improve localization accuracy. Because the angular displacements have an influence on the final accuracy, by attaching a measuring system to the platform, the texture image of platform base bulkhead can be collected in a real-time manner. Through the image registration, the displacement vector of the platform relative to its bulkhead can be calculated to further determine angular displacements. After being decomposed and superposed on the three attitude angles of the UAV, the angular displacements can reduce the coordinate transformation errors and thus improve the localization accuracy. Even a simple kind of method can improve the localization accuracy by 14.3%. PMID:28273845

A Novel System for Correction of Relative Angular Displacement between Airborne Platform and UAV in Target Localization.

PubMed

Liu, Chenglong; Liu, Jinghong; Song, Yueming; Liang, Huaidan

2017-03-04

This paper provides a system and method for correction of relative angular displacements between an Unmanned Aerial Vehicle (UAV) and its onboard strap-down photoelectric platform to improve localization accuracy. Because the angular displacements have an influence on the final accuracy, by attaching a measuring system to the platform, the texture image of platform base bulkhead can be collected in a real-time manner. Through the image registration, the displacement vector of the platform relative to its bulkhead can be calculated to further determine angular displacements. After being decomposed and superposed on the three attitude angles of the UAV, the angular displacements can reduce the coordinate transformation errors and thus improve the localization accuracy. Even a simple kind of method can improve the localization accuracy by 14.3%.

Newspaper Coverage of the 1992 Presidential Campaign: A Content Analysis of Character/Competence/Image Issues versus Platform/Political Issues.

ERIC Educational Resources Information Center

Sims, Judy R.; Giordano, Joseph

A research study assessed the amount of front page newspaper coverage allotted to "character/competence/image" issues versus "platform/political" issues in the 1992 presidential campaign. Using textual analysis, methodology of content analysis, researchers coded the front page of the following 5 newspapers between August 1 and…

High throughput field plant phenotyping facility at University of Nebraska-Lincoln and the first year experience

NASA Astrophysics Data System (ADS)

Ge, Y.; Bai, G.; Irmak, S.; Awada, T.; Stoerger, V.; Graef, G.; Scoby, D.; Schnable, J.

2017-12-01

University of Nebraska - Lincoln's high throughput field plant phenotyping facility is a cable robot based system built on a 1-ac field. The sensor platform is tethered with eight cables via four poles at the corners of the field for its precise control and positioning. The sensor modules on the platform include a 4-band RGB-NIR camera, a thermal infrared camera, a 3D LiDAR, VNIR spectrometers, and environmental sensors. These sensors are used to collect multifaceted physiological, structural and chemical properties of plants from the field plots. A subsurface drip irrigation system is established in this field which allows a controlled amount of water and fertilizers to be delivered to individual plots. An extensive soil moisture sensor network is also established to monitor soil water status, and serve as a feedback loop for irrigation scheduling. In the first year of operation, the field is planted maize and soybean. Weekly ground truth data were collected from the plots to validate image and sensor data from the phenotyping system. This presentation will provide an overview of this state-of-the-art field plant phenotyping facility, and present preliminary data from the first year operation of the system.

Big capabilities in small packages: hyperspectral imaging from a compact platform

NASA Astrophysics Data System (ADS)

Beasley, Matthew; Goldberg, Hannah; Voorhees, Christopher; Illsley, Peter

2016-09-01

We present the Compact Holographic Aberration-corrected Platform (CHAP) instrument, designed and developed at Planetary Resources Development Corporation. By combining a dispersive element with the secondary of a telescope, we are able to produce a relatively long focal length with moderate dispersion at the focal plane. This design enables us to build a capable hyperspectral imaging instrument within the size constraints of the Cubesat form-factor. The advantages of our design revolves around its simplicity: there are only two optical elements, producing both a white light and diffracted image. With the use of a replicated grating, we can produce a long focal length hyperspectral imager at a price point far below other spaceflight instruments. The design is scalable for larger platforms and since it has no transmitting optics and only two reflective surfaces could be designed to function at any desired wavelength. Our system will be capable of spectral imaging across the 400 to 900 nm spectral range for use in small body surveys.

ART-ML: a new markup language for modelling and representation of biological processes in cardiovascular diseases.

PubMed

Karvounis, E C; Exarchos, T P; Fotiou, E; Sakellarios, A I; Iliopoulou, D; Koutsouris, D; Fotiadis, D I

2013-01-01

With an ever increasing number of biological models available on the internet, a standardized modelling framework is required to allow information to be accessed and visualized. In this paper we propose a novel Extensible Markup Language (XML) based format called ART-ML that aims at supporting the interoperability and the reuse of models of geometry, blood flow, plaque progression and stent modelling, exported by any cardiovascular disease modelling software. ART-ML has been developed and tested using ARTool. ARTool is a platform for the automatic processing of various image modalities of coronary and carotid arteries. The images and their content are fused to develop morphological models of the arteries in 3D representations. All the above described procedures integrate disparate data formats, protocols and tools. ART-ML proposes a representation way, expanding ARTool, for interpretability of the individual resources, creating a standard unified model for the description of data and, consequently, a format for their exchange and representation that is machine independent. More specifically, ARTool platform incorporates efficient algorithms which are able to perform blood flow simulations and atherosclerotic plaque evolution modelling. Integration of data layers between different modules within ARTool are based upon the interchange of information included in the ART-ML model repository. ART-ML provides a markup representation that enables the representation and management of embedded models within the cardiovascular disease modelling platform, the storage and interchange of well-defined information. The corresponding ART-ML model incorporates all relevant information regarding geometry, blood flow, plaque progression and stent modelling procedures. All created models are stored in a model repository database which is accessible to the research community using efficient web interfaces, enabling the interoperability of any cardiovascular disease modelling software models. ART-ML can be used as a reference ML model in multiscale simulations of plaque formation and progression, incorporating all scales of the biological processes.

Home dialysis and the Internet: designing an e-learning platform via brainstorming sessions.

PubMed

Piccoli, Giorgina Barbara; Ferraresi, Martina; Murciano, Antonio; Pereno, Amina; Consiglio, Valentina; Scognamiglio, Stefania; Deagostini, Maria Chiara; Randone, Olga; Digiorgio, Gerardo; Calderale, Mario Pasquale

2012-01-01

The resurgence of home hemodialysis (HHD) underlines the importance of educational programs. Brainstorming is a powerful tool for innovation, widely employed in industry but seldom used in medicine. The aim of this study was to define an e-learning Web platform for HHD patients via a brainstorming approach. Four brainstorming sessions were held 2-6 weeks apart. Twelve people were involved: 2 dialysis physicians, 2 nurses, 2 HHD patients, 2 caregivers, a filmmaker, 2 computer experts (1 with a psychology degree) and a senior engineer. Each session was summarized as the starting point for the following one. The topics discussed were the platform structure and its logo. For the platform, the following requirements were defined: teaching should be extensive and tailored to different levels of knowledge; all available teaching tools (tutorials, demonstrations, recorded and written materials) should be used; films enhance emotional participation and can be used to reduce fears; the contents should include general information on chronic kidney disease, details of all types of renal replacement therapy (RRT) (how and why), dialysis accidents, blood and imaging tests, laws and reimbursements, direct experiences and history of RRT. Remote monitoring and visual interactions are important for reassurance about HHD and should be provided. The requirements for the logo were that it be innovative, related to daily life, representative of a holistic approach and convey happiness. The logo "Hom-e-hem" was created, playing on the assonance between the religious term Om and the word home, with the e of electronic linking it with hem, short for hemodialysis. Brainstorming sessions can be used to design patient-tailored educational interventions. The key message, "self-care is a bridge from illness back to life," may apply to a wider context.

HipMatch: an object-oriented cross-platform program for accurate determination of cup orientation using 2D-3D registration of single standard X-ray radiograph and a CT volume.

PubMed

Zheng, Guoyan; Zhang, Xuan; Steppacher, Simon D; Murphy, Stephen B; Siebenrock, Klaus A; Tannast, Moritz

2009-09-01

The widely used procedure of evaluation of cup orientation following total hip arthroplasty using single standard anteroposterior (AP) radiograph is known inaccurate, largely due to the wide variability in individual pelvic orientation relative to X-ray plate. 2D-3D image registration methods have been introduced for an accurate determination of the post-operative cup alignment with respect to an anatomical reference extracted from the CT data. Although encouraging results have been reported, their extensive usage in clinical routine is still limited. This may be explained by their requirement of a CAD model of the prosthesis, which is often difficult to be organized from the manufacturer due to the proprietary issue, and by their requirement of either multiple radiographs or a radiograph-specific calibration, both of which are not available for most retrospective studies. To address these issues, we developed and validated an object-oriented cross-platform program called "HipMatch" where a hybrid 2D-3D registration scheme combining an iterative landmark-to-ray registration with a 2D-3D intensity-based registration was implemented to estimate a rigid transformation between a pre-operative CT volume and the post-operative X-ray radiograph for a precise estimation of cup alignment. No CAD model of the prosthesis is required. Quantitative and qualitative results evaluated on cadaveric and clinical datasets are given, which indicate the robustness and the accuracy of the program. HipMatch is written in object-oriented programming language C++ using cross-platform software Qt (TrollTech, Oslo, Norway), VTK, and Coin3D and is transportable to any platform.

GGEMS-Brachy: GPU GEant4-based Monte Carlo simulation for brachytherapy applications

NASA Astrophysics Data System (ADS)

Lemaréchal, Yannick; Bert, Julien; Falconnet, Claire; Després, Philippe; Valeri, Antoine; Schick, Ulrike; Pradier, Olivier; Garcia, Marie-Paule; Boussion, Nicolas; Visvikis, Dimitris

2015-07-01

In brachytherapy, plans are routinely calculated using the AAPM TG43 formalism which considers the patient as a simple water object. An accurate modeling of the physical processes considering patient heterogeneity using Monte Carlo simulation (MCS) methods is currently too time-consuming and computationally demanding to be routinely used. In this work we implemented and evaluated an accurate and fast MCS on Graphics Processing Units (GPU) for brachytherapy low dose rate (LDR) applications. A previously proposed Geant4 based MCS framework implemented on GPU (GGEMS) was extended to include a hybrid GPU navigator, allowing navigation within voxelized patient specific images and analytically modeled 125I seeds used in LDR brachytherapy. In addition, dose scoring based on track length estimator including uncertainty calculations was incorporated. The implemented GGEMS-brachy platform was validated using a comparison with Geant4 simulations and reference datasets. Finally, a comparative dosimetry study based on the current clinical standard (TG43) and the proposed platform was performed on twelve prostate cancer patients undergoing LDR brachytherapy. Considering patient 3D CT volumes of 400  × 250  × 65 voxels and an average of 58 implanted seeds, the mean patient dosimetry study run time for a 2% dose uncertainty was 9.35 s (≈500 ms 10-6 simulated particles) and 2.5 s when using one and four GPUs, respectively. The performance of the proposed GGEMS-brachy platform allows envisaging the use of Monte Carlo simulation based dosimetry studies in brachytherapy compatible with clinical practice. Although the proposed platform was evaluated for prostate cancer, it is equally applicable to other LDR brachytherapy clinical applications. Future extensions will allow its application in high dose rate brachytherapy applications.

Synthesis and Characterization of Functional Nanofilm-Coated Live Immune Cells.

PubMed

Hwang, Jangsun; Choi, Daheui; Choi, Moonhyun; Seo, Youngmin; Son, Jaewoo; Hong, Jinkee; Choi, Jonghoon

2018-05-30

Layer-by-layer (LbL) assembly techniques have been extensively studied in cell biology because of their simplicity of preparation and versatility. The applications of the LbL platform technology using polysaccharides, silicon, and graphene have been investigated. However, the applications of the above-mentioned technology using living cells remain to be fully understood. This study demonstrates a living cell-based LbL platform using various types of living cells. In addition, it confirms that the surplus charge on the outer surface of the coated cells can be used to bind the target protein. We develop a living cell-based LbL platform technology by stacking layers of hyaluronic acid (HA) and poly-l-lysine (PLL). The HA/PLL stacking results in three bilayers with a thickness of 4 ± 1 nm on the cell surface. Furthermore, the multilayer nanofilms on the cells are completely degraded after 3 days of the application of the LbL method. We also evaluate and visualize three bilayers of the nanofilm on adherent (AML-12 cells)-, nonadherent (trypsin-treated AML-12 cells)-, and circulation type [peripheral blood mononuclear cells (PBMCs)] cells by analyzing the zeta potential, cell viability, and imaging via scanning electron microscopy and confocal microscopy. Finally, we study the cytotoxicity of the nanofilm and characteristic functions of the immune cells after the nanofilm coating. The multilayer nanofilms are not acutely cytotoxic and did not inhibit the immune response of the PBMCs against stimulant. We conclude that a two bilayer nanofilm would be ideal for further study in any cell type. The living cell-based LbL platform is expected to be useful for a variety of applications in cell biology.

Inspection of Pole-Like Structures Using a Visual-Inertial Aided VTOL Platform with Shared Autonomy

PubMed Central

Sa, Inkyu; Hrabar, Stefan; Corke, Peter

2015-01-01

This paper presents an algorithm and a system for vertical infrastructure inspection using a vertical take-off and landing (VTOL) unmanned aerial vehicle and shared autonomy. Inspecting vertical structures such as light and power distribution poles is a difficult task that is time-consuming, dangerous and expensive. Recently, micro VTOL platforms (i.e., quad-, hexa- and octa-rotors) have been rapidly gaining interest in research, military and even public domains. The unmanned, low-cost and VTOL properties of these platforms make them ideal for situations where inspection would otherwise be time-consuming and/or hazardous to humans. There are, however, challenges involved with developing such an inspection system, for example flying in close proximity to a target while maintaining a fixed stand-off distance from it, being immune to wind gusts and exchanging useful information with the remote user. To overcome these challenges, we require accurate and high-update rate state estimation and high performance controllers to be implemented onboard the vehicle. Ease of control and a live video feed are required for the human operator. We demonstrate a VTOL platform that can operate at close-quarters, whilst maintaining a safe stand-off distance and rejecting environmental disturbances. Two approaches are presented: Position-Based Visual Servoing (PBVS) using an Extended Kalman Filter (EKF) and estimator-free Image-Based Visual Servoing (IBVS). Both use monocular visual, inertia, and sonar data, allowing the approaches to be applied for indoor or GPS-impaired environments. We extensively compare the performances of PBVS and IBVS in terms of accuracy, robustness and computational costs. Results from simulations and indoor/outdoor (day and night) flight experiments demonstrate the system is able to successfully inspect and circumnavigate a vertical pole. PMID:26340631

3D range-gated super-resolution imaging based on stereo matching for moving platforms and targets

NASA Astrophysics Data System (ADS)

Sun, Liang; Wang, Xinwei; Zhou, Yan

2017-11-01

3D range-gated superresolution imaging is a novel 3D reconstruction technique for target detection and recognition with good real-time performance. However, for moving targets or platforms such as airborne, shipborne, remote operated vehicle and autonomous vehicle, 3D reconstruction has a large error or failure. In order to overcome this drawback, we propose a method of stereo matching for 3D range-gated superresolution reconstruction algorithm. In experiment, the target is a doll of Mario with a height of 38cm at the location of 34m, and we obtain two successive frame images of the Mario. To confirm our method is effective, we transform the original images with translation, rotation, scale and perspective, respectively. The experimental result shows that our method has a good result of 3D reconstruction for moving targets or platforms.

Fast Metabolic Response to Drug Intervention through Analysis on a Miniaturized, Highly Integrated Molecular Imaging System

PubMed Central

Wang, Jun; Hwang, Kiwook; Braas, Daniel; Dooraghi, Alex; Nathanson, David; Campbell, Dean O.; Gu, Yuchao; Sandberg, Troy; Mischel, Paul; Radu, Caius; Chatziioannou, Arion F.; Phelps, Michael E.; Christofk, Heather; Heath, James R.

2014-01-01

We report on a radiopharmaceutical imaging platform designed to capture the kinetics of cellular responses to drugs. Methods A portable in vitro molecular imaging system, comprised of a microchip and a beta-particle imaging camera, permits routine cell-based radioassays on small number of either suspension or adherent cells. We investigate the response kinetics of model lymphoma and glioblastoma cancer cell lines to [18F]fluorodeoxyglucose ([18F]FDG) uptake following drug exposure. Those responses are correlated with kinetic changes in the cell cycle, or with changes in receptor-tyrosine kinase signaling. Results The platform enables radioassays directly on multiple cell types, and yields results comparable to conventional approaches, but uses smaller sample sizes, permits a higher level of quantitation, and doesn’t require cell lysis. Conclusion The kinetic analysis enabled by the platform provides a rapid (~1 hour) drug screening assay. PMID:23978446

Experiment research on inertia-aided adaptive electronic image stabilization of optical stable platform

NASA Astrophysics Data System (ADS)

Lu, Xiaodong; Wu, Tianze; Zhou, Jun; Zhao, Bin; Ma, Xiaoyuan; Tang, Xiucheng

2016-03-01

An electronic image stabilization method compounded with inertia information, which can compensate the coupling interference caused by the pitch-yaw movement of the optical stable platform system, has been proposed in this paper. Firstly the mechanisms of coning rotation and lever-arm translation of line of sight (LOS) are analyzed during the stabilization process under moving carriers, and the mathematical model which describes the relationship between LOS rotation angle and platform attitude angle are derived. Then the image spin angle caused by coning rotation is estimated by using inertia information. Furthermore, an adaptive block matching method, which based on image edge and angular point, is proposed to smooth the jitter created by the lever-arm translation. This method optimizes the matching process and strategies. Finally, the results of hardware-in-the-loop simulation verified the effectiveness and real-time performance of the proposed method.

Collaborating with Your Clients Using Social Media & Mobile Communications

ERIC Educational Resources Information Center

Typhina, Eli; Bardon, Robert E.; Gharis, Laurie W.

2015-01-01

Many Extension educators are still learning how to effectively integrate social media into their programs. By using the right social media platforms and mobile applications to create engaged, online communities, Extension educators can collaborate with clients to produce and to share information expanding and enhancing their social media and…

Pinterest for Parent Education

ERIC Educational Resources Information Center

Routh, Brianna; Langworthy, Sara; Jastram, Hannah

2014-01-01

As more parents are using the Internet to answer their questions, Extension needs to provide practical, research-based resources in an accessible format. Pinterest is a platform that can be used by Extension educators to provide continued education and make reputable resources more discoverable for parents. Based on Knowles adult learning theory…

Developing a Successful Asynchronous Online Extension Program for Forest Landowners

ERIC Educational Resources Information Center

Zobrist, Kevin W.

2014-01-01

Asynchronous online Extension classes can reach a wide audience, is convenient for the learner, and minimizes ongoing demands on instructor time. However, producing such classes takes significant effort up front. Advance planning and good communication with contributors are essential to success. Considerations include delivery platforms, content…

A game-based platform for crowd-sourcing biomedical image diagnosis and standardized remote training and education of diagnosticians

NASA Astrophysics Data System (ADS)

Feng, Steve; Woo, Minjae; Chandramouli, Krithika; Ozcan, Aydogan

2015-03-01

Over the past decade, crowd-sourcing complex image analysis tasks to a human crowd has emerged as an alternative to energy-inefficient and difficult-to-implement computational approaches. Following this trend, we have developed a mathematical framework for statistically combining human crowd-sourcing of biomedical image analysis and diagnosis through games. Using a web-based smart game (BioGames), we demonstrated this platform's effectiveness for telediagnosis of malaria from microscopic images of individual red blood cells (RBCs). After public release in early 2012 (http://biogames.ee.ucla.edu), more than 3000 gamers (experts and non-experts) used this BioGames platform to diagnose over 2800 distinct RBC images, marking them as positive (infected) or negative (non-infected). Furthermore, we asked expert diagnosticians to tag the same set of cells with labels of positive, negative, or questionable (insufficient information for a reliable diagnosis) and statistically combined their decisions to generate a gold standard malaria image library. Our framework utilized minimally trained gamers' diagnoses to generate a set of statistical labels with an accuracy that is within 98% of our gold standard image library, demonstrating the "wisdom of the crowd". Using the same image library, we have recently launched a web-based malaria training and educational game allowing diagnosticians to compare their performance with their peers. After diagnosing a set of ~500 cells per game, diagnosticians can compare their quantified scores against a leaderboard and view their misdiagnosed cells. Using this platform, we aim to expand our gold standard library with new RBC images and provide a quantified digital tool for measuring and improving diagnostician training globally.

Digital shaded relief image of a carbonate platform (northern Great Bahama Bank): Scenery seen and unseen

NASA Astrophysics Data System (ADS)

Boss, Stephen K.

1996-11-01

A mosaic image of the northern Great Bahama Bank was created from separate gray-scale Landsat images using photo-editing and image analysis software that is commercially available for desktop computers. Measurements of pixel gray levels (relative scale from 0 to 255 referred to as digital number, DN) on the mosaic image were compared to bank-top bathymetry (determined from a network of single-channel, high-resolution seismic profiles), bottom type (coarse sand, sandy mud, barren rock, or reef determined from seismic profiles and diver observations), and vegetative cover (presence and/or absence and relative density of the marine angiosperm Thalassia testudinum determined from diver observations). Results of these analyses indicate that bank-top bathymetry is a primary control on observed pixel DN, bottom type is a secondary control on pixel DN, and vegetative cover is a tertiary influence on pixel DN. Consequently, processing of the gray-scale Landsat mosaic with a directional gradient edge-detection filter generated a physiographic shaded relief image resembling bank-top bathymetric patterns related to submerged physiographic features across the platform. The visibility of submerged karst landforms, Pleistocene eolianite ridges, islands, and possible paleo-drainage patterns created during sea-level lowstands is significantly enhanced on processed images relative to the original mosaic. Bank-margin ooid shoals, platform interior sand bodies, reef edifices, and bidirectional sand waves are features resulting from Holocene carbonate deposition that are also more clearly visible on the new physiographic images. Combined with observational data (single-channel, high-resolution seismic profiles, bottom observations by SCUBA divers, sediment and rock cores) across the northern Great Bahama Bank, these physiographic images facilitate comprehension of areal relations among antecedent platform topography, physical processes, and ensuing depositional patterns during sea-level rise.

MUSE: MUlti-atlas region Segmentation utilizing Ensembles of registration algorithms and parameters, and locally optimal atlas selection

PubMed Central

Ou, Yangming; Resnick, Susan M.; Gur, Ruben C.; Gur, Raquel E.; Satterthwaite, Theodore D.; Furth, Susan; Davatzikos, Christos

2016-01-01

Atlas-based automated anatomical labeling is a fundamental tool in medical image segmentation, as it defines regions of interest for subsequent analysis of structural and functional image data. The extensive investigation of multi-atlas warping and fusion techniques over the past 5 or more years has clearly demonstrated the advantages of consensus-based segmentation. However, the common approach is to use multiple atlases with a single registration method and parameter set, which is not necessarily optimal for every individual scan, anatomical region, and problem/data-type. Different registration criteria and parameter sets yield different solutions, each providing complementary information. Herein, we present a consensus labeling framework that generates a broad ensemble of labeled atlases in target image space via the use of several warping algorithms, regularization parameters, and atlases. The label fusion integrates two complementary sources of information: a local similarity ranking to select locally optimal atlases and a boundary modulation term to refine the segmentation consistently with the target image's intensity profile. The ensemble approach consistently outperforms segmentations using individual warping methods alone, achieving high accuracy on several benchmark datasets. The MUSE methodology has been used for processing thousands of scans from various datasets, producing robust and consistent results. MUSE is publicly available both as a downloadable software package, and as an application that can be run on the CBICA Image Processing Portal (https://ipp.cbica.upenn.edu), a web based platform for remote processing of medical images. PMID:26679328

Theranostics and metabolotheranostics for precision medicine in oncology

NASA Astrophysics Data System (ADS)

Bhujwalla, Zaver M.; Kakkad, Samata; Chen, Zhihang; Jin, Jiefu; Hapuarachchige, Sudath; Artemov, Dmitri; Penet, Marie-France

2018-06-01

Most diseases, especially cancer, would significantly benefit from precision medicine where treatment is shaped for the individual. The concept of theragnostics or theranostics emerged around 2002 to describe the incorporation of diagnostic assays into the selection of therapy for this purpose. Increasingly, theranostics has been used for strategies that combine noninvasive imaging-based diagnostics with therapy. Within the past decade theranostic imaging has transformed into a rapidly expanding field that is located at the interface of diagnosis and therapy. A critical need in cancer treatment is to minimize damage to normal tissue. Molecular imaging can be applied to identify targets specific to cancer with imaging, design agents against these targets to visualize their delivery, and monitor response to treatment, with the overall purpose of minimizing collateral damage. Genomic and proteomic profiling can provide an extensive 'fingerprint' of each tumor. With this cancer fingerprint, theranostic agents can be designed to personalize treatment for precision medicine of cancer, and minimize damage to normal tissue. Here, for the first time, we have introduced the term 'metabolotheranostics' to describe strategies where disease-based alterations in metabolic pathways detected by MRS are specifically targeted with image-guided delivery platforms to achieve disease-specific therapy. The versatility of MRI and MRS in molecular and functional imaging makes these technologies especially important in theranostic MRI and 'metabolotheranostics'. Our purpose here is to provide insights into the capabilities and applications of this exciting new field in cancer treatment with a focus on MRI and MRS.

Open source acceleration of wave optics simulations on energy efficient high-performance computing platforms

NASA Astrophysics Data System (ADS)

Beck, Jeffrey; Bos, Jeremy P.

2017-05-01

We compare several modifications to the open-source wave optics package, WavePy, intended to improve execution time. Specifically, we compare the relative performance of the Intel MKL, a CPU based OpenCV distribution, and GPU-based version. Performance is compared between distributions both on the same compute platform and between a fully-featured computing workstation and the NVIDIA Jetson TX1 platform. Comparisons are drawn in terms of both execution time and power consumption. We have found that substituting the Fast Fourier Transform operation from OpenCV provides a marked improvement on all platforms. In addition, we show that embedded platforms offer some possibility for extensive improvement in terms of efficiency compared to a fully featured workstation.

A Review of Imaging Techniques for Plant Phenotyping

PubMed Central

Li, Lei; Zhang, Qin; Huang, Danfeng

2014-01-01

Given the rapid development of plant genomic technologies, a lack of access to plant phenotyping capabilities limits our ability to dissect the genetics of quantitative traits. Effective, high-throughput phenotyping platforms have recently been developed to solve this problem. In high-throughput phenotyping platforms, a variety of imaging methodologies are being used to collect data for quantitative studies of complex traits related to the growth, yield and adaptation to biotic or abiotic stress (disease, insects, drought and salinity). These imaging techniques include visible imaging (machine vision), imaging spectroscopy (multispectral and hyperspectral remote sensing), thermal infrared imaging, fluorescence imaging, 3D imaging and tomographic imaging (MRT, PET and CT). This paper presents a brief review on these imaging techniques and their applications in plant phenotyping. The features used to apply these imaging techniques to plant phenotyping are described and discussed in this review. PMID:25347588

Semiautomated confocal imaging of fungal pathogenesis on plants: Microscopic analysis of macroscopic specimens.

PubMed

Minker, Katharine R; Biedrzycki, Meredith L; Kolagunda, Abhishek; Rhein, Stephen; Perina, Fabiano J; Jacobs, Samuel S; Moore, Michael; Jamann, Tiffany M; Yang, Qin; Nelson, Rebecca; Balint-Kurti, Peter; Kambhamettu, Chandra; Wisser, Randall J; Caplan, Jeffrey L

2018-02-01

The study of phenotypic variation in plant pathogenesis provides fundamental information about the nature of disease resistance. Cellular mechanisms that alter pathogenesis can be elucidated with confocal microscopy; however, systematic phenotyping platforms-from sample processing to image analysis-to investigate this do not exist. We have developed a platform for 3D phenotyping of cellular features underlying variation in disease development by fluorescence-specific resolution of host and pathogen interactions across time (4D). A confocal microscopy phenotyping platform compatible with different maize-fungal pathosystems (fungi: Setosphaeria turcica, Cochliobolus heterostrophus, and Cercospora zeae-maydis) was developed. Protocols and techniques were standardized for sample fixation, optical clearing, species-specific combinatorial fluorescence staining, multisample imaging, and image processing for investigation at the macroscale. The sample preparation methods presented here overcome challenges to fluorescence imaging such as specimen thickness and topography as well as physiological characteristics of the samples such as tissue autofluorescence and presence of cuticle. The resulting imaging techniques provide interesting qualitative and quantitative information not possible with conventional light or electron 2D imaging. Microsc. Res. Tech., 81:141-152, 2018. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Using advanced computer vision algorithms on small mobile robots

NASA Astrophysics Data System (ADS)

Kogut, G.; Birchmore, F.; Biagtan Pacis, E.; Everett, H. R.

2006-05-01

The Technology Transfer project employs a spiral development process to enhance the functionality and autonomy of mobile robot systems in the Joint Robotics Program (JRP) Robotic Systems Pool by converging existing component technologies onto a transition platform for optimization. An example of this approach is the implementation of advanced computer vision algorithms on small mobile robots. We demonstrate the implementation and testing of the following two algorithms useful on mobile robots: 1) object classification using a boosted Cascade of classifiers trained with the Adaboost training algorithm, and 2) human presence detection from a moving platform. Object classification is performed with an Adaboost training system developed at the University of California, San Diego (UCSD) Computer Vision Lab. This classification algorithm has been used to successfully detect the license plates of automobiles in motion in real-time. While working towards a solution to increase the robustness of this system to perform generic object recognition, this paper demonstrates an extension to this application by detecting soda cans in a cluttered indoor environment. The human presence detection from a moving platform system uses a data fusion algorithm which combines results from a scanning laser and a thermal imager. The system is able to detect the presence of humans while both the humans and the robot are moving simultaneously. In both systems, the two aforementioned algorithms were implemented on embedded hardware and optimized for use in real-time. Test results are shown for a variety of environments.

Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology.

PubMed

Markiewicz, Tomasz

2011-03-30

The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server database. The internet platform was tested on PC Intel Core2 Duo T9600 2.8 GHz 4 GB RAM server with 768x576 pixel size, 1.28 Mb tiff format images reffering to meningioma tumour (x400, Ki-67/MIB-1). The time consumption was as following: at analysis by CAMI, locally on a server - 3.5 seconds, at remote analysis - 26 seconds, from which 22 seconds were used for data transfer via internet connection. At jpg format image (102 Kb) the consumption time was reduced to 14 seconds. The results have confirmed that designed remote platform can be useful for pathology image analysis. The time consumption is depended mainly on the image size and speed of the internet connections. The presented implementation can be used for many types of analysis at different staining, tissue, morphometry approaches, etc. The significant problem is the implementation of the JSP page in the multithread form, that can be used parallelly by many users. The presented platform for image analysis in pathology can be especially useful for small laboratory without its own image analysis system.

Using MATLAB software with Tomcat server and Java platform for remote image analysis in pathology

PubMed Central

2011-01-01

Background The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. Methods In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. Results The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server database. The internet platform was tested on PC Intel Core2 Duo T9600 2.8GHz 4GB RAM server with 768x576 pixel size, 1.28Mb tiff format images reffering to meningioma tumour (x400, Ki-67/MIB-1). The time consumption was as following: at analysis by CAMI, locally on a server – 3.5 seconds, at remote analysis – 26 seconds, from which 22 seconds were used for data transfer via internet connection. At jpg format image (102 Kb) the consumption time was reduced to 14 seconds. Conclusions The results have confirmed that designed remote platform can be useful for pathology image analysis. The time consumption is depended mainly on the image size and speed of the internet connections. The presented implementation can be used for many types of analysis at different staining, tissue, morphometry approaches, etc. The significant problem is the implementation of the JSP page in the multithread form, that can be used parallelly by many users. The presented platform for image analysis in pathology can be especially useful for small laboratory without its own image analysis system. PMID:21489188

Effect of Antenna Pointing Errors on SAR Imaging Considering the Change of the Point Target Location

NASA Astrophysics Data System (ADS)

Zhang, Xin; Liu, Shijie; Yu, Haifeng; Tong, Xiaohua; Huang, Guoman

2018-04-01

Towards spaceborne spotlight SAR, the antenna is regulated by the SAR system with specific regularity, so the shaking of the internal mechanism is inevitable. Moreover, external environment also has an effect on the stability of SAR platform. Both of them will cause the jitter of the SAR platform attitude. The platform attitude instability will introduce antenna pointing error on both the azimuth and range directions, and influence the acquisition of SAR original data and ultimate imaging quality. In this paper, the relations between the antenna pointing errors and the three-axis attitude errors are deduced, then the relations between spaceborne spotlight SAR imaging of the point target and antenna pointing errors are analysed based on the paired echo theory, meanwhile, the change of the azimuth antenna gain is considered as the spotlight SAR platform moves ahead. The simulation experiments manifest the effects on spotlight SAR imaging caused by antenna pointing errors are related to the target location, that is, the pointing errors of the antenna beam will severely influence the area far away from the scene centre of azimuth direction in the illuminated scene.

Compact and light-weight automated semen analysis platform using lensfree on-chip microscopy.

PubMed

Su, Ting-Wei; Erlinger, Anthony; Tseng, Derek; Ozcan, Aydogan

2010-10-01

We demonstrate a compact and lightweight platform to conduct automated semen analysis using a lensfree on-chip microscope. This holographic on-chip imaging platform weighs ∼46 g, measures ∼4.2 × 4.2 × 5.8 cm, and does not require any lenses, lasers or other bulky optical components to achieve phase and amplitude imaging of sperms over ∼24 mm(2) field-of-view with an effective numerical aperture of ∼0.2. Using this wide-field lensfree on-chip microscope, semen samples are imaged for ∼10 s, capturing a total of ∼20 holographic frames. Digital subtraction of these consecutive lensfree frames, followed by appropriate processing of the reconstructed images, enables automated quantification of the count, the speed and the dynamic trajectories of motile sperms, while summation of the same frames permits counting of immotile sperms. Such a compact and lightweight automated semen analysis platform running on a wide-field lensfree on-chip microscope could be especially important for fertility clinics, personal male fertility tests, as well as for field use in veterinary medicine such as in stud farming and animal breeding applications.

Institute for Molecular Medicine Research Program

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

Phelps, Michael E

2012-12-14

The objectives of the project are the development of new Positron Emission Tomography (PET) imaging instrumentation, chemistry technology platforms and new molecular imaging probes to examine the transformations from normal cellular and biological processes to those of disease in pre-clinical animal models. These technology platforms and imaging probes provide the means to: 1. Study the biology of disease using pre-clinical mouse models and cells. 2. Develop molecular imaging probes for imaging assays of proteins in pre-clinical models. 3. Develop imaging assays in pre-clinical models to provide to other scientists the means to guide and improve the processes for discovering newmore » drugs. 4. Develop imaging assays in pre-clinical models for others to use in judging the impact of drugs on the biology of disease.« less

Platform for efficient switching between multiple devices in the intensive care unit.

PubMed

De Backere, F; Vanhove, T; Dejonghe, E; Feys, M; Herinckx, T; Vankelecom, J; Decruyenaere, J; De Turck, F

2015-01-01

This article is part of the Focus Theme of METHODS of Information in Medicine on "Managing Interoperability and Complexity in Health Systems". Handheld computers, such as tablets and smartphones, are becoming more and more accessible in the clinical care setting and in Intensive Care Units (ICUs). By making the most useful and appropriate data available on multiple devices and facilitate the switching between those devices, staff members can efficiently integrate them in their workflow, allowing for faster and more accurate decisions. This paper addresses the design of a platform for the efficient switching between multiple devices in the ICU. The key functionalities of the platform are the integration of the platform into the workflow of the medical staff and providing tailored and dynamic information at the point of care. The platform is designed based on a 3-tier architecture with a focus on extensibility, scalability and an optimal user experience. After identification to a device using Near Field Communication (NFC), the appropriate medical information will be shown on the selected device. The visualization of the data is adapted to the type of the device. A web-centric approach was used to enable extensibility and portability. A prototype of the platform was thoroughly evaluated. The scalability, performance and user experience were evaluated. Performance tests show that the response time of the system scales linearly with the amount of data. Measurements with up to 20 devices have shown no performance loss due to the concurrent use of multiple devices. The platform provides a scalable and responsive solution to enable the efficient switching between multiple devices. Due to the web-centric approach new devices can easily be integrated. The performance and scalability of the platform have been evaluated and it was shown that the response time and scalability of the platform was within an acceptable range.

SurfaceSlide: a multitouch digital pathology platform.

PubMed

Wang, Yinhai; Williamson, Kate E; Kelly, Paul J; James, Jacqueline A; Hamilton, Peter W

2012-01-01

Digital pathology provides a digital environment for the management and interpretation of pathological images and associated data. It is becoming increasing popular to use modern computer based tools and applications in pathological education, tissue based research and clinical diagnosis. Uptake of this new technology is stymied by its single user orientation and its prerequisite and cumbersome combination of mouse and keyboard for navigation and annotation. In this study we developed SurfaceSlide, a dedicated viewing platform which enables the navigation and annotation of gigapixel digitised pathological images using fingertip touch. SurfaceSlide was developed using the Microsoft Surface, a 30 inch multitouch tabletop computing platform. SurfaceSlide users can perform direct panning and zooming operations on digitised slide images. These images are downloaded onto the Microsoft Surface platform from a remote server on-demand. Users can also draw annotations and key in texts using an on-screen virtual keyboard. We also developed a smart caching protocol which caches the surrounding regions of a field of view in multi-resolutions thus providing a smooth and vivid user experience and reducing the delay for image downloading from the internet. We compared the usability of SurfaceSlide against Aperio ImageScope and PathXL online viewer. SurfaceSlide is intuitive, fast and easy to use. SurfaceSlide represents the most direct, effective and intimate human-digital slide interaction experience. It is expected that SurfaceSlide will significantly enhance digital pathology tools and applications in education and clinical practice.

SurfaceSlide: A Multitouch Digital Pathology Platform

PubMed Central

Wang, Yinhai; Williamson, Kate E.; Kelly, Paul J.; James, Jacqueline A.; Hamilton, Peter W.

2012-01-01

Background Digital pathology provides a digital environment for the management and interpretation of pathological images and associated data. It is becoming increasing popular to use modern computer based tools and applications in pathological education, tissue based research and clinical diagnosis. Uptake of this new technology is stymied by its single user orientation and its prerequisite and cumbersome combination of mouse and keyboard for navigation and annotation. Methodology In this study we developed SurfaceSlide, a dedicated viewing platform which enables the navigation and annotation of gigapixel digitised pathological images using fingertip touch. SurfaceSlide was developed using the Microsoft Surface, a 30 inch multitouch tabletop computing platform. SurfaceSlide users can perform direct panning and zooming operations on digitised slide images. These images are downloaded onto the Microsoft Surface platform from a remote server on-demand. Users can also draw annotations and key in texts using an on-screen virtual keyboard. We also developed a smart caching protocol which caches the surrounding regions of a field of view in multi-resolutions thus providing a smooth and vivid user experience and reducing the delay for image downloading from the internet. We compared the usability of SurfaceSlide against Aperio ImageScope and PathXL online viewer. Conclusion SurfaceSlide is intuitive, fast and easy to use. SurfaceSlide represents the most direct, effective and intimate human–digital slide interaction experience. It is expected that SurfaceSlide will significantly enhance digital pathology tools and applications in education and clinical practice. PMID:22292040

An Extensible Sensing and Control Platform for Building Energy Management

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

Rowe, Anthony; Berges, Mario; Martin, Christopher

2016-04-03

The goal of this project is to develop Mortar.io, an open-source BAS platform designed to simplify data collection, archiving, event scheduling and coordination of cross-system interactions. Mortar.io is optimized for (1) robustness to network outages, (2) ease of installation using plug-and-play and (3) scalable support for small to large buildings and campuses.

Image Sharing in Radiology-A Primer.

PubMed

Chatterjee, Arindam R; Stalcup, Seth; Sharma, Arjun; Sato, T Shawn; Gupta, Pushpender; Lee, Yueh Z; Malone, Christopher; McBee, Morgan; Hotaling, Elise L; Kansagra, Akash P

2017-03-01

By virtue of its information technology-oriented infrastructure, the specialty of radiology is uniquely positioned to be at the forefront of efforts to promote data sharing across the healthcare enterprise, including particularly image sharing. The potential benefits of image sharing for clinical, research, and educational applications in radiology are immense. In this work, our group-the Association of University Radiologists (AUR) Radiology Research Alliance Task Force on Image Sharing-reviews the benefits of implementing image sharing capability, introduces current image sharing platforms and details their unique requirements, and presents emerging platforms that may see greater adoption in the future. By understanding this complex ecosystem of image sharing solutions, radiologists can become important advocates for the successful implementation of these powerful image sharing resources. Copyright © 2017 The Association of University Radiologists. Published by Elsevier Inc. All rights reserved.

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.

fMRat: an extension of SPM for a fully automatic analysis of rodent brain functional magnetic resonance series.

PubMed

Chavarrías, Cristina; García-Vázquez, Verónica; Alemán-Gómez, Yasser; Montesinos, Paula; Pascau, Javier; Desco, Manuel

2016-05-01

The purpose of this study was to develop a multi-platform automatic software tool for full processing of fMRI rodent studies. Existing tools require the usage of several different plug-ins, a significant user interaction and/or programming skills. Based on a user-friendly interface, the tool provides statistical parametric brain maps (t and Z) and percentage of signal change for user-provided regions of interest. The tool is coded in MATLAB (MathWorks(®)) and implemented as a plug-in for SPM (Statistical Parametric Mapping, the Wellcome Trust Centre for Neuroimaging). The automatic pipeline loads default parameters that are appropriate for preclinical studies and processes multiple subjects in batch mode (from images in either Nifti or raw Bruker format). In advanced mode, all processing steps can be selected or deselected and executed independently. Processing parameters and workflow were optimized for rat studies and assessed using 460 male-rat fMRI series on which we tested five smoothing kernel sizes and three different hemodynamic models. A smoothing kernel of FWHM = 1.2 mm (four times the voxel size) yielded the highest t values at the somatosensorial primary cortex, and a boxcar response function provided the lowest residual variance after fitting. fMRat offers the features of a thorough SPM-based analysis combined with the functionality of several SPM extensions in a single automatic pipeline with a user-friendly interface. The code and sample images can be downloaded from https://github.com/HGGM-LIM/fmrat .

High-speed quantitative phase imaging using time-stretch spectral shearing contrast (Conference Presentation)

NASA Astrophysics Data System (ADS)

Bosworth, Bryan; Foster, Mark A.

2017-02-01

Photonic time-stretch microscopy (TSM) provides an ideal platform for high-throughput imaging flow cytometry, affording extremely high shutter speeds and frame rates with high sensitivity. In order to resolve weakly scattering cells in biofluid and solve the issue of signal-to-noise in cell labeling specificity of biomarkers in imaging flow cytometry, several quantitative phase (QP) techniques have recently been adapted to TSM. However, these techniques have relied primarily on sensitive free-space optical configurations to generate full electric field measurements. The present work draws from the field of ultrashort pulse characterization to leverage the coherence of the ultrashort optical pulses integral to all TSM systems in order to do self-referenced single-shot quantitative phase imaging in a TSM system. Self-referencing is achieved via spectral shearing interferometry in an exceptionally stable and straightforward Sagnac loop incorporating an electro-optic phase modulator and polarization-maintaining fiber that produce sheared and unsheared copies of the pulse train with an inter-pulse delay determined by polarization mode dispersion. The spectral interferogram then yields a squared amplitude and a phase derivative image that can be integrated for conventional phase. We apply this spectral shearing contrast microscope to acquire QP images on a high-speed flow microscope at 90-MHz line rates with <400 pixels per line. We also consider the extension of this technique to compressed sensing (CS) acquisition by intensity modulating the interference spectra with pseudorandom binary waveforms to reconstruct the images from a highly sub-Nyquist number of random inner products, providing a path to even higher operating rates and reduced data storage requirements.

a Kml-Based Approach for Distributed Collaborative Interpretation of Remote Sensing Images in the Geo-Browser

NASA Astrophysics Data System (ADS)

Huang, L.; Zhu, X.; Guo, W.; Xiang, L.; Chen, X.; Mei, Y.

2012-07-01

Existing implementations of collaborative image interpretation have many limitations for very large satellite imageries, such as inefficient browsing, slow transmission, etc. This article presents a KML-based approach to support distributed, real-time, synchronous collaborative interpretation for remote sensing images in the geo-browser. As an OGC standard, KML (Keyhole Markup Language) has the advantage of organizing various types of geospatial data (including image, annotation, geometry, etc.) in the geo-browser. Existing KML elements can be used to describe simple interpretation results indicated by vector symbols. To enlarge its application, this article expands KML elements to describe some complex image processing operations, including band combination, grey transformation, geometric correction, etc. Improved KML is employed to describe and share interpretation operations and results among interpreters. Further, this article develops some collaboration related services that are collaboration launch service, perceiving service and communication service. The launch service creates a collaborative interpretation task and provides a unified interface for all participants. The perceiving service supports interpreters to share collaboration awareness. Communication service provides interpreters with written words communication. Finally, the GeoGlobe geo-browser (an extensible and flexible geospatial platform developed in LIESMARS) is selected to perform experiments of collaborative image interpretation. The geo-browser, which manage and visualize massive geospatial information, can provide distributed users with quick browsing and transmission. Meanwhile in the geo-browser, GIS data (for example DEM, DTM, thematic map and etc.) can be integrated to assist in improving accuracy of interpretation. Results show that the proposed method is available to support distributed collaborative interpretation of remote sensing image

Real-time self-calibration of a tracked augmented reality display

NASA Astrophysics Data System (ADS)

Baum, Zachary; Lasso, Andras; Ungi, Tamas; Fichtinger, Gabor

2016-03-01

PURPOSE: Augmented reality systems have been proposed for image-guided needle interventions but they have not become widely used in clinical practice due to restrictions such as limited portability, low display refresh rates, and tedious calibration procedures. We propose a handheld tablet-based self-calibrating image overlay system. METHODS: A modular handheld augmented reality viewbox was constructed from a tablet computer and a semi-transparent mirror. A consistent and precise self-calibration method, without the use of any temporary markers, was designed to achieve an accurate calibration of the system. Markers attached to the viewbox and patient are simultaneously tracked using an optical pose tracker to report the position of the patient with respect to a displayed image plane that is visualized in real-time. The software was built using the open-source 3D Slicer application platform's SlicerIGT extension and the PLUS toolkit. RESULTS: The accuracy of the image overlay with image-guided needle interventions yielded a mean absolute position error of 0.99 mm (95th percentile 1.93 mm) in-plane of the overlay and a mean absolute position error of 0.61 mm (95th percentile 1.19 mm) out-of-plane. This accuracy is clinically acceptable for tool guidance during various procedures, such as musculoskeletal injections. CONCLUSION: A self-calibration method was developed and evaluated for a tracked augmented reality display. The results show potential for the use of handheld image overlays in clinical studies with image-guided needle interventions.

Using R-Project for Free Statistical Analysis in Extension Research

ERIC Educational Resources Information Center

Mangiafico, Salvatore S.

2013-01-01

One option for Extension professionals wishing to use free statistical software is to use online calculators, which are useful for common, simple analyses. A second option is to use a free computing environment capable of performing statistical analyses, like R-project. R-project is free, cross-platform, powerful, and respected, but may be…

Targeted nanoparticles for image-guided treatment of triple-negative breast cancer: clinical significance and technological advances.

PubMed

Miller-Kleinhenz, Jasmine M; Bozeman, Erica N; Yang, Lily

2015-01-01

Effective treatment of triple-negative breast cancer (TNBC) with its aggressive tumor biology, highly heterogeneous tumor cells, and poor prognosis requires an integrated therapeutic approach that addresses critical issues in cancer therapy. Multifunctional nanoparticles with the abilities of targeted drug delivery and noninvasive imaging for monitoring drug delivery and responses to therapy, such as theranostic nanoparticles, hold great promise toward the development of novel therapeutic approaches for the treatment of TNBC using a single therapeutic platform. The biological and pathological characteristics of TNBC provide insight into several potential molecular targets for current and future nanoparticle-based therapeutics. Extensive tumor stroma, highly proliferative cells, and a high rate of drug resistance are all barriers that must be appropriately addressed in order for these nanotherapeutic platforms to be effective. Utilization of the enhanced permeability and retention effect coupled with active targeting of cell surface receptors expressed by TNBC cells, and tumor-associated endothelial cells, stromal fibroblasts, and macrophages is likely to overcome such barriers to facilitate more effective drug delivery. An in-depth summary of current studies investigating targeted nanoparticles in preclinical TNBC mouse and human xenograft models is presented. This review aims to outline the current status of nanotherapeutic options for TNBC patients, identification of promising molecular targets, challenges associated with the development of targeted nanotherapeutics, the research done by our group as well as by others, and future perspectives on the nanomedicine field and ways to translate current preclinical studies into the clinic. © 2015 Wiley Periodicals, Inc.

Targeted exploration and analysis of large cross-platform human transcriptomic compendia

PubMed Central

Zhu, Qian; Wong, Aaron K; Krishnan, Arjun; Aure, Miriam R; Tadych, Alicja; Zhang, Ran; Corney, David C; Greene, Casey S; Bongo, Lars A; Kristensen, Vessela N; Charikar, Moses; Li, Kai; Troyanskaya, Olga G.

2016-01-01

We present SEEK (http://seek.princeton.edu), a query-based search engine across very large transcriptomic data collections, including thousands of human data sets from almost 50 microarray and next-generation sequencing platforms. SEEK uses a novel query-level cross-validation-based algorithm to automatically prioritize data sets relevant to the query and a robust search approach to identify query-coregulated genes, pathways, and processes. SEEK provides cross-platform handling, multi-gene query search, iterative metadata-based search refinement, and extensive visualization-based analysis options. PMID:25581801

A client/server system for Internet access to biomedical text/image databanks.

PubMed

Thoma, G R; Long, L R; Berman, L E

1996-01-01

Internet access to mixed text/image databanks is finding application in the medical world. An example is a database of medical X-rays and associated data consisting of demographic, socioeconomic, physician's exam, medical laboratory and other information collected as part of a nationwide health survey conducted by the government. Another example is a collection of digitized cryosection images, CT and MR taken of cadavers as part of the National Library of Medicine's Visible Human Project. In both cases, the challenge is to provide access to both the image and the associated text for a wide end user community to create atlases, conduct epidemiological studies, to develop image-specific algorithms for compression, enhancement and other types of image processing, among many other applications. The databanks mentioned above are being created in prototype form. This paper describes the prototype system developed for the archiving of the data and the client software to enable a broad range of end users to access the archive, retrieve text and image data, display the data and manipulate the images. System design considerations include; data organization in a relational database management system with object-oriented extensions; a hierarchical organization of the image data by different resolution levels for different user classes; client design based on common hardware and software platforms incorporating SQL search capability, X Window, Motif and TAE (a development environment supporting rapid prototyping and management of graphic-oriented user interfaces); potential to include ultra high resolution display monitors as a user option; intuitive user interface paradigm for building complex queries; and contrast enhancement, magnification and mensuration tools for better viewing by the user.

Predictive value of magnetic resonance imaging determined tumor contact length for extracapsular extension of prostate cancer.

PubMed

Baco, Eduard; Rud, Erik; Vlatkovic, Ljiljana; Svindland, Aud; Eggesbø, Heidi B; Hung, Andrew J; Matsugasumi, Toru; Bernhard, Jean-Christophe; Gill, Inderbir S; Ukimura, Osamu

2015-02-01

Tumor contact length is defined as the amount of prostate cancer in contact with the prostatic capsule. We evaluated the ability of magnetic resonance imaging determined tumor contact length to predict microscopic extracapsular extension compared to existing predictors of extracapsular extension. We retrospectively analyzed the records of 111 consecutive patients with magnetic resonance imaging/ultrasound fusion targeted, biopsy proven prostate cancer who underwent radical prostatectomy from January 2010 to July 2013. Median patient age was 64 years and median prostate specific antigen was 8.9 ng/ml. Clinical stage was cT1 in 93 cases (84%) and cT2 in 18 (16%). Postoperative pathological analysis confirmed pT2 in 71 patients (64%) and pT3 in 40 (36%). We evaluated 1) in the radical prostatectomy specimen the correlation of microscopic extracapsular extension with pathological cancer volume, pathological tumor contact length and Gleason score, 2) the correlation between microscopic extracapsular extension and magnetic resonance imaging tumor contact length, and 3) the ability of preoperative variables to predict microscopic extracapsular extension. Logistic regression analysis revealed that pathological tumor contact length correlated better with microscopic extracapsular extension than the predictive power of pathological cancer volume (0.821 vs 0.685). The Spearman correlation between pathological and magnetic resonance imaging tumor contact length was r = 0.839 (p <0.0001). ROC AUC analysis revealed that magnetic resonance imaging tumor contact length outperformed cancer core involvement on targeted biopsy and the Partin tables to predict microscopic extracapsular extension (0.88 vs 0.70 and 0.63, respectively). At a magnetic resonance imaging tumor contact length threshold of 20 mm the accuracy for diagnosing microscopic extracapsular extension was superior to that of conventional magnetic resonance imaging criteria (82% vs 67%, p = 0.015). We developed a predicted probability plot curve of extracapsular extension according to magnetic resonance imaging tumor contact length. Magnetic resonance imaging determined tumor contact length could be a promising quantitative predictor of microscopic extracapsular extension. Copyright © 2015 American Urological Association Education and Research, Inc. Published by Elsevier Inc. All rights reserved.

Recent advances and future prospects of iron oxide nanoparticles in biomedicine and diagnostics.

PubMed

Vallabani, N V Srikanth; Singh, Sanjay

2018-06-01

Superparamagnetic iron oxide nanoparticles (SPIONs) are considered as chemically inert materials and, therefore, being extensively applied in the areas of imaging, targeting, drug delivery and biosensors. Their unique properties such as low toxicity, biocompatibility, potent magnetic and catalytic behavior and superior role in multifunctional modalities have epitomized them as an appropriate candidate for biomedical applications. Recent developments in the area of materials science have enabled the facile synthesis of Iron oxide nanoparticles (IONPs) offering easy tuning of surface properties and surface functionalization with desired biomolecules. Such developments have enabled IONPs to be easily accommodated in nanocomposite platform or devices. Additionally, the tag of biocompatible material has realized their potential in myriad applications of nanomedicines including imaging modalities, sensing, and therapeutics. Further, IONPs enzyme mimetic activity pronounced their role as nanozymes in detecting biomolecules like glucose, and cholesterol etc. Hence, based on their versatile applications in biomedicine, the present review article focusses on the current trends, developments and future prospects of IONPs in MRI, hyperthermia, photothermal therapy, biomolecules detection, chemotherapy, antimicrobial activity and also their role as the multifunctional agent in diagnosis and nanomedicines.

Silhouette-based approach of 3D image reconstruction for automated image acquisition using robotic arm

NASA Astrophysics Data System (ADS)

Azhar, N.; Saad, W. H. M.; Manap, N. A.; Saad, N. M.; Syafeeza, A. R.

2017-06-01

This study presents the approach of 3D image reconstruction using an autonomous robotic arm for the image acquisition process. A low cost of the automated imaging platform is created using a pair of G15 servo motor connected in series to an Arduino UNO as a main microcontroller. Two sets of sequential images were obtained using different projection angle of the camera. The silhouette-based approach is used in this study for 3D reconstruction from the sequential images captured from several different angles of the object. Other than that, an analysis based on the effect of different number of sequential images on the accuracy of 3D model reconstruction was also carried out with a fixed projection angle of the camera. The effecting elements in the 3D reconstruction are discussed and the overall result of the analysis is concluded according to the prototype of imaging platform.

Xi-cam: Flexible High Throughput Data Processing for GISAXS

NASA Astrophysics Data System (ADS)

Pandolfi, Ronald; Kumar, Dinesh; Venkatakrishnan, Singanallur; Sarje, Abinav; Krishnan, Hari; Pellouchoud, Lenson; Ren, Fang; Fournier, Amanda; Jiang, Zhang; Tassone, Christopher; Mehta, Apurva; Sethian, James; Hexemer, Alexander

With increasing capabilities and data demand for GISAXS beamlines, supporting software is under development to handle larger data rates, volumes, and processing needs. We aim to provide a flexible and extensible approach to GISAXS data treatment as a solution to these rising needs. Xi-cam is the CAMERA platform for data management, analysis, and visualization. The core of Xi-cam is an extensible plugin-based GUI platform which provides users an interactive interface to processing algorithms. Plugins are available for SAXS/GISAXS data and data series visualization, as well as forward modeling and simulation through HipGISAXS. With Xi-cam's advanced mode, data processing steps are designed as a graph-based workflow, which can be executed locally or remotely. Remote execution utilizes HPC or de-localized resources, allowing for effective reduction of high-throughput data. Xi-cam is open-source and cross-platform. The processing algorithms in Xi-cam include parallel cpu and gpu processing optimizations, also taking advantage of external processing packages such as pyFAI. Xi-cam is available for download online.

Synchronised integrated online e-health profiles.

PubMed

Liang, Jian; Iannella, Renato; Sahama, Tony

2011-01-01

Web-based social networking applications have become increasingly important in recent years. The current applications in the healthcare sphere can support the health management, but to date there is no patient-controlled integrator. This paper proposes a platform called Multiple Profile Manager (MPM) that enables a user to create and manage an integrated profile that can be shared across numerous social network sites. Moreover, it is able to facilitate the collection of personal healthcare data, which makes a contribution to the development of public health informatics. Here we want to illustrate how patients and physicians can be benefited from enabling the platform for online social network sites. The MPM simplifies the management of patients' profiles and allows health professionals to obtain a more complete picture of the patients' background so that they can provide better health care. To do so, we demonstrate a prototype of the platform and describe its protocol specification, which is an XMPP (Extensible Messaging and Presence Protocol) [1] extension, for sharing and synchronising profile data (vCard²) between different social networks.

An ARM Mobile Facility Designed for Marine Deployments

NASA Astrophysics Data System (ADS)

Wiscombe, W. J.

2007-05-01

The U.S. Dept. of Energy's ARM (Atmospheric Radiation Measurements) Program is designing a Mobile Facility exclusively for marine deployments. This marine facility is patterned after ARM's land Mobile Facility, which had its inaugural deployment at Point Reyes, California, in 2005, followed by deployments to Niger in 2006 and Germany in 2007 (ongoing), and a planned deployment to China in 2008. These facilities are primarily intended for the study of clouds, radiation, aerosols, and surface processes with a goal to include these processes accurately in climate models. They are preferably embedded within larger field campaigns which provide context. They carry extensive instrumentation (in several large containers) including: cloud radar, lidar, microwave radiometers, infrared spectrometers, broadband and narrowband radiometers, sonde-launching facilities, extensive surface aerosol measurements, sky imagers, and surface latent and sensible heat flux devices. ARM's Mobile Facilities are designed for 6-10 month deployments in order to capture climatically-relevant datasets. They are available to any scientist, U.S. or international, who wishes to submit a proposal during the annual Spring call. The marine facility will be adapted to, and ruggedized for, the harsh marine environment and will add a scanning two-frequency radar, a boundary-layer wind profiler, a shortwave spectrometer, and aerosol instrumentation adapted to typical marine aerosols like sea salt. Plans also include the use of roving small UAVs, automated small boats, and undersea autonomous vehicles in order to address the point-to-area-average problem which is so crucial for informing climate models. Initial deployments are planned for small islands in climatically- interesting cloud regimes, followed by deployments on oceanic platforms (like decommissioned oil rigs and the quasi-permanent platform of this session's title) and eventually on large ships like car carriers plying routine routes.

Imaging enabled platforms for development of therapeutics

NASA Astrophysics Data System (ADS)

Celli, Jonathan; Rizvi, Imran; Blanden, Adam R.; Evans, Conor L.; Abu-Yousif, Adnan O.; Spring, Bryan Q.; Muzikansky, Alona; Pogue, Brian W.; Finkelstein, Dianne M.; Hasan, Tayyaba

2011-03-01

Advances in imaging and spectroscopic technologies have enabled the optimization of many therapeutic modalities in cancer and noncancer pathologies either by earlier disease detection or by allowing therapy monitoring. Amongst the therapeutic options benefiting from developments in imaging technologies, photodynamic therapy (PDT) is exceptional. PDT is a photochemistry-based therapeutic approach where a light-sensitive molecule (photosensitizer) is activated with light of appropriate energy (wavelength) to produce reactive molecular species such as free radicals and singlet oxygen. These molecular entities then react with biological targets such as DNA, membranes and other cellular components to impair their function and lead to eventual cell and tissue death. Development of PDT-based imaging also provides a platform for rapid screening of new therapeutics in novel in vitro models prior to expensive and labor-intensive animal studies. In this study we demonstrate how an imaging platform can be used for strategizing a novel combination treatment strategy for multifocal ovarian cancer. Using an in vitro 3D model for micrometastatic ovarian cancer in conjunction with quantitative imaging we examine dose and scheduling strategies for PDT in combination with carboplatin, a chemotherapeutic agent presently in clinical use for management of this deadly form of cancer.

Multimodality bonchoscopic imaging of tracheopathica osteochondroplastica

NASA Astrophysics Data System (ADS)

Colt, Henri; Murgu, Septimiu D.; Ahn, Yeh-Chan; Brenner, Matt

2009-05-01

Results of a commercial optical coherence tomography system used as part of a multimodality diagnostic bronchoscopy platform are presented for a 61-year-old patient with central airway obstruction from tracheopathica osteochondroplastica. Comparison to results of white-light bronchoscopy, histology, and endobronchial ultrasound examination are accompanied by a discussion of resolution, penetration depth, contrast, and field of view of these imaging modalities. White-light bronchoscopy revealed irregularly shaped, firm submucosal nodules along cartilaginous structures of the anterior and lateral walls of the trachea, sparing the muscular posterior membrane. Endobronchial ultrasound showed a hyperechoic density of 0.4 cm thickness. optical coherence tomography (OCT) was performed using a commercially available, compact time-domain OCT system (Niris System, Imalux Corp., Cleveland, Ohio) with a magnetically actuating probe (two-dimensional, front imaging, and inside actuation). Images showed epithelium, upper submucosa, and osseous submucosal nodule layers corresponding with histopathology. To our knowledge, this is the first time these commercially available systems are used as part of a multimodality bronchoscopy platform to study diagnostic imaging of a benign disease causing central airway obstruction. Further studies are needed to optimize these systems for pulmonary applications and to determine how new-generation imaging modalities will be integrated into a multimodality bronchoscopy platform.

Lens-free shadow image based high-throughput continuous cell monitoring technique.

PubMed

Jin, Geonsoo; Yoo, In-Hwa; Pack, Seung Pil; Yang, Ji-Woon; Ha, Un-Hwan; Paek, Se-Hwan; Seo, Sungkyu

2012-01-01

A high-throughput continuous cell monitoring technique which does not require any labeling reagents or destruction of the specimen is demonstrated. More than 6000 human alveolar epithelial A549 cells are monitored for up to 72 h simultaneously and continuously with a single digital image within a cost and space effective lens-free shadow imaging platform. In an experiment performed within a custom built incubator integrated with the lens-free shadow imaging platform, the cell nucleus division process could be successfully characterized by calculating the signal-to-noise ratios (SNRs) and the shadow diameters (SDs) of the cell shadow patterns. The versatile nature of this platform also enabled a single cell viability test followed by live cell counting. This study firstly shows that the lens-free shadow imaging technique can provide a continuous cell monitoring without any staining/labeling reagent and destruction of the specimen. This high-throughput continuous cell monitoring technique based on lens-free shadow imaging may be widely utilized as a compact, low-cost, and high-throughput cell monitoring tool in the fields of drug and food screening or cell proliferation and viability testing. Copyright © 2012 Elsevier B.V. All rights reserved.

Design of the compact high-resolution imaging spectrometer (CHRIS), and future developments

NASA Astrophysics Data System (ADS)

Cutter, Mike; Lobb, Dan

2017-11-01

The CHRIS instrument was launched on ESA's PROBA platform in October 2001, and is providing hyperspectral images of selected ground areas at 17m ground sampling distance, in the spectral range 415nm to 1050nm. Platform agility allows image sets to be taken at multiple view angles in each overpass. The design of the instrument is briefly outlined, including design of optics, structures, detection and in-flight calibration system. Lessons learnt from construction and operation of the experimental system, and possible design directions for future hyperspectral systems, are discussed.

Multiphysics and multiscale modelling, data-model fusion and integration of organ physiology in the clinic: ventricular cardiac mechanics.

PubMed

Chabiniok, Radomir; Wang, Vicky Y; Hadjicharalambous, Myrianthi; Asner, Liya; Lee, Jack; Sermesant, Maxime; Kuhl, Ellen; Young, Alistair A; Moireau, Philippe; Nash, Martyn P; Chapelle, Dominique; Nordsletten, David A

2016-04-06

With heart and cardiovascular diseases continually challenging healthcare systems worldwide, translating basic research on cardiac (patho)physiology into clinical care is essential. Exacerbating this already extensive challenge is the complexity of the heart, relying on its hierarchical structure and function to maintain cardiovascular flow. Computational modelling has been proposed and actively pursued as a tool for accelerating research and translation. Allowing exploration of the relationships between physics, multiscale mechanisms and function, computational modelling provides a platform for improving our understanding of the heart. Further integration of experimental and clinical data through data assimilation and parameter estimation techniques is bringing computational models closer to use in routine clinical practice. This article reviews developments in computational cardiac modelling and how their integration with medical imaging data is providing new pathways for translational cardiac modelling.

Sensor deployment on unmanned ground vehicles

NASA Astrophysics Data System (ADS)

Gerhart, Grant R.; Witus, Gary

2007-10-01

TARDEC has been developing payloads for small robots as part of its unmanned ground vehicle (UGV) development programs. These platforms typically weigh less than 100 lbs and are used for various physical security and force protection applications. This paper will address a number of technical issues including platform mobility, payload positioning, sensor configuration and operational tradeoffs. TARDEC has developed a number of robots with different mobility mechanisms including track, wheel and hybrid track/wheel running gear configurations. An extensive discussion will focus upon omni-directional vehicle (ODV) platforms with enhanced intrinsic mobility for positioning sensor payloads. This paper also discusses tradeoffs between intrinsic platform mobility and articulated arm complexity for end point positioning of modular sensor packages.

SU-E-T-428: Feasibility Study of 4D Image Reconstruction by Organ Motion Vector Extension Based On Portal Images

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

Yoon, J; Jung, J; Yeo, I

2015-06-15

Purpose: To develop and to test a method to generate a new 4D CT images of the treatment day from the old 4D CT and the portal images of the day when the motion extent exceeded from that represented by plan CTs. Methods: A motion vector of a moving tumor in a patient may be extended to reconstruct the tumor position when the motion extent exceeded from that represented by plan CTs. To test this, 1. a phantom that consists of a polystyrene cylinder (tumor) embedded in cork (lung) was placed on a moving platform with 4 sec/cycle and amplitudesmore » of 1 cm and 2 cm, and was 4D-scanned. 2. A 6MV photon beam was irradiated on the moving phantoms and cineEPID images were obtained. 3. A motion vector of the tumor was acquired from 4D CT images of the phantom with 1 cm amplitude. 4. From cine EPID images of the phantom with the 2 cm amplitude, various motion extents (0.3 cm, 0.5 cm, etc) were acquired and programmed into the motion vector, producing CT images at each position. 5. The reconstructed CT images were then compared with pre-acquired “reference” 4D CT images at each position (i.e. phase). Results: The CT image was reconstructed and compared with the reference image, showing a slight mismatch in the transition direction limited by voxel size (slice thickness) in CT image. Due to the rigid nature of the phantom studied, the modeling the displacement of the center of object was sufficient. When deformable tumors are to be modeled, more complex scheme is necessary, which utilize cine EPID and 4D CT images. Conclusion: The new idea of CT image reconstruction was demonstrated. Deformable tumor movements need to be considered in the future.« less

Correlative imaging across microscopy platforms using the fast and accurate relocation of microscopic experimental regions (FARMER) method

NASA Astrophysics Data System (ADS)

Huynh, Toan; Daddysman, Matthew K.; Bao, Ying; Selewa, Alan; Kuznetsov, Andrey; Philipson, Louis H.; Scherer, Norbert F.

2017-05-01

Imaging specific regions of interest (ROIs) of nanomaterials or biological samples with different imaging modalities (e.g., light and electron microscopy) or at subsequent time points (e.g., before and after off-microscope procedures) requires relocating the ROIs. Unfortunately, relocation is typically difficult and very time consuming to achieve. Previously developed techniques involve the fabrication of arrays of features, the procedures for which are complex, and the added features can interfere with imaging the ROIs. We report the Fast and Accurate Relocation of Microscopic Experimental Regions (FARMER) method, which only requires determining the coordinates of 3 (or more) conspicuous reference points (REFs) and employs an algorithm based on geometric operators to relocate ROIs in subsequent imaging sessions. The 3 REFs can be quickly added to various regions of a sample using simple tools (e.g., permanent markers or conductive pens) and do not interfere with the ROIs. The coordinates of the REFs and the ROIs are obtained in the first imaging session (on a particular microscope platform) using an accurate and precise encoded motorized stage. In subsequent imaging sessions, the FARMER algorithm finds the new coordinates of the ROIs (on the same or different platforms), using the coordinates of the manually located REFs and the previously recorded coordinates. FARMER is convenient, fast (3-15 min/session, at least 10-fold faster than manual searches), accurate (4.4 μm average error on a microscope with a 100x objective), and precise (almost all errors are <8 μm), even with deliberate rotating and tilting of the sample well beyond normal repositioning accuracy. We demonstrate this versatility by imaging and re-imaging a diverse set of samples and imaging methods: live mammalian cells at different time points; fixed bacterial cells on two microscopes with different imaging modalities; and nanostructures on optical and electron microscopes. FARMER can be readily adapted to any imaging system with an encoded motorized stage and can facilitate multi-session and multi-platform imaging experiments in biology, materials science, photonics, and nanoscience.

Image2000: A Free, Innovative, Java Based Imaging Package

NASA Technical Reports Server (NTRS)

Pell, Nicholas; Wheeler, Phil; Cornwell, Carl; Matusow, David; Obenschain, Arthur F. (Technical Monitor)

2001-01-01

The National Aeronautics and Space Administration (NASA) Goddard Space Flight Center's (GSFC) Scientific and Educational Endeavors (SEE) and the Center for Image Processing in Education (CIPE) use satellite image processing as part of their science lessons developed for students and educators. The image processing products that they use, as part of these lessons, no longer fulfill the needs of SEE and CIPE because these products are either dependent on a particular computing platform, hard to customize and extend, or do not have enough functionality. SEE and CIPE began looking for what they considered the "perfect" image processing tool that was platform independent, rich in functionality and could easily be extended and customized for their purposes. At the request of SEE, NASA's GSFC, code 588 the Advanced Architectures and Automation Branch developed a powerful new Java based image processing endeavors.

Versatile illumination platform and fast optical switch to give standard observation camera gated active imaging capacity

NASA Astrophysics Data System (ADS)

Grasser, R.; Peyronneaudi, Benjamin; Yon, Kevin; Aubry, Marie

2015-10-01

CILAS, subsidiary of Airbus Defense and Space, develops, manufactures and sales laser-based optronics equipment for defense and homeland security applications. Part of its activity is related to active systems for threat detection, recognition and identification. Active surveillance and active imaging systems are often required to achieve identification capacity in case for long range observation in adverse conditions. In order to ease the deployment of active imaging systems often complex and expensive, CILAS suggests a new concept. It consists on the association of two apparatus working together. On one side, a patented versatile laser platform enables high peak power laser illumination for long range observation. On the other side, a small camera add-on works as a fast optical switch to select photons with specific time of flight only. The association of the versatile illumination platform and the fast optical switch presents itself as an independent body, so called "flash module", giving to virtually any passive observation systems gated active imaging capacity in NIR and SWIR.

A New Instrument for Measurement of the Solar Aureole Radiance Distribution from Unstable Platforms

NASA Technical Reports Server (NTRS)

Ritter, Joseph M.; Voss, Kenneth J.

1999-01-01

A novel imaging solar aureole radiometer, which can obtain absolute radiometric measurements of the solar aureole when operated on an unstable platform is described. A CCD array is used to image the aureole, while a neutral density occulter on a long pole blocks the direct solar radiation. This ensures accurate direction registration as the sun appears in acquired images, and the total circumsolar region is measured simultaneously. The imaging nature of this instrument along with a special triggering device permit acquisition of the circumsolar sky radiance within 7.5 degrees of the center of the solar disk, and within 1 degree of the edge of the solar disk. This innovation makes possible for the first time, reliable and accurate radiometric measurements of the solar aureole from unstable mobile platforms such as ships. This allows determination small angle atmospheric scattering. The instrument has been used in field studies of atmospheric aerosols and will be used in satellite validation and calibration campaigns.

An image processing and analysis tool for identifying and analysing complex plant root systems in 3D soil using non-destructive analysis: Root1.

PubMed

Flavel, Richard J; Guppy, Chris N; Rabbi, Sheikh M R; Young, Iain M

2017-01-01

The objective of this study was to develop a flexible and free image processing and analysis solution, based on the Public Domain ImageJ platform, for the segmentation and analysis of complex biological plant root systems in soil from x-ray tomography 3D images. Contrasting root architectures from wheat, barley and chickpea root systems were grown in soil and scanned using a high resolution micro-tomography system. A macro (Root1) was developed that reliably identified with good to high accuracy complex root systems (10% overestimation for chickpea, 1% underestimation for wheat, 8% underestimation for barley) and provided analysis of root length and angle. In-built flexibility allowed the user interaction to (a) amend any aspect of the macro to account for specific user preferences, and (b) take account of computational limitations of the platform. The platform is free, flexible and accurate in analysing root system metrics.

Unmanned aerial vehicle: A unique platform for low-altitude remote sensing for crop management

USDA-ARS?s Scientific Manuscript database

Unmanned aerial vehicles (UAV) provide a unique platform for remote sensing to monitor crop fields that complements remote sensing from satellite, aircraft and ground-based platforms. The UAV-based remote sensing is versatile at ultra-low altitude to be able to provide an ultra-high-resolution imag...

Development of embedded real-time and high-speed vision platform

NASA Astrophysics Data System (ADS)

Ouyang, Zhenxing; Dong, Yimin; Yang, Hua

2015-12-01

Currently, high-speed vision platforms are widely used in many applications, such as robotics and automation industry. However, a personal computer (PC) whose over-large size is not suitable and applicable in compact systems is an indispensable component for human-computer interaction in traditional high-speed vision platforms. Therefore, this paper develops an embedded real-time and high-speed vision platform, ER-HVP Vision which is able to work completely out of PC. In this new platform, an embedded CPU-based board is designed as substitution for PC and a DSP and FPGA board is developed for implementing image parallel algorithms in FPGA and image sequential algorithms in DSP. Hence, the capability of ER-HVP Vision with size of 320mm x 250mm x 87mm can be presented in more compact condition. Experimental results are also given to indicate that the real-time detection and counting of the moving target at a frame rate of 200 fps at 512 x 512 pixels under the operation of this newly developed vision platform are feasible.

A theoretical-experimental methodology for assessing the sensitivity of biomedical spectral imaging platforms, assays, and analysis methods.

PubMed

Leavesley, Silas J; Sweat, Brenner; Abbott, Caitlyn; Favreau, Peter; Rich, Thomas C

2018-01-01

Spectral imaging technologies have been used for many years by the remote sensing community. More recently, these approaches have been applied to biomedical problems, where they have shown great promise. However, biomedical spectral imaging has been complicated by the high variance of biological data and the reduced ability to construct test scenarios with fixed ground truths. Hence, it has been difficult to objectively assess and compare biomedical spectral imaging assays and technologies. Here, we present a standardized methodology that allows assessment of the performance of biomedical spectral imaging equipment, assays, and analysis algorithms. This methodology incorporates real experimental data and a theoretical sensitivity analysis, preserving the variability present in biomedical image data. We demonstrate that this approach can be applied in several ways: to compare the effectiveness of spectral analysis algorithms, to compare the response of different imaging platforms, and to assess the level of target signature required to achieve a desired performance. Results indicate that it is possible to compare even very different hardware platforms using this methodology. Future applications could include a range of optimization tasks, such as maximizing detection sensitivity or acquisition speed, providing high utility for investigators ranging from design engineers to biomedical scientists. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On abrupt transpression to transtension transition in the South Baikal rift system (Tunka - South Baikal segment)

NASA Astrophysics Data System (ADS)

Sankov, Vladimir; Parfeevets, Anna; Lukhnev, Andrey; Miroshnitchenko, Andrey; Ashurkov, Sergey; Sankov, Alexey; Usynin, Leonid; Eskin, Alexander; Bryzhak, Evgeny

2013-04-01

This work addresses to relation of transpression and extension stress-strain conditions in intracontinental rift system. In our investigation we use a new structural, shallow geophysics, GPS geodetic data and paleostress reconstructions. The surroundings of southern tip of Siberian platform is the region of three Late Cenozoic structures conjugation: sublatitudinal Obruchev fault (OF) controlling the northern boundary of the South Baikal basin, NW trending Main Sayan fault (MSF) as the strike-slip boundary between Siberian platform and East Sayan block and WNW trending eastern segment of Tunka fault (TF) as part of the Tunka basins system northern boundary. A new evidences of superposition of compression and extension fault structures were revealed near the southern extremity of Baikal lake. We've find a very close vicinity of Late Pleistocene - Holocene strike-slip, thrust and normal faulting in the MSF and OF junction zone. The on-land Holocene normal faulting can be considered as secondary fault paragenesis within the main strike-slip zone (Sankov et al., 2009). Active strike-slip, thrust and reverse faulting characterize the MSF and TF junction zone. The transpression conditions are replaced very sharply by transtension and extension ones in eastern direction from zone of structures conjugation - the active normal faulting is dominated within the South Baikal basin. The Bystraya rift basin located in the west shows the tectonic inversion since Middle Pleistocene as a result of the strike-slip movements partitioning between TF and MSF and inset of edition compression stress. The active strike-slip and intrabasin extension conditions are dominated father to the west in Tunka basin. The results of our GPS measurements show the present day convergence and east movements of Khamar-Daban block and eastern Tunka basins relative to Siberian platform along MSF and TF with NE-SW shortening domination. The clear NW-SE divergence across Baikal basin is documented. Holocene and present-day left lateral relative motions of about 3 mm/yr (Sankov et al., 2004) between of Siberian platform and its mounting frame are accommodated along south-eastern segment of MSF. We consider two main factors of sharp transition between transpression and transtension to extension conditions in Tunka-South Baikal segment of Baikal rift system. The first one is the influence of geometry of southern tip of Siberian platform as a first order ancient lithosphere heterogeneity in agreement with (Petit et al., 1996). The second factor is the interaction in this region of two tectonic forces driving the Cenozoic geodynamics. The initial opening of the Tunka and South Baikal basins since Oligocene time as well as father Baikal rift system development caused by long lived asthenosphere flow along NW-SE direction (Sankov et al., 2011). The addition NE-SW compression started during Pliocene (Parfeevets, Sankov, 2006) as the result of the Hindustan and Eurasia convergence. The former caused transpression deformations and clockwise horizontal block rotations along south-western boundary of the platform with their SE movements to the "free space" opened by the divergence of Siberian platform and Transbaikal block (Sankov et al., 2002, 2005).

An FPGA-based heterogeneous image fusion system design method

NASA Astrophysics Data System (ADS)

Song, Le; Lin, Yu-chi; Chen, Yan-hua; Zhao, Mei-rong

2011-08-01

Taking the advantages of FPGA's low cost and compact structure, an FPGA-based heterogeneous image fusion platform is established in this study. Altera's Cyclone IV series FPGA is adopted as the core processor of the platform, and the visible light CCD camera and infrared thermal imager are used as the image-capturing device in order to obtain dualchannel heterogeneous video images. Tailor-made image fusion algorithms such as gray-scale weighted averaging, maximum selection and minimum selection methods are analyzed and compared. VHDL language and the synchronous design method are utilized to perform a reliable RTL-level description. Altera's Quartus II 9.0 software is applied to simulate and implement the algorithm modules. The contrast experiments of various fusion algorithms show that, preferably image quality of the heterogeneous image fusion can be obtained on top of the proposed system. The applied range of the different fusion algorithms is also discussed.

Considering IIOT and security for the DoD

NASA Astrophysics Data System (ADS)

Klawon, Kevin; Gold, Josh; Bachman, Kristen; Landoll, Darren

2016-05-01

The Internet of Things (IoT) has come of age and domestic and industrial devices are all "smart". But how can they be universally classified and queried? How do we know that the underlying architecture is secure enough to deploy on a defense network? By leverage existing platforms designed for interoperability, extensibility, and security that can manage data across multiple domains and runs on any platform.

MMX-I: data-processing software for multimodal X-ray imaging and tomography.

PubMed

Bergamaschi, Antoine; Medjoubi, Kadda; Messaoudi, Cédric; Marco, Sergio; Somogyi, Andrea

2016-05-01

A new multi-platform freeware has been developed for the processing and reconstruction of scanning multi-technique X-ray imaging and tomography datasets. The software platform aims to treat different scanning imaging techniques: X-ray fluorescence, phase, absorption and dark field and any of their combinations, thus providing an easy-to-use data processing tool for the X-ray imaging user community. A dedicated data input stream copes with the input and management of large datasets (several hundred GB) collected during a typical multi-technique fast scan at the Nanoscopium beamline and even on a standard PC. To the authors' knowledge, this is the first software tool that aims at treating all of the modalities of scanning multi-technique imaging and tomography experiments.

A comparative analysis of high-throughput platforms for validation of a circulating microRNA signature in diabetic retinopathy.

PubMed

Farr, Ryan J; Januszewski, Andrzej S; Joglekar, Mugdha V; Liang, Helena; McAulley, Annie K; Hewitt, Alex W; Thomas, Helen E; Loudovaris, Tom; Kay, Thomas W H; Jenkins, Alicia; Hardikar, Anandwardhan A

2015-06-02

MicroRNAs are now increasingly recognized as biomarkers of disease progression. Several quantitative real-time PCR (qPCR) platforms have been developed to determine the relative levels of microRNAs in biological fluids. We systematically compared the detection of cellular and circulating microRNA using a standard 96-well platform, a high-content microfluidics platform and two ultra-high content platforms. We used extensive analytical tools to compute inter- and intra-run variability and concordance measured using fidelity scoring, coefficient of variation and cluster analysis. We carried out unprejudiced next generation sequencing to identify a microRNA signature for Diabetic Retinopathy (DR) and systematically assessed the validation of this signature on clinical samples using each of the above four qPCR platforms. The results indicate that sensitivity to measure low copy number microRNAs is inversely related to qPCR reaction volume and that the choice of platform for microRNA biomarker validation should be made based on the abundance of miRNAs of interest.

The fusion of satellite and UAV data: simulation of high spatial resolution band

NASA Astrophysics Data System (ADS)

Jenerowicz, Agnieszka; Siok, Katarzyna; Woroszkiewicz, Malgorzata; Orych, Agata

2017-10-01

Remote sensing techniques used in the precision agriculture and farming that apply imagery data obtained with sensors mounted on UAV platforms became more popular in the last few years due to the availability of low- cost UAV platforms and low- cost sensors. Data obtained from low altitudes with low- cost sensors can be characterised by high spatial and radiometric resolution but quite low spectral resolution, therefore the application of imagery data obtained with such technology is quite limited and can be used only for the basic land cover classification. To enrich the spectral resolution of imagery data acquired with low- cost sensors from low altitudes, the authors proposed the fusion of RGB data obtained with UAV platform with multispectral satellite imagery. The fusion is based on the pansharpening process, that aims to integrate the spatial details of the high-resolution panchromatic image with the spectral information of lower resolution multispectral or hyperspectral imagery to obtain multispectral or hyperspectral images with high spatial resolution. The key of pansharpening is to properly estimate the missing spatial details of multispectral images while preserving their spectral properties. In the research, the authors presented the fusion of RGB images (with high spatial resolution) obtained with sensors mounted on low- cost UAV platforms and multispectral satellite imagery with satellite sensors, i.e. Landsat 8 OLI. To perform the fusion of UAV data with satellite imagery, the simulation of the panchromatic bands from RGB data based on the spectral channels linear combination, was conducted. Next, for simulated bands and multispectral satellite images, the Gram-Schmidt pansharpening method was applied. As a result of the fusion, the authors obtained several multispectral images with very high spatial resolution and then analysed the spatial and spectral accuracies of processed images.

Preliminary Electrical Designs for CTEX and AFIT Satellite Ground Station

DTIC Science & Technology

2010-03-01

with additional IO High-Speed Piezo Tip/Tilt Platforms S-340 Platform Recommended Models Mirror Aluminum Aluminum S-340.Ax Invar Zerodur glass S-340...developed by RC Optics that uses internal steer- able mirrors that point the optics without slewing the entire instrument. The imaging system is composed of...Determination System Telescope Assembly CTEx Imaging System DCCU Camera Motor/Encoder Assemby FSM & Control Electronics Dwell Mirror w/ 2

A Versatile Phenotyping System and Analytics Platform Reveals Diverse Temporal Responses to Water Availability in Setaria.

PubMed

Fahlgren, Noah; Feldman, Maximilian; Gehan, Malia A; Wilson, Melinda S; Shyu, Christine; Bryant, Douglas W; Hill, Steven T; McEntee, Colton J; Warnasooriya, Sankalpi N; Kumar, Indrajit; Ficor, Tracy; Turnipseed, Stephanie; Gilbert, Kerrigan B; Brutnell, Thomas P; Carrington, James C; Mockler, Todd C; Baxter, Ivan

2015-10-05

Phenotyping has become the rate-limiting step in using large-scale genomic data to understand and improve agricultural crops. Here, the Bellwether Phenotyping Platform for controlled-environment plant growth and automated multimodal phenotyping is described. The system has capacity for 1140 plants, which pass daily through stations to record fluorescence, near-infrared, and visible images. Plant Computer Vision (PlantCV) was developed as open-source, hardware platform-independent software for quantitative image analysis. In a 4-week experiment, wild Setaria viridis and domesticated Setaria italica had fundamentally different temporal responses to water availability. While both lines produced similar levels of biomass under limited water conditions, Setaria viridis maintained the same water-use efficiency under water replete conditions, while Setaria italica shifted to less efficient growth. Overall, the Bellwether Phenotyping Platform and PlantCV software detected significant effects of genotype and environment on height, biomass, water-use efficiency, color, plant architecture, and tissue water status traits. All ∼ 79,000 images acquired during the course of the experiment are publicly available. Copyright © 2015 The Author. Published by Elsevier Inc. All rights reserved.

Molecular Platform for Design and Synthesis of Targeted Dual-Modality Imaging Probes

PubMed Central

2015-01-01

We report a versatile dendritic structure based platform for construction of targeted dual-modality imaging probes. The platform contains multiple copies of 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) branching out from a 1,4,7-triazacyclononane-N,N′,N″-triacetic acid (NOTA) core. The specific coordination chemistries of the NOTA and DOTA moieties offer specific loading of 68/67Ga3+ and Gd3+, respectively, into a common molecular scaffold. The platform also contains three amino groups which can potentiate targeted dual-modality imaging of PET/MRI or SPECT/MRI (PET: positron emission tomography; SPECT: single photon emission computed tomography; MRI: magnetic resonance imaging) when further functionalized by targeting vectors of interest. To validate this design concept, a bimetallic complex was synthesized with six peripheral Gd-DOTA units and one Ga-NOTA core at the center, whose ion T1 relaxivity per gadolinium atom was measured to be 15.99 mM–1 s–1 at 20 MHz. Further, the bimetallic agent demonstrated its anticipated in vivo stability, tissue distribution, and pharmacokinetic profile when labeled with 67Ga. When conjugated with a model targeting peptide sequence, the trivalent construct was able to visualize tumors in a mouse xenograft model by both PET and MRI via a single dose injection. PMID:25615011

Scalable, High-performance 3D Imaging Software Platform: System Architecture and Application to Virtual Colonoscopy

PubMed Central

Yoshida, Hiroyuki; Wu, Yin; Cai, Wenli; Brett, Bevin

2013-01-01

One of the key challenges in three-dimensional (3D) medical imaging is to enable the fast turn-around time, which is often required for interactive or real-time response. This inevitably requires not only high computational power but also high memory bandwidth due to the massive amount of data that need to be processed. In this work, we have developed a software platform that is designed to support high-performance 3D medical image processing for a wide range of applications using increasingly available and affordable commodity computing systems: multi-core, clusters, and cloud computing systems. To achieve scalable, high-performance computing, our platform (1) employs size-adaptive, distributable block volumes as a core data structure for efficient parallelization of a wide range of 3D image processing algorithms; (2) supports task scheduling for efficient load distribution and balancing; and (3) consists of a layered parallel software libraries that allow a wide range of medical applications to share the same functionalities. We evaluated the performance of our platform by applying it to an electronic cleansing system in virtual colonoscopy, with initial experimental results showing a 10 times performance improvement on an 8-core workstation over the original sequential implementation of the system. PMID:23366803

Videoexoscopic real-time intraoperative navigation for spinal neurosurgery: a novel co-adaptation of two existing technology platforms, technical note.

PubMed

Huang, Meng; Barber, Sean Michael; Steele, William James; Boghani, Zain; Desai, Viren Rajendrakumar; Britz, Gavin Wayne; West, George Alexander; Trask, Todd Wilson; Holman, Paul Joseph

2018-06-01

Image-guided approaches to spinal instrumentation and interbody fusion have been widely popularized in the last decade [1-5]. Navigated pedicle screws are significantly less likely to breach [2, 3, 5, 6]. Navigation otherwise remains a point reference tool because the projection is off-axis to the surgeon's inline loupe or microscope view. The Synaptive robotic brightmatter drive videoexoscope monitor system represents a new paradigm for off-axis high-definition (HD) surgical visualization. It has many advantages over the traditional microscope and loupes, which have already been demonstrated in a cadaveric study [7]. An auxiliary, but powerful capability of this system is projection of a second, modifiable image in a split-screen configuration. We hypothesized that integration of both Medtronic and Synaptive platforms could permit the visualization of reconstructed navigation and surgical field images simultaneously. By utilizing navigated instruments, this configuration has the ability to support live image-guided surgery or real-time navigation (RTN). Medtronic O-arm/Stealth S7 navigation, MetRx, NavLock, and SureTrak spinal systems were implemented on a prone cadaveric specimen with a stream output to the Synaptive Display. Surgical visualization was provided using a Storz Image S1 platform and camera mounted to the Synaptive robotic brightmatter drive. We were able to successfully technically co-adapt both platforms. A minimally invasive transforaminal lumbar interbody fusion (MIS TLIF) and an open pedicle subtraction osteotomy (PSO) were performed using a navigated high-speed drill under RTN. Disc Shaver and Trials under RTN were implemented on the MIS TLIF. The synergy of Synaptive HD videoexoscope robotic drive and Medtronic Stealth platforms allow for live image-guided surgery or real-time navigation (RTN). Off-axis projection also allows upright neutral cervical spine operative ergonomics for the surgeons and improved surgical team visualization and education compared to traditional means. This technique has the potential to augment existing minimally invasive and open approaches, but will require long-term outcome measurements for efficacy.

The NifTK software platform for image-guided interventions: platform overview and NiftyLink messaging.

PubMed

Clarkson, Matthew J; Zombori, Gergely; Thompson, Steve; Totz, Johannes; Song, Yi; Espak, Miklos; Johnsen, Stian; Hawkes, David; Ourselin, Sébastien

2015-03-01

To perform research in image-guided interventions, researchers need a wide variety of software components, and assembling these components into a flexible and reliable system can be a challenging task. In this paper, the NifTK software platform is presented. A key focus has been high-performance streaming of stereo laparoscopic video data, ultrasound data and tracking data simultaneously. A new messaging library called NiftyLink is introduced that uses the OpenIGTLink protocol and provides the user with easy-to-use asynchronous two-way messaging, high reliability and comprehensive error reporting. A small suite of applications called NiftyGuide has been developed, containing lightweight applications for grabbing data, currently from position trackers and ultrasound scanners. These applications use NiftyLink to stream data into NiftyIGI, which is a workstation-based application, built on top of MITK, for visualisation and user interaction. Design decisions, performance characteristics and initial applications are described in detail. NiftyLink was tested for latency when transmitting images, tracking data, and interleaved imaging and tracking data. NiftyLink can transmit tracking data at 1,024 frames per second (fps) with latency of 0.31 milliseconds, and 512 KB images with latency of 6.06 milliseconds at 32 fps. NiftyIGI was tested, receiving stereo high-definition laparoscopic video at 30 fps, tracking data from 4 rigid bodies at 20-30 fps and ultrasound data at 20 fps with rendering refresh rates between 2 and 20 Hz with no loss of user interaction. These packages form part of the NifTK platform and have proven to be successful in a variety of image-guided surgery projects. Code and documentation for the NifTK platform are available from http://www.niftk.org . NiftyLink is provided open-source under a BSD license and available from http://github.com/NifTK/NiftyLink . The code for this paper is tagged IJCARS-2014.

Adding XML to the MIS Curriculum: Lessons from the Classroom

ERIC Educational Resources Information Center

Wagner, William P.; Pant, Vik; Hilken, Ralph

2008-01-01

eXtensible Markup Language (XML) is a new technology that is currently being extolled by many industry experts and software vendors. Potentially it represents a platform independent language for sharing information over networks in a way that is much more seamless than with previous technologies. It is extensible in that XML serves as a "meta"…

The Manifesto for Extension and Engagement: A Perspective on Family and Consumer Sciences for the Future

ERIC Educational Resources Information Center

Carroll, Jan B.; Chamberlin, Barbara; Devall, Esther; Dinstel, Roxie; Hauser-Lindstrom, Doreen; Petty, Barbara D.

2017-01-01

Extension professionals in the Western Region proclaimed The Timberline Manifesto at their 100-year celebration, "Centennial on the Summit," at Mount Hood, OR, in 2014. Family and consumer sciences (FCS) leaders relate this platform to the future of FCS: our opportunities for success in engagement, integration, technology, demand-driven…

Satellite Image Classification of Building Damages Using Airborne and Satellite Image Samples in a Deep Learning Approach

NASA Astrophysics Data System (ADS)

Duarte, D.; Nex, F.; Kerle, N.; Vosselman, G.

2018-05-01

The localization and detailed assessment of damaged buildings after a disastrous event is of utmost importance to guide response operations, recovery tasks or for insurance purposes. Several remote sensing platforms and sensors are currently used for the manual detection of building damages. However, there is an overall interest in the use of automated methods to perform this task, regardless of the used platform. Owing to its synoptic coverage and predictable availability, satellite imagery is currently used as input for the identification of building damages by the International Charter, as well as the Copernicus Emergency Management Service for the production of damage grading and reference maps. Recently proposed methods to perform image classification of building damages rely on convolutional neural networks (CNN). These are usually trained with only satellite image samples in a binary classification problem, however the number of samples derived from these images is often limited, affecting the quality of the classification results. The use of up/down-sampling image samples during the training of a CNN, has demonstrated to improve several image recognition tasks in remote sensing. However, it is currently unclear if this multi resolution information can also be captured from images with different spatial resolutions like satellite and airborne imagery (from both manned and unmanned platforms). In this paper, a CNN framework using residual connections and dilated convolutions is used considering both manned and unmanned aerial image samples to perform the satellite image classification of building damages. Three network configurations, trained with multi-resolution image samples are compared against two benchmark networks where only satellite image samples are used. Combining feature maps generated from airborne and satellite image samples, and refining these using only the satellite image samples, improved nearly 4 % the overall satellite image classification of building damages.

An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses

DOE PAGES

Fischer, Curt R.; Ruebel, Oliver; Bowen, Benjamin P.

2015-09-11

Mass spectrometry imaging (MSI) is used in an increasing number of biological applications. Typical MSI datasets contain unique, high-resolution mass spectra from tens of thousands of spatial locations, resulting in raw data sizes of tens of gigabytes per sample. In this paper, we review technical progress that is enabling new biological applications and that is driving an increase in the complexity and size of MSI data. Handling such data often requires specialized computational infrastructure, software, and expertise. OpenMSI, our recently described platform, makes it easy to explore and share MSI datasets via the web – even when larger than 50more » GB. Here we describe the integration of OpenMSI with IPython notebooks for transparent, sharable, and replicable MSI research. An advantage of this approach is that users do not have to share raw data along with analyses; instead, data is retrieved via OpenMSI's web API. The IPython notebook interface provides a low-barrier entry point for data manipulation that is accessible for scientists without extensive computational training. Via these notebooks, analyses can be easily shared without requiring any data movement. We provide example notebooks for several common MSI analysis types including data normalization, plotting, clustering, and classification, and image registration.« less

RAY-UI: A powerful and extensible user interface for RAY

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

Baumgärtel, P., E-mail: peter.baumgaertel@helmholtz-berlin.de; Erko, A.; Schäfers, F.

2016-07-27

The RAY-UI project started as a proof-of-concept for an interactive and graphical user interface (UI) for the well-known ray tracing software RAY [1]. In the meantime, it has evolved into a powerful enhanced version of RAY that will serve as the platform for future development and improvement of associated tools. The software as of today supports nearly all sophisticated simulation features of RAY. Furthermore, it delivers very significant usability and work efficiency improvements. Beamline elements can be quickly added or removed in the interactive sequence view. Parameters of any selected element can be accessed directly and in arbitrary order. Withmore » a single click, parameter changes can be tested and new simulation results can be obtained. All analysis results can be explored interactively right after ray tracing by means of powerful integrated image viewing and graphing tools. Unlimited image planes can be positioned anywhere in the beamline, and bundles of image planes can be created for moving the plane along the beam to identify the focus position with live updates of the simulated results. In addition to showing the features and workflow of RAY-UI, we will give an overview of the underlying software architecture as well as examples for use and an outlook for future developments.« less

A Markov chain model for image ranking system in social networks

NASA Astrophysics Data System (ADS)

Zin, Thi Thi; Tin, Pyke; Toriu, Takashi; Hama, Hiromitsu

2014-03-01

In today world, different kinds of networks such as social, technological, business and etc. exist. All of the networks are similar in terms of distributions, continuously growing and expanding in large scale. Among them, many social networks such as Facebook, Twitter, Flickr and many others provides a powerful abstraction of the structure and dynamics of diverse kinds of inter personal connection and interaction. Generally, the social network contents are created and consumed by the influences of all different social navigation paths that lead to the contents. Therefore, identifying important and user relevant refined structures such as visual information or communities become major factors in modern decision making world. Moreover, the traditional method of information ranking systems cannot be successful due to their lack of taking into account the properties of navigation paths driven by social connections. In this paper, we propose a novel image ranking system in social networks by using the social data relational graphs from social media platform jointly with visual data to improve the relevance between returned images and user intentions (i.e., social relevance). Specifically, we propose a Markov chain based Social-Visual Ranking algorithm by taking social relevance into account. By using some extensive experiments, we demonstrated the significant and effectiveness of the proposed social-visual ranking method.

ProteinShader: illustrative rendering of macromolecules

PubMed Central

Weber, Joseph R

2009-01-01

Background Cartoon-style illustrative renderings of proteins can help clarify structural features that are obscured by space filling or balls and sticks style models, and recent advances in programmable graphics cards offer many new opportunities for improving illustrative renderings. Results The ProteinShader program, a new tool for macromolecular visualization, uses information from Protein Data Bank files to produce illustrative renderings of proteins that approximate what an artist might create by hand using pen and ink. A combination of Hermite and spherical linear interpolation is used to draw smooth, gradually rotating three-dimensional tubes and ribbons with a repeating pattern of texture coordinates, which allows the application of texture mapping, real-time halftoning, and smooth edge lines. This free platform-independent open-source program is written primarily in Java, but also makes extensive use of the OpenGL Shading Language to modify the graphics pipeline. Conclusion By programming to the graphics processor unit, ProteinShader is able to produce high quality images and illustrative rendering effects in real-time. The main feature that distinguishes ProteinShader from other free molecular visualization tools is its use of texture mapping techniques that allow two-dimensional images to be mapped onto the curved three-dimensional surfaces of ribbons and tubes with minimum distortion of the images. PMID:19331660

GOES-12 SXI Operational Calibration

NASA Astrophysics Data System (ADS)

Pizzo, V. J.; Hill, S. M.; Balch, C.

2002-12-01

The prototype Solar X-ray Imager (SXI) was lofted into orbit aboard the NOAA GOES-12 spacecraft on 23 July 2001. The results of pre-launch ground-based optical tests have been combined with an extensive set of imagery taken during the post-launch checkout period from late August through mid December 2001 to establish an operational calibration for the full instrument performance. Although the nickel-coated mirror is a conventional Wolter-I grazing incidence optic, the detector consists of an MCP-enhanced CCD configuration not previously used for direct solar imaging. A full set of calibration data for each optical component (mirror, filters, detector) as well as for net system throughput have been derived and are available on the SXI website (http://sec.noaa.gov/sxi/ScienceUserGuide.html). In addition, a wide variety of information on instrument spatial resolution, point-spread function, dynamic range, photon statistics, and gain dependence (related to voltage settings for the MCP) have been derived. An improved background correction has been developed and applied to the recent release of the post-launch data now publicly available in FITS format. Special instrument topics including issues related to solar pointing and image timing aboard a geo-synchronous platform, CCD blooming properties, detector flat-field effects, and response to SEP events are also detailed.

An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses.

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

Fischer, CR; Ruebel, O; Bowen, BP

Mass spectrometry imaging (MSI) is used in an increasing number of biological applications. Typical MSI datasets contain unique, high-resolution mass spectra from tens of thousands of spatial locations, resulting in raw data sizes of tens of gigabytes per sample. In this paper, we review technical progress that is enabling new biological applications and that is driving an increase in the complexity and size of MSI data. Handling such data often requires specialized computational infrastructure, software, and expertise. OpenMSI, our recently described platform, makes it easy to explore and share MSI datasets via the web - even when larger than 50 GB.more » Here we describe the integration of OpenMSI with IPython notebooks for transparent, sharable, and replicable MSI research. An advantage of this approach is that users do not have to share raw data along with analyses; instead, data is retrieved via OpenMSI's web API. The IPython notebook interface provides a low-barrier entry point for data manipulation that is accessible for scientists without extensive computational training. Via these notebooks, analyses can be easily shared without requiring any data movement. We provide example notebooks for several common MSI analysis types including data normalization, plotting, clustering, and classification, and image registration.« less

An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses

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

Fischer, Curt R.; Ruebel, Oliver; Bowen, Benjamin P.

Mass spectrometry imaging (MSI) is used in an increasing number of biological applications. Typical MSI datasets contain unique, high-resolution mass spectra from tens of thousands of spatial locations, resulting in raw data sizes of tens of gigabytes per sample. In this paper, we review technical progress that is enabling new biological applications and that is driving an increase in the complexity and size of MSI data. Handling such data often requires specialized computational infrastructure, software, and expertise. OpenMSI, our recently described platform, makes it easy to explore and share MSI datasets via the web – even when larger than 50more » GB. Here we describe the integration of OpenMSI with IPython notebooks for transparent, sharable, and replicable MSI research. An advantage of this approach is that users do not have to share raw data along with analyses; instead, data is retrieved via OpenMSI's web API. The IPython notebook interface provides a low-barrier entry point for data manipulation that is accessible for scientists without extensive computational training. Via these notebooks, analyses can be easily shared without requiring any data movement. We provide example notebooks for several common MSI analysis types including data normalization, plotting, clustering, and classification, and image registration.« less

An application framework for computer-aided patient positioning in radiation therapy.

PubMed

Liebler, T; Hub, M; Sanner, C; Schlegel, W

2003-09-01

The importance of exact patient positioning in radiation therapy increases with the ongoing improvements in irradiation planning and treatment. Therefore, new ways to overcome precision limitations of current positioning methods in fractionated treatment have to be found. The Department of Medical Physics at the German Cancer Research Centre (DKFZ) follows different video-based approaches to increase repositioning precision. In this context, the modular software framework FIVE (Fast Integrated Video-based Environment) has been designed and implemented. It is both hardware- and platform-independent and supports merging position data by integrating various computer-aided patient positioning methods. A highly precise optical tracking system and several subtraction imaging techniques have been realized as modules to supply basic video-based repositioning techniques. This paper describes the common framework architecture, the main software modules and their interfaces. An object-oriented software engineering process has been applied using the UML, C + + and the Qt library. The significance of the current framework prototype for the application in patient positioning as well as the extension to further application areas will be discussed. Particularly in experimental research, where special system adjustments are often necessary, the open design of the software allows problem-oriented extensions and adaptations.

[Central online quality assurance in radiology: an IT solution exemplified by the German Breast Cancer Screening Program].

PubMed

Czwoydzinski, J; Girnus, R; Sommer, A; Heindel, W; Lenzen, H

2011-09-01

Physical-technical quality assurance is one of the essential tasks of the National Reference Centers in the German Breast Cancer Screening Program. For this purpose the mammography units are required to transfer the measured values of the constancy tests on a daily basis and all phantom images created for this purpose on a weekly basis to the reference centers. This is a serious logistical challenge. To meet these requirements, we developed an innovative software tool. By the end of 2005, we had already developed web-based software (MammoControl) allowing the transmission of constancy test results via entry forms. For automatic analysis and transmission of the phantom images, we then introduced an extension (MammoControl DIANA). This was based on Java, Java Web Start, the NetBeans Rich Client Platform, the Pixelmed Java DICOM Toolkit and the ImageJ library. MammoControl DIANA was designed to run locally in the mammography units. This allows automated on-site image analysis. Both results and compressed images can then be transmitted to the reference center. We developed analysis modules for the daily and monthly consistency tests and additionally for a homogeneity test. The software we developed facilitates the immediate availability of measurement results, phantom images, and DICOM header data in all reference centers. This allows both targeted guidance and short response time in the case of errors. We achieved a consistent IT-based evaluation with standardized tools for the entire screening program in Germany. © Georg Thieme Verlag KG Stuttgart · New York.

NOTE: MMCTP: a radiotherapy research environment for Monte Carlo and patient-specific treatment planning

NASA Astrophysics Data System (ADS)

Alexander, A.; DeBlois, F.; Stroian, G.; Al-Yahya, K.; Heath, E.; Seuntjens, J.

2007-07-01

Radiotherapy research lacks a flexible computational research environment for Monte Carlo (MC) and patient-specific treatment planning. The purpose of this study was to develop a flexible software package on low-cost hardware with the aim of integrating new patient-specific treatment planning with MC dose calculations suitable for large-scale prospective and retrospective treatment planning studies. We designed the software package 'McGill Monte Carlo treatment planning' (MMCTP) for the research development of MC and patient-specific treatment planning. The MMCTP design consists of a graphical user interface (GUI), which runs on a simple workstation connected through standard secure-shell protocol to a cluster for lengthy MC calculations. Treatment planning information (e.g., images, structures, beam geometry properties and dose distributions) is converted into a convenient MMCTP local file storage format designated, the McGill RT format. MMCTP features include (a) DICOM_RT, RTOG and CADPlan CART format imports; (b) 2D and 3D visualization views for images, structure contours, and dose distributions; (c) contouring tools; (d) DVH analysis, and dose matrix comparison tools; (e) external beam editing; (f) MC transport calculation from beam source to patient geometry for photon and electron beams. The MC input files, which are prepared from the beam geometry properties and patient information (e.g., images and structure contours), are uploaded and run on a cluster using shell commands controlled from the MMCTP GUI. The visualization, dose matrix operation and DVH tools offer extensive options for plan analysis and comparison between MC plans and plans imported from commercial treatment planning systems. The MMCTP GUI provides a flexible research platform for the development of patient-specific MC treatment planning for photon and electron external beam radiation therapy. The impact of this tool lies in the fact that it allows for systematic, platform-independent, large-scale MC treatment planning for different treatment sites. Patient recalculations were performed to validate the software and ensure proper functionality.

Digital image analysis of Ki67 proliferation index in breast cancer using virtual dual staining on whole tissue sections: clinical validation and inter-platform agreement.

PubMed

Koopman, Timco; Buikema, Henk J; Hollema, Harry; de Bock, Geertruida H; van der Vegt, Bert

2018-05-01

The Ki67 proliferation index is a prognostic and predictive marker in breast cancer. Manual scoring is prone to inter- and intra-observer variability. The aims of this study were to clinically validate digital image analysis (DIA) of Ki67 using virtual dual staining (VDS) on whole tissue sections and to assess inter-platform agreement between two independent DIA platforms. Serial whole tissue sections of 154 consecutive invasive breast carcinomas were stained for Ki67 and cytokeratin 8/18 with immunohistochemistry in a clinical setting. Ki67 proliferation index was determined using two independent DIA platforms, implementing VDS to identify tumor tissue. Manual Ki67 score was determined using a standardized manual counting protocol. Inter-observer agreement between manual and DIA scores and inter-platform agreement between both DIA platforms were determined and calculated using Spearman's correlation coefficients. Correlations and agreement were assessed with scatterplots and Bland-Altman plots. Spearman's correlation coefficients were 0.94 (p < 0.001) for inter-observer agreement between manual counting and platform A, 0.93 (p < 0.001) between manual counting and platform B, and 0.96 (p < 0.001) for inter-platform agreement. Scatterplots and Bland-Altman plots revealed no skewness within specific data ranges. In the few cases with ≥ 10% difference between manual counting and DIA, results by both platforms were similar. DIA using VDS is an accurate method to determine the Ki67 proliferation index in breast cancer, as an alternative to manual scoring of whole sections in clinical practice. Inter-platform agreement between two different DIA platforms was excellent, suggesting vendor-independent clinical implementability.

HoloGondel: in situ cloud observations on a cable car in the Swiss Alps using a holographic imager

NASA Astrophysics Data System (ADS)

Beck, Alexander; Henneberger, Jan; Schöpfer, Sarah; Fugal, Jacob; Lohmann, Ulrike

2017-02-01

In situ observations of cloud properties in complex alpine terrain where research aircraft cannot sample are commonly conducted at mountain-top research stations and limited to single-point measurements. The HoloGondel platform overcomes this limitation by using a cable car to obtain vertical profiles of the microphysical and meteorological cloud parameters. The main component of the HoloGondel platform is the HOLographic Imager for Microscopic Objects (HOLIMO 3G), which uses digital in-line holography to image cloud particles. Based on two-dimensional images the microphysical cloud parameters for the size range from small cloud particles to large precipitation particles are obtained for the liquid and ice phase. The low traveling velocity of a cable car on the order of 10 m s-1 allows measurements with high spatial resolution; however, at the same time it leads to an unstable air speed towards the HoloGondel platform. Holographic cloud imagers, which have a sample volume that is independent of the air speed, are therefore well suited for measurements on a cable car. Example measurements of the vertical profiles observed in a liquid cloud and a mixed-phase cloud at the Eggishorn in the Swiss Alps in the winters 2015 and 2016 are presented. The HoloGondel platform reliably observes cloud droplets larger than 6.5 µm, partitions between cloud droplets and ice crystals for a size larger than 25 µm and obtains a statistically significantly size distribution for every 5 m in vertical ascent.

Constrained VPH+: a local path planning algorithm for a bio-inspired crawling robot with customized ultrasonic scanning sensor.

PubMed

Rao, Akshay; Elara, Mohan Rajesh; Elangovan, Karthikeyan

This paper aims to develop a local path planning algorithm for a bio-inspired, reconfigurable crawling robot. A detailed description of the robotic platform is first provided, and the suitability for deployment of each of the current state-of-the-art local path planners is analyzed after an extensive literature review. The Enhanced Vector Polar Histogram algorithm is described and reformulated to better fit the requirements of the platform. The algorithm is deployed on the robotic platform in crawling configuration and favorably compared with other state-of-the-art local path planning algorithms.

LOOS: an extensible platform for the structural analysis of simulations.

PubMed

Romo, Tod D; Grossfield, Alan

2009-01-01

We have developed LOOS (Lightweight Object-Oriented Structure-analysis library) as an object-oriented library designed to facilitate the rapid development of tools for the structural analysis of simulations. LOOS supports the native file formats of most common simulation packages including AMBER, CHARMM, CNS, Gromacs, NAMD, Tinker, and X-PLOR. Encapsulation and polymorphism are used to simultaneously provide a stable interface to the programmer and make LOOS easily extensible. A rich atom selection language based on the C expression syntax is included as part of the library. LOOS enables students and casual programmer-scientists to rapidly write their own analytical tools in a compact and expressive manner resembling scripting. LOOS is written in C++ and makes extensive use of the Standard Template Library and Boost, and is freely available under the GNU General Public License (version 3) LOOS has been tested on Linux and MacOS X, but is written to be portable and should work on most Unix-based platforms.

Gulf of Mexico

Atmospheric Science Data Center

2014-05-15

article title:  Unique Views of Gulf Oil Slick     View Larger Image ... image. The red symbol indicates the former location of the drilling platform. The image dimensions are 346 by 258 kilometers (215 by 160 ...

A Microfluidic Platform for Correlative Live-Cell and Super-Resolution Microscopy

PubMed Central

Tam, Johnny; Cordier, Guillaume Alan; Bálint, Štefan; Sandoval Álvarez, Ángel; Borbely, Joseph Steven; Lakadamyali, Melike

2014-01-01

Recently, super-resolution microscopy methods such as stochastic optical reconstruction microscopy (STORM) have enabled visualization of subcellular structures below the optical resolution limit. Due to the poor temporal resolution, however, these methods have mostly been used to image fixed cells or dynamic processes that evolve on slow time-scales. In particular, fast dynamic processes and their relationship to the underlying ultrastructure or nanoscale protein organization cannot be discerned. To overcome this limitation, we have recently developed a correlative and sequential imaging method that combines live-cell and super-resolution microscopy. This approach adds dynamic background to ultrastructural images providing a new dimension to the interpretation of super-resolution data. However, currently, it suffers from the need to carry out tedious steps of sample preparation manually. To alleviate this problem, we implemented a simple and versatile microfluidic platform that streamlines the sample preparation steps in between live-cell and super-resolution imaging. The platform is based on a microfluidic chip with parallel, miniaturized imaging chambers and an automated fluid-injection device, which delivers a precise amount of a specified reagent to the selected imaging chamber at a specific time within the experiment. We demonstrate that this system can be used for live-cell imaging, automated fixation, and immunostaining of adherent mammalian cells in situ followed by STORM imaging. We further demonstrate an application by correlating mitochondrial dynamics, morphology, and nanoscale mitochondrial protein distribution in live and super-resolution images. PMID:25545548

A cloud-based multimodality case file for mobile devices.

PubMed

Balkman, Jason D; Loehfelm, Thomas W

2014-01-01

Recent improvements in Web and mobile technology, along with the widespread use of handheld devices in radiology education, provide unique opportunities for creating scalable, universally accessible, portable image-rich radiology case files. A cloud database and a Web-based application for radiologic images were developed to create a mobile case file with reasonable usability, download performance, and image quality for teaching purposes. A total of 75 radiology cases related to breast, thoracic, gastrointestinal, musculoskeletal, and neuroimaging subspecialties were included in the database. Breast imaging cases are the focus of this article, as they best demonstrate handheld display capabilities across a wide variety of modalities. This case subset also illustrates methods for adapting radiologic content to cloud platforms and mobile devices. Readers will gain practical knowledge about storage and retrieval of cloud-based imaging data, an awareness of techniques used to adapt scrollable and high-resolution imaging content for the Web, and an appreciation for optimizing images for handheld devices. The evaluation of this software demonstrates the feasibility of adapting images from most imaging modalities to mobile devices, even in cases of full-field digital mammograms, where high resolution is required to represent subtle pathologic features. The cloud platform allows cases to be added and modified in real time by using only a standard Web browser with no application-specific software. Challenges remain in developing efficient ways to generate, modify, and upload radiologic and supplementary teaching content to this cloud-based platform. Online supplemental material is available for this article. ©RSNA, 2014.

High resolution computational on-chip imaging of biological samples using sparsity constraint (Conference Presentation)

NASA Astrophysics Data System (ADS)

Rivenson, Yair; Wu, Chris; Wang, Hongda; Zhang, Yibo; Ozcan, Aydogan

2017-03-01

Microscopic imaging of biological samples such as pathology slides is one of the standard diagnostic methods for screening various diseases, including cancer. These biological samples are usually imaged using traditional optical microscopy tools; however, the high cost, bulkiness and limited imaging throughput of traditional microscopes partially restrict their deployment in resource-limited settings. In order to mitigate this, we previously demonstrated a cost-effective and compact lens-less on-chip microscopy platform with a wide field-of-view of >20-30 mm^2. The lens-less microscopy platform has shown its effectiveness for imaging of highly connected biological samples, such as pathology slides of various tissue samples and smears, among others. This computational holographic microscope requires a set of super-resolved holograms acquired at multiple sample-to-sensor distances, which are used as input to an iterative phase recovery algorithm and holographic reconstruction process, yielding high-resolution images of the samples in phase and amplitude channels. Here we demonstrate that in order to reconstruct clinically relevant images with high resolution and image contrast, we require less than 50% of the previously reported nominal number of holograms acquired at different sample-to-sensor distances. This is achieved by incorporating a loose sparsity constraint as part of the iterative holographic object reconstruction. We demonstrate the success of this sparsity-based computational lens-less microscopy platform by imaging pathology slides of breast cancer tissue and Papanicolaou (Pap) smears.

Design Analysis of a Space Based Chromotomographic Hyperspectral Imaging Experiment

DTIC Science & Technology

2010-03-01

Tilt Platforms S-340 Platform Recommended Models Mirror Aluminum Aluminum S-340.Ax Invar Zerodur glass S-340.ix Titanium BK7 glass S-340.Tx Steel S-340...composed of a telescope, two grating spectrometers, calibration lamps, and focal plane electronics and cooling system. The telescope is a three mirror ...advanced hyperspectral imager for coastal bathymetry is that the experiment will closely mirror that of the proposed space-based chromotomographic hy

Platform for Automated Real-Time High Performance Analytics on Medical Image Data.

PubMed

Allen, William J; Gabr, Refaat E; Tefera, Getaneh B; Pednekar, Amol S; Vaughn, Matthew W; Narayana, Ponnada A

2018-03-01

Biomedical data are quickly growing in volume and in variety, providing clinicians an opportunity for better clinical decision support. Here, we demonstrate a robust platform that uses software automation and high performance computing (HPC) resources to achieve real-time analytics of clinical data, specifically magnetic resonance imaging (MRI) data. We used the Agave application programming interface to facilitate communication, data transfer, and job control between an MRI scanner and an off-site HPC resource. In this use case, Agave executed the graphical pipeline tool GRAphical Pipeline Environment (GRAPE) to perform automated, real-time, quantitative analysis of MRI scans. Same-session image processing will open the door for adaptive scanning and real-time quality control, potentially accelerating the discovery of pathologies and minimizing patient callbacks. We envision this platform can be adapted to other medical instruments, HPC resources, and analytics tools.

Data integration: Combined imaging and electrophysiology data in the cloud.

PubMed

Kini, Lohith G; Davis, Kathryn A; Wagenaar, Joost B

2016-01-01

There has been an increasing effort to correlate electrophysiology data with imaging in patients with refractory epilepsy over recent years. IEEG.org provides a free-access, rapidly growing archive of imaging data combined with electrophysiology data and patient metadata. It currently contains over 1200 human and animal datasets, with multiple data modalities associated with each dataset (neuroimaging, EEG, EKG, de-identified clinical and experimental data, etc.). The platform is developed around the concept that scientific data sharing requires a flexible platform that allows sharing of data from multiple file formats. IEEG.org provides high- and low-level access to the data in addition to providing an environment in which domain experts can find, visualize, and analyze data in an intuitive manner. Here, we present a summary of the current infrastructure of the platform, available datasets and goals for the near future. Copyright © 2015 Elsevier Inc. All rights reserved.

Data integration: Combined Imaging and Electrophysiology data in the cloud

PubMed Central

Kini, Lohith G.; Davis, Kathryn A.; Wagenaar, Joost B.

2015-01-01

There has been an increasing effort to correlate electrophysiology data with imaging in patients with refractory epilepsy over recent years. IEEG.org provides a free-access, rapidly growing archive of imaging data combined with electrophysiology data and patient metadata. It currently contains over 1200 human and animal datasets, with multiple data modalities associated with each dataset (neuroimaging, EEG, EKG, de-identified clinical and experimental data, etc.). The platform is developed around the concept that scientific data sharing requires a flexible platform that allows sharing of data from multiple file-formats. IEEG.org provides high and low-level access to the data in addition to providing an environment in which domain experts can find, visualize, and analyze data in an intuitive manner. Here, we present a summary of the current infrastructure of the platform, available datasets and goals for the near future. PMID:26044858

Gyrocopter-Based Remote Sensing Platform

NASA Astrophysics Data System (ADS)

Weber, I.; Jenal, A.; Kneer, C.; Bongartz, J.

2015-04-01

In this paper the development of a lightweight and highly modularized airborne sensor platform for remote sensing applications utilizing a gyrocopter as a carrier platform is described. The current sensor configuration consists of a high resolution DSLR camera for VIS-RGB recordings. As a second sensor modality, a snapshot hyperspectral camera was integrated in the aircraft. Moreover a custom-developed thermal imaging system composed of a VIS-PAN camera and a LWIR-camera is used for aerial recordings in the thermal infrared range. Furthermore another custom-developed highly flexible imaging system for high resolution multispectral image acquisition with up to six spectral bands in the VIS-NIR range is presented. The performance of the overall system was tested during several flights with all sensor modalities and the precalculated demands with respect to spatial resolution and reliability were validated. The collected data sets were georeferenced, georectified, orthorectified and then stitched to mosaics.

Using dynamic interferometric synthetic aperature radar (InSAR) to image fast-moving surface waves

DOEpatents

Vincent, Paul

2005-06-28

A new differential technique and system for imaging dynamic (fast moving) surface waves using Dynamic Interferometric Synthetic Aperture Radar (InSAR) is introduced. This differential technique and system can sample the fast-moving surface displacement waves from a plurality of moving platform positions in either a repeat-pass single-antenna or a single-pass mode having a single-antenna dual-phase receiver or having dual physically separate antennas, and reconstruct a plurality of phase differentials from a plurality of platform positions to produce a series of desired interferometric images of the fast moving waves.

The Science of a Sundae: Using the Principle of Colligative Properties in Food Science Outreach Activities for Middle and High School Students

ERIC Educational Resources Information Center

Wickware, Carmen L.; Day, Charles T.C.; Adams, Michael; Orta-Ramirez, Alicia; Snyder, Abigail B.

2017-01-01

The opportunities for outreach activities for professionals and academics in food science are extensive, as too are the range of participants' experience levels and platforms for delivery. Here, we present a set of activities that are readily adaptable for a range of students (ages 10 to 18) in multiple platforms (demonstration table and hands-on…

Extending IPsec for Efficient Remote Attestation

NASA Astrophysics Data System (ADS)

Sadeghi, Ahmad-Reza; Schulz, Steffen

When establishing a VPN to connect different sites of a network, the integrity of the involved VPN endpoints is often a major security concern. Based on the Trusted Platform Module (TPM), available in many computing platforms today, remote attestation mechanisms can be used to evaluate the internal state of remote endpoints automatically. However, existing protocols and extensions are either unsuited for use with IPsec or impose considerable additional implementation complexity and protocol overhead.

P-TRAP: a Panicle TRAit Phenotyping tool.

PubMed

A L-Tam, Faroq; Adam, Helene; Anjos, António dos; Lorieux, Mathias; Larmande, Pierre; Ghesquière, Alain; Jouannic, Stefan; Shahbazkia, Hamid Reza

2013-08-29

In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user-friendly environment for experiments. The experimental results showed very good accuracy compared to field operator, expert verification and well-known academic methods.

P-TRAP: a Panicle Trait Phenotyping tool

PubMed Central

2013-01-01

Background In crops, inflorescence complexity and the shape and size of the seed are among the most important characters that influence yield. For example, rice panicles vary considerably in the number and order of branches, elongation of the axis, and the shape and size of the seed. Manual low-throughput phenotyping methods are time consuming, and the results are unreliable. However, high-throughput image analysis of the qualitative and quantitative traits of rice panicles is essential for understanding the diversity of the panicle as well as for breeding programs. Results This paper presents P-TRAP software (Panicle TRAit Phenotyping), a free open source application for high-throughput measurements of panicle architecture and seed-related traits. The software is written in Java and can be used with different platforms (the user-friendly Graphical User Interface (GUI) uses Netbeans Platform 7.3). The application offers three main tools: a tool for the analysis of panicle structure, a spikelet/grain counting tool, and a tool for the analysis of seed shape. The three tools can be used independently or simultaneously for analysis of the same image. Results are then reported in the Extensible Markup Language (XML) and Comma Separated Values (CSV) file formats. Images of rice panicles were used to evaluate the efficiency and robustness of the software. Compared to data obtained by manual processing, P-TRAP produced reliable results in a much shorter time. In addition, manual processing is not repeatable because dry panicles are vulnerable to damage. The software is very useful, practical and collects much more data than human operators. Conclusions P-TRAP is a new open source software that automatically recognizes the structure of a panicle and the seeds on the panicle in numeric images. The software processes and quantifies several traits related to panicle structure, detects and counts the grains, and measures their shape parameters. In short, P-TRAP offers both efficient results and a user-friendly environment for experiments. The experimental results showed very good accuracy compared to field operator, expert verification and well-known academic methods. PMID:23987653

The Effect of Lithospheric Discontinuities on the Composition of Lavas From the Northern Galápagos Platform Extension

NASA Astrophysics Data System (ADS)

Schlitzer, W.; Harpp, K. S.; Mittelstaedt, E. L.; Kurz, M. D.; Geist, D.

2011-12-01

The platform supporting the Galápagos Archipelago extends ~50 km NW toward the Galápagos Spreading Center (GSC) into the Northern Galapagos Volcanic Province (NGVP), where it underlies Pinta, Marchena, and Genovesa Islands. Approximately 45 km north of Pinta is the southern termination of a ~100-km long transform fault, at 90o50'W. The seafloor surrounding the NGVP was surveyed and dredged during the 2010 MV1007 and 2001 DRIFT04 cruises. All the large volcanoes, including the islands, have elongate bathymetric footprints with extensive submarine ridges. Lavas from this small region (<150 km in diameter) exhibit isotopic and trace element signatures that span the compositional range of the entire Galápagos Archipelago. Pinta and its submarine extension have the most enriched signatures, whereas at the eastern end of the platform extension, Genovesa is indistinguishable from normal MORB. Samples dredged around Pinta and Marchena have intermediate compositions. In contrast, lavas from the adjacent transform fault are more depleted than those from Genovesa and anywhere along the GSC for hundreds of km in both directions. Lavas from this region exhibit a range of 3He/4He (6.5-9.5 Ra), significantly lower than the high 3He/4He signature of material erupted by the plume-rich western Galápagos shield volcanoes (>25 Ra). Whereas the compositions of lavas erupted on the Nazca Plate in the NGVP require 3 or more distinct mantle endmembers to explain their compositions, our data indicate that the platform extension region only requires components previously described for the Galápagos Islands. In addition, Sm/Yb decreases abruptly along an E-W transect from Pinta to Genovesa. Gibson and Geist (2010) concluded that Sm/Yb ratios reflect variations in surface wave velocities (Villagomez et al., 2007), enabling them to predict lithospheric thickness. We apply the relationship defined by Gibson and Geist to map lithospheric thickness across our study area. Our results suggest that the lithosphere (and thus minimum melt generation depth) gets progressively shallower from Pinta to Genovesa; this phenomenon may explain unexpected Holocene volcanism in the NGVP. The wide range in Sm/Yb further suggests a complex lithospheric structure underlying the platform extension, which we propose reflects formation of the adjacent GSC transform fault within the last ~3 Ma, possibly through a series of ridge jumps as suggested by modeling of new magnetic data. We propose a model in which heterogeneous plume material with enriched and depleted components (Ito and Mahoney, 2005) is migrating toward the GSC along the base of the lithosphere, having previously lost its primordial helium signature during deep melting near the western shield volcanoes. As the material crosses the complex lithospheric thickness variations in the NGVP, melt generation becomes progressively shallower. The enriched compositions at Pinta thus result from limited, deep melting of enriched compositions owing to a thick lithospheric cap. East of Pinta, the plume melts more extensively and to shallower depths, producing progressively depleted signatures toward Genovesa.

Ultrasound estimates of muscle quality in older adults: reliability and comparison of Photoshop and ImageJ for the grayscale analysis of muscle echogenicity

PubMed Central

Seamon, Bryant A.; Teixeira, Carla; Ismail, Catheeja

2016-01-01

Background. Quantitative diagnostic ultrasound imaging has been proposed as a method of estimating muscle quality using measures of echogenicity. The Rectangular Marquee Tool (RMT) and the Free Hand Tool (FHT) are two types of editing features used in Photoshop and ImageJ for determining a region of interest (ROI) within an ultrasound image. The primary objective of this study is to determine the intrarater and interrater reliability of Photoshop and ImageJ for the estimate of muscle tissue echogenicity in older adults via grayscale histogram analysis. The secondary objective is to compare the mean grayscale values obtained using both the RMT and FHT methods across both image analysis platforms. Methods. This cross-sectional observational study features 18 community-dwelling men (age = 61.5 ± 2.32 years). Longitudinal views of the rectus femoris were captured using B-mode ultrasound. The ROI for each scan was selected by 2 examiners using the RMT and FHT methods from each software program. Their reliability is assessed using intraclass correlation coefficients (ICCs) and the standard error of the measurement (SEM). Measurement agreement for these values is depicted using Bland-Altman plots. A paired t-test is used to determine mean differences in echogenicity expressed as grayscale values using the RMT and FHT methods to select the post-image acquisition ROI. The degree of association among ROI selection methods and image analysis platforms is analyzed using the coefficient of determination (R2). Results. The raters demonstrated excellent intrarater and interrater reliability using the RMT and FHT methods across both platforms (lower bound 95% CI ICC = .97–.99, p < .001). Mean differences between the echogenicity estimates obtained with the RMT and FHT methods was .87 grayscale levels (95% CI [.54–1.21], p < .0001) using data obtained with both programs. The SEM for Photoshop was .97 and 1.05 grayscale levels when using the RMT and FHT ROI selection methods, respectively. Comparatively, the SEM values were .72 and .81 grayscale levels, respectively, when using the RMT and FHT ROI selection methods in ImageJ. Uniform coefficients of determination (R2 = .96–.99, p < .001) indicate strong positive associations among the grayscale histogram analysis measurement conditions independent of the ROI selection methods and imaging platform. Conclusion. Our method for evaluating muscle echogenicity demonstrated a high degree of intrarater and interrater reliability using both the RMT and FHT methods across 2 common image analysis platforms. The minimal measurement error exhibited by the examiners demonstrates that the ROI selection methods used with Photoshop and ImageJ are suitable for the post-acquisition image analysis of tissue echogenicity in older adults. PMID:26925339

Simple platform for chronic imaging of hippocampal activity during spontaneous behaviour in an awake mouse

PubMed Central

Villette, Vincent; Levesque, Mathieu; Miled, Amine; Gosselin, Benoit; Topolnik, Lisa

2017-01-01

Chronic electrophysiological recordings of neuronal activity combined with two-photon Ca2+ imaging give access to high resolution and cellular specificity. In addition, awake drug-free experimentation is required for investigating the physiological mechanisms that operate in the brain. Here, we developed a simple head fixation platform, which allows simultaneous chronic imaging and electrophysiological recordings to be obtained from the hippocampus of awake mice. We performed quantitative analyses of spontaneous animal behaviour, the associated network states and the cellular activities in the dorsal hippocampus as well as estimated the brain stability limits to image dendritic processes and individual axonal boutons. Ca2+ imaging recordings revealed a relatively stereotyped hippocampal activity despite a high inter-animal and inter-day variability in the mouse behavior. In addition to quiet state and locomotion behavioural patterns, the platform allowed the reliable detection of walking steps and fine speed variations. The brain motion during locomotion was limited to ~1.8 μm, thus allowing for imaging of small sub-cellular structures to be performed in parallel with recordings of network and behavioural states. This simple device extends the drug-free experimentation in vivo, enabling high-stability optophysiological experiments with single-bouton resolution in the mouse awake brain. PMID:28240275

Iron oxide core oil-in-water emulsions as a multifunctional nanoparticle platform for tumor targeting and imaging

PubMed Central

Jarzyna, Peter A.; Skajaa, Torjus; Gianella, Anita; Cormode, David P.; Samber, Dan D.; Dickson, Stephen D.; Chen, Wei; Griffioen, Arjan W.; Fayad, Zahi A.; Mulder, Willem J. M.

2009-01-01

Nanoemulsions are increasingly investigated for the delivery of hydrophobic drugs to improve their bioavailability or make their administration possible. In the current study, oil-in-water emulsions with three different mean diameters (30, 60, and 95 nm) were developed as a new multimodality nanoparticle platform for tumor targeting and imaging. To that aim, hydrophobically coated iron oxide particles were included in the soybean oil core of the nanoemulsions to enable their detection with magnetic resonance imaging (MRI), while the conjugation of a near infrared fluorophore allowed optical imaging. The accumulation of this novel nanocomposite in subcutaneous human tumors in nude mice was demonstrated with MRI and fluorescence imaging in vivo, and with Perl’s staining of histological tumor sections ex vivo. PMID:19783295

MMX-I: data-processing software for multimodal X-ray imaging and tomography

PubMed Central

Bergamaschi, Antoine; Medjoubi, Kadda; Messaoudi, Cédric; Marco, Sergio; Somogyi, Andrea

2016-01-01

A new multi-platform freeware has been developed for the processing and reconstruction of scanning multi-technique X-ray imaging and tomography datasets. The software platform aims to treat different scanning imaging techniques: X-ray fluorescence, phase, absorption and dark field and any of their combinations, thus providing an easy-to-use data processing tool for the X-ray imaging user community. A dedicated data input stream copes with the input and management of large datasets (several hundred GB) collected during a typical multi-technique fast scan at the Nanoscopium beamline and even on a standard PC. To the authors’ knowledge, this is the first software tool that aims at treating all of the modalities of scanning multi-technique imaging and tomography experiments. PMID:27140159

A Control System and Streaming DAQ Platform with Image-Based Trigger for X-ray Imaging

NASA Astrophysics Data System (ADS)

Stevanovic, Uros; Caselle, Michele; Cecilia, Angelica; Chilingaryan, Suren; Farago, Tomas; Gasilov, Sergey; Herth, Armin; Kopmann, Andreas; Vogelgesang, Matthias; Balzer, Matthias; Baumbach, Tilo; Weber, Marc

2015-06-01

High-speed X-ray imaging applications play a crucial role for non-destructive investigations of the dynamics in material science and biology. On-line data analysis is necessary for quality assurance and data-driven feedback, leading to a more efficient use of a beam time and increased data quality. In this article we present a smart camera platform with embedded Field Programmable Gate Array (FPGA) processing that is able to stream and process data continuously in real-time. The setup consists of a Complementary Metal-Oxide-Semiconductor (CMOS) sensor, an FPGA readout card, and a readout computer. It is seamlessly integrated in a new custom experiment control system called Concert that provides a more efficient way of operating a beamline by integrating device control, experiment process control, and data analysis. The potential of the embedded processing is demonstrated by implementing an image-based trigger. It records the temporal evolution of physical events with increased speed while maintaining the full field of view. The complete data acquisition system, with Concert and the smart camera platform was successfully integrated and used for fast X-ray imaging experiments at KIT's synchrotron radiation facility ANKA.

Feature-aided multiple target tracking in the image plane

NASA Astrophysics Data System (ADS)

Brown, Andrew P.; Sullivan, Kevin J.; Miller, David J.

2006-05-01

Vast quantities of EO and IR data are collected on airborne platforms (manned and unmanned) and terrestrial platforms (including fixed installations, e.g., at street intersections), and can be exploited to aid in the global war on terrorism. However, intelligent preprocessing is required to enable operator efficiency and to provide commanders with actionable target information. To this end, we have developed an image plane tracker which automatically detects and tracks multiple targets in image sequences using both motion and feature information. The effects of platform and camera motion are compensated via image registration, and a novel change detection algorithm is applied for accurate moving target detection. The contiguous pixel blob on each moving target is segmented for use in target feature extraction and model learning. Feature-based target location measurements are used for tracking through move-stop-move maneuvers, close target spacing, and occlusion. Effective clutter suppression is achieved using joint probabilistic data association (JPDA), and confirmed target tracks are indicated for further processing or operator review. In this paper we describe the algorithms implemented in the image plane tracker and present performance results obtained with video clips from the DARPA VIVID program data collection and from a miniature unmanned aerial vehicle (UAV) flight.

An overview on development and application of an experimental platform for quantitative cardiac imaging research in rabbit models of myocardial infarction

PubMed Central

Feng, Yuanbo; Bogaert, Jan; Oyen, Raymond

2014-01-01

To exploit the advantages of using rabbits for cardiac imaging research and to tackle the technical obstacles, efforts have been made under the framework of a doctoral research program. In this overview article, by cross-referencing the current literature, we summarize how we have developed a preclinical cardiac research platform based on modified models of reperfused myocardial infarction (MI) in rabbits; how the in vivo manifestations of cardiac imaging could be closely matched with those ex vivo macro- and microscopic findings; how these imaging outcomes could be quantitatively analyzed, validated and demonstrated; and how we could apply this cardiac imaging platform to provide possible solutions to certain lingering diagnostic and therapeutic problems in experimental cardiology. In particular, tissue components in acute cardiac ischemia have been stratified and characterized, post-infarct lipomatous metaplasia (LM) as a common but hardly illuminated clinical pathology has been identified in rabbit models, and a necrosis avid tracer as well as an anti-ischemic drug have been successfully assessed for their potential utilities in clinical cardiology. These outcomes may interest the researchers in the related fields and help strengthen translational research in cardiovascular diseases. PMID:25392822

An overview on development and application of an experimental platform for quantitative cardiac imaging research in rabbit models of myocardial infarction.

PubMed

Feng, Yuanbo; Bogaert, Jan; Oyen, Raymond; Ni, Yicheng

2014-10-01

To exploit the advantages of using rabbits for cardiac imaging research and to tackle the technical obstacles, efforts have been made under the framework of a doctoral research program. In this overview article, by cross-referencing the current literature, we summarize how we have developed a preclinical cardiac research platform based on modified models of reperfused myocardial infarction (MI) in rabbits; how the in vivo manifestations of cardiac imaging could be closely matched with those ex vivo macro- and microscopic findings; how these imaging outcomes could be quantitatively analyzed, validated and demonstrated; and how we could apply this cardiac imaging platform to provide possible solutions to certain lingering diagnostic and therapeutic problems in experimental cardiology. In particular, tissue components in acute cardiac ischemia have been stratified and characterized, post-infarct lipomatous metaplasia (LM) as a common but hardly illuminated clinical pathology has been identified in rabbit models, and a necrosis avid tracer as well as an anti-ischemic drug have been successfully assessed for their potential utilities in clinical cardiology. These outcomes may interest the researchers in the related fields and help strengthen translational research in cardiovascular diseases.

Development of a carbonate platform with potential for large discoveries - an example from Vietnam

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

Mayall, M.; Bent, A.; Dale, B.

1996-01-01

In offshore central and southern Vietnam a number of carbonate accumulations can be recognized. Platform carbonates form basin-wide units of carbonate characterized by strong, continuous parallel seismic reflectors. Facies are dominated by bioclastic wackestones with poor-moderate reservoir quality. On the more isolated highs, large buildups developed. These are typically 5-10 km across and 300 m thick. They unconformably overlie the platform carbonate facies which are extensively karstified. In places these are pinnacles, typically 2-5 km across, 300 m+ thick with chaotic or mounded internal seismic facies. The large carbonate buildups are characterized by steep sided slopes with talus cones, reef-marginmore » rims usually developed around only part of the buildup, and a prominent back-stepping geometry. Buildup interior facies form the main potential reservoirs They are dominated by fine to coarse grained coralgal packstones. Fine grained carbonates are associated with deeper water events and multiple karst surfaces can also be identified. Reservoir quality is excellent, largely controlled by extensive dissolution and dolomitization believed to be related to the exposure events. Gas has been found in a number of reservoirs. Heterogeneities can be recognized which could potentially effect production. These include the extensive finer grained facies, cementation or open fissures associated with the karst surfaces, a more cemented reef rim, shallowing upwards facies cycles and faults.« less

Development of a carbonate platform with potential for large discoveries - an example from Vietnam

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

Mayall, M.; Bent, A.; Dale, B.

1996-12-31

In offshore central and southern Vietnam a number of carbonate accumulations can be recognized. Platform carbonates form basin-wide units of carbonate characterized by strong, continuous parallel seismic reflectors. Facies are dominated by bioclastic wackestones with poor-moderate reservoir quality. On the more isolated highs, large buildups developed. These are typically 5-10 km across and 300 m thick. They unconformably overlie the platform carbonate facies which are extensively karstified. In places these are pinnacles, typically 2-5 km across, 300 m+ thick with chaotic or mounded internal seismic facies. The large carbonate buildups are characterized by steep sided slopes with talus cones, reef-marginmore » rims usually developed around only part of the buildup, and a prominent back-stepping geometry. Buildup interior facies form the main potential reservoirs They are dominated by fine to coarse grained coralgal packstones. Fine grained carbonates are associated with deeper water events and multiple karst surfaces can also be identified. Reservoir quality is excellent, largely controlled by extensive dissolution and dolomitization believed to be related to the exposure events. Gas has been found in a number of reservoirs. Heterogeneities can be recognized which could potentially effect production. These include the extensive finer grained facies, cementation or open fissures associated with the karst surfaces, a more cemented reef rim, shallowing upwards facies cycles and faults.« less

Imaging at ultrahigh magnetic fields: History, challenges, and solutions.

PubMed

Uğurbil, Kamil

2018-03-01

Following early efforts in applying nuclear magnetic resonance (NMR) spectroscopy to study biological processes in intact systems, and particularly since the introduction of 4 T human scanners circa 1990, rapid progress was made in imaging and spectroscopy studies of humans at 4 T and animal models at 9.4 T, leading to the introduction of 7 T and higher magnetic fields for human investigation at about the turn of the century. Work conducted on these platforms has provided numerous technological solutions to challenges posed at these ultrahigh fields, and demonstrated the existence of significant advantages in signal-to-noise ratio and biological information content. Primary difference from lower fields is the deviation from the near field regime at the radiofrequencies (RF) corresponding to hydrogen resonance conditions. At such ultrahigh fields, the RF is characterized by attenuated traveling waves in the human body, which leads to image non-uniformities for a given sample-coil configuration because of destructive and constructive interferences. These non-uniformities were initially considered detrimental to progress of imaging at high field strengths. However, they are advantageous for parallel imaging in signal reception and transmission, two critical technologies that account, to a large extend, for the success of ultrahigh fields. With these technologies and improvements in instrumentation and imaging methods, today ultrahigh fields have provided unprecedented gains in imaging of brain function and anatomy, and started to make inroads into investigation of the human torso and extremities. As extensive as they are, these gains still constitute a prelude to what is to come given the increasingly larger effort committed to ultrahigh field research and development of ever better instrumentation and techniques. Copyright © 2017 Elsevier Inc. All rights reserved.

SlicerRT: radiation therapy research toolkit for 3D Slicer.

PubMed

Pinter, Csaba; Lasso, Andras; Wang, An; Jaffray, David; Fichtinger, Gabor

2012-10-01

Interest in adaptive radiation therapy research is constantly growing, but software tools available for researchers are mostly either expensive, closed proprietary applications, or free open-source packages with limited scope, extensibility, reliability, or user support. To address these limitations, we propose SlicerRT, a customizable, free, and open-source radiation therapy research toolkit. SlicerRT aspires to be an open-source toolkit for RT research, providing fast computations, convenient workflows for researchers, and a general image-guided therapy infrastructure to assist clinical translation of experimental therapeutic approaches. It is a medium into which RT researchers can integrate their methods and algorithms, and conduct comparative testing. SlicerRT was implemented as an extension for the widely used 3D Slicer medical image visualization and analysis application platform. SlicerRT provides functionality specifically designed for radiation therapy research, in addition to the powerful tools that 3D Slicer offers for visualization, registration, segmentation, and data management. The feature set of SlicerRT was defined through consensus discussions with a large pool of RT researchers, including both radiation oncologists and medical physicists. The development processes used were similar to those of 3D Slicer to ensure software quality. Standardized mechanisms of 3D Slicer were applied for documentation, distribution, and user support. The testing and validation environment was configured to automatically launch a regression test upon each software change and to perform comparison with ground truth results provided by other RT applications. Modules have been created for importing and loading DICOM-RT data, computing and displaying dose volume histograms, creating accumulated dose volumes, comparing dose volumes, and visualizing isodose lines and surfaces. The effectiveness of using 3D Slicer with the proposed SlicerRT extension for radiation therapy research was demonstrated on multiple use cases. A new open-source software toolkit has been developed for radiation therapy research. SlicerRT can import treatment plans from various sources into 3D Slicer for visualization, analysis, comparison, and processing. The provided algorithms are extensively tested and they are accessible through a convenient graphical user interface as well as a flexible application programming interface.

TRIO Platform: A Novel Low Profile In vivo Imaging Support and Restraint System for Mice.

PubMed

Voziyanov, Vladislav; Kemp, Benjamin S; Dressel, Chelsea A; Ponder, Kayla; Murray, Teresa A

2016-01-01

High resolution, in vivo optical imaging of the mouse brain over time often requires anesthesia, which necessitates maintaining the animal's body temperature and level of anesthesia, as well as securing the head in an optimal, stable position. Controlling each parameter usually requires using multiple systems. Assembling multiple components into the small space on a standard microscope stage can be difficult and some commercially available parts simply do not fit. Furthermore, it is time-consuming to position an animal in the identical position over multiple imaging sessions for longitudinal studies. This is especially true when using an implanted gradient index (GRIN) lens for deep brain imaging. The multiphoton laser beam must be parallel with the shaft of the lens because even a slight tilt of the lens can degrade image quality. In response to these challenges, we have designed a compact, integrated in vivo imaging support system to overcome the problems created by using separate systems during optical imaging in mice. It is a single platform that provides (1) sturdy head fixation, (2) an integrated gas anesthesia mask, and (3) safe warm water heating. This THREE-IN-ONE (TRIO) Platform has a small footprint and a low profile that positions a mouse's head only 20 mm above the microscope stage. This height is about one half to one third the height of most commercially available immobilization devices. We have successfully employed this system, using isoflurane in over 40 imaging sessions with an average of 2 h per session with no leaks or other malfunctions. Due to its smaller size, the TRIO Platform can be used with a wider range of upright microscopes and stages. Most of the components were designed in SOLIDWORKS® and fabricated using a 3D printer. This additive manufacturing approach also readily permits size modifications for creating systems for other small animals.

TRIO Platform: A Novel Low Profile In vivo Imaging Support and Restraint System for Mice

PubMed Central

Voziyanov, Vladislav; Kemp, Benjamin S.; Dressel, Chelsea A.; Ponder, Kayla; Murray, Teresa A.

2016-01-01

High resolution, in vivo optical imaging of the mouse brain over time often requires anesthesia, which necessitates maintaining the animal's body temperature and level of anesthesia, as well as securing the head in an optimal, stable position. Controlling each parameter usually requires using multiple systems. Assembling multiple components into the small space on a standard microscope stage can be difficult and some commercially available parts simply do not fit. Furthermore, it is time-consuming to position an animal in the identical position over multiple imaging sessions for longitudinal studies. This is especially true when using an implanted gradient index (GRIN) lens for deep brain imaging. The multiphoton laser beam must be parallel with the shaft of the lens because even a slight tilt of the lens can degrade image quality. In response to these challenges, we have designed a compact, integrated in vivo imaging support system to overcome the problems created by using separate systems during optical imaging in mice. It is a single platform that provides (1) sturdy head fixation, (2) an integrated gas anesthesia mask, and (3) safe warm water heating. This THREE-IN-ONE (TRIO) Platform has a small footprint and a low profile that positions a mouse's head only 20 mm above the microscope stage. This height is about one half to one third the height of most commercially available immobilization devices. We have successfully employed this system, using isoflurane in over 40 imaging sessions with an average of 2 h per session with no leaks or other malfunctions. Due to its smaller size, the TRIO Platform can be used with a wider range of upright microscopes and stages. Most of the components were designed in SOLIDWORKS® and fabricated using a 3D printer. This additive manufacturing approach also readily permits size modifications for creating systems for other small animals. PMID:27199633

Imaging cell picker: A morphology-based automated cell separation system on a photodegradable hydrogel culture platform.

PubMed

Shibuta, Mayu; Tamura, Masato; Kanie, Kei; Yanagisawa, Masumi; Matsui, Hirofumi; Satoh, Taku; Takagi, Toshiyuki; Kanamori, Toshiyuki; Sugiura, Shinji; Kato, Ryuji

2018-06-09

Cellular morphology on and in a scaffold composed of extracellular matrix generally represents the cellular phenotype. Therefore, morphology-based cell separation should be interesting method that is applicable to cell separation without staining surface markers in contrast to conventional cell separation methods (e.g., fluorescence activated cell sorting and magnetic activated cell sorting). In our previous study, we have proposed a cloning technology using a photodegradable gelatin hydrogel to separate the individual cells on and in hydrogels. To further expand the applicability of this photodegradable hydrogel culture platform, we here report an image-based cell separation system imaging cell picker for the morphology-based cell separation on a photodegradable hydrogel. We have developed the platform which enables the automated workflow of image acquisition, image processing and morphology analysis, and collection of a target cells. We have shown the performance of the morphology-based cell separation through the optimization of the critical parameters that determine the system's performance, such as (i) culture conditions, (ii) imaging conditions, and (iii) the image analysis scheme, to actually clone the cells of interest. Furthermore, we demonstrated the morphology-based cloning performance of cancer cells in the mixture of cells by automated hydrogel degradation by light irradiation and pipetting. Copyright © 2018 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

A platform for European CMOS image sensors for space applications

NASA Astrophysics Data System (ADS)

Minoglou, K.; San Segundo Bello, D.; Sabuncuoglu Tezcan, D.; Haspeslagh, L.; Van Olmen, J.; Merry, B.; Cavaco, C.; Mazzamuto, F.; Toqué-Trésonne, I.; Moirin, R.; Brouwer, M.; Toccafondi, M.; Preti, G.; Rosmeulen, M.; De Moor, P.

2017-11-01

Both ESA and the EC have identified the need for a supply chain of CMOS imagers for space applications which uses solely European sources. An essential requirement on this supply chain is the platformization of the process modules, in particular when it comes to very specific processing steps, such as those required for the manufacturing of backside illuminated image sensors. This is the goal of the European (EC/FP7/SPACE) funded project EUROCIS. All EUROCIS partners have excellent know-how and track record in the expertise fields required. Imec has been leading the imager chip design and the front side and backside processing. LASSE, as a major player in the laser annealing supplier sector, has been focusing on the optimization of the process related to the backside passivation of the image sensors. TNO, known worldwide as a top developer of instruments for scientific research, including space research and sensors for satellites, has contributed in the domain of optical layers for space instruments and optimized antireflective coatings. Finally, Selex ES, as a world-wide leader for manufacturing instruments with expertise in various space missions and programs, has defined the image sensor specifications and is taking care of the final device characterization. In this paper, an overview of the process flow, the results on test structures and imagers processed using this platform will be presented.

Silicon nanomaterials platform for bioimaging, biosensing, and cancer therapy.

PubMed

Peng, Fei; Su, Yuanyuan; Zhong, Yiling; Fan, Chunhai; Lee, Shuit-Tong; He, Yao

2014-02-18

Silicon nanomaterials are an important class of nanomaterials with great potential for technologies including energy, catalysis, and biotechnology, because of their many unique properties, including biocompatibility, abundance, and unique electronic, optical, and mechanical properties, among others. Silicon nanomaterials are known to have little or no toxicity due to favorable biocompatibility of silicon, which is an important precondition for biological and biomedical applications. In addition, huge surface-to-volume ratios of silicon nanomaterials are responsible for their unique optical, mechanical, or electronic properties, which offer exciting opportunities for design of high-performance silicon-based functional nanoprobes, nanosensors, and nanoagents for biological analysis and detection and disease treatment. Moreover, silicon is the second most abundant element (after oxygen) on earth, providing plentiful and inexpensive resources for large-scale and low-cost preparation of silicon nanomaterials for practical applications. Because of these attractive traits, and in parallel with a growing interest in their design and synthesis, silicon nanomaterials are extensively investigated for wide-ranging applications, including energy, catalysis, optoelectronics, and biology. Among them, bioapplications of silicon nanomaterials are of particular interest. In the past decade, scientists have made an extensive effort to construct a silicon nanomaterials platform for various biological and biomedical applications, such as biosensors, bioimaging, and cancer treatment, as new and powerful tools for disease diagnosis and therapy. Nonetheless, there are few review articles covering these important and promising achievements to promote the awareness of development of silicon nanobiotechnology. In this Account, we summarize recent representative works to highlight the recent developments of silicon functional nanomaterials for a new, powerful platform for biological and biomedical applications, including biosensor, bioimaging, and cancer therapy. First, we show that the interesting photoluminescence properties (e.g., strong fluorescence and robust photostability) and excellent biocompatibility of silicon nanoparticles (SiNPs) are superbly suitable for direct and long-term visualization of biological systems. The strongly fluorescent SiNPs are highly effective for bioimaging applications, especially for long-term cellular labeling, cancer cell detection, and tumor imaging in vitro and in vivo with high sensitivity. Next, we discuss the utilization of silicon nanomaterials to construct high-performance biosensors, such as silicon-based field-effect transistors (FET) and surface-enhanced Raman scattering (SERS) sensors, which hold great promise for ultrasensitive and selective detection of biological species (e.g., DNA and protein). Then, we introduce recent exciting research findings on the applications of silicon nanomaterials for cancer therapy with encouraging therapeutic outcomes. Lastly, we highlight the major challenges and promises in this field, and the prospect of a new nanobiotechnology platform based on silicon nanomaterials.

The effect of platform switching on the levels of metal ion release from different implant–abutment couples

PubMed Central

Alrabeah, Ghada O; Knowles, Jonathan C; Petridis, Haralampos

2016-01-01

The improved peri-implant bone response demonstrated by platform switching may be the result of reduced amounts of metal ions released to the surrounding tissues. The aim of this study was to compare the levels of metal ions released from platform-matched and platform-switched implant–abutment couples as a result of accelerated corrosion. Thirty-six titanium alloy (Ti-6Al-4V) and cobalt–chrome alloy abutments were coupled with titanium cylinders forming either platform-switched or platform-matched groups (n=6). In addition, 18 unconnected samples served as controls. The specimens were subjected to accelerated corrosion by static immersion in 1% lactic acid for 1 week. The amount of metal ions ion of each test tube was measured using inductively coupled plasma mass spectrometry. Scanning electron microscope (SEM) images and energy dispersive spectroscopy X-ray analyses were performed pre- and post-immersion to assess corrosion at the interface. The platform-matched groups demonstrated higher ion release for vanadium, aluminium, cobalt, chrome, and molybdenum compared with the platform-switched groups (P<0.05). Titanium was the highest element to be released regardless of abutment size or connection (P<0.05). SEM images showed pitting corrosion prominent on the outer borders of the implant and abutment platform surfaces. In conclusion, implant–abutment couples underwent an active corrosion process resulting in metal ions release into the surrounding environment. The highest amount of metal ions released was recorded for the platform-matched groups, suggesting that platform-switching concept has a positive effect in reducing the levels of metal ion release from the implant–abutment couples. PMID:27357323

Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance*

PubMed Central

Paulovich, Amanda G.; Billheimer, Dean; Ham, Amy-Joan L.; Vega-Montoto, Lorenzo; Rudnick, Paul A.; Tabb, David L.; Wang, Pei; Blackman, Ronald K.; Bunk, David M.; Cardasis, Helene L.; Clauser, Karl R.; Kinsinger, Christopher R.; Schilling, Birgit; Tegeler, Tony J.; Variyath, Asokan Mulayath; Wang, Mu; Whiteaker, Jeffrey R.; Zimmerman, Lisa J.; Fenyo, David; Carr, Steven A.; Fisher, Susan J.; Gibson, Bradford W.; Mesri, Mehdi; Neubert, Thomas A.; Regnier, Fred E.; Rodriguez, Henry; Spiegelman, Cliff; Stein, Stephen E.; Tempst, Paul; Liebler, Daniel C.

2010-01-01

Optimal performance of LC-MS/MS platforms is critical to generating high quality proteomics data. Although individual laboratories have developed quality control samples, there is no widely available performance standard of biological complexity (and associated reference data sets) for benchmarking of platform performance for analysis of complex biological proteomes across different laboratories in the community. Individual preparations of the yeast Saccharomyces cerevisiae proteome have been used extensively by laboratories in the proteomics community to characterize LC-MS platform performance. The yeast proteome is uniquely attractive as a performance standard because it is the most extensively characterized complex biological proteome and the only one associated with several large scale studies estimating the abundance of all detectable proteins. In this study, we describe a standard operating protocol for large scale production of the yeast performance standard and offer aliquots to the community through the National Institute of Standards and Technology where the yeast proteome is under development as a certified reference material to meet the long term needs of the community. Using a series of metrics that characterize LC-MS performance, we provide a reference data set demonstrating typical performance of commonly used ion trap instrument platforms in expert laboratories; the results provide a basis for laboratories to benchmark their own performance, to improve upon current methods, and to evaluate new technologies. Additionally, we demonstrate how the yeast reference, spiked with human proteins, can be used to benchmark the power of proteomics platforms for detection of differentially expressed proteins at different levels of concentration in a complex matrix, thereby providing a metric to evaluate and minimize preanalytical and analytical variation in comparative proteomics experiments. PMID:19858499

Lensfree Computational Microscopy Tools and their Biomedical Applications

NASA Astrophysics Data System (ADS)

Sencan, Ikbal

Conventional microscopy has been a revolutionary tool for biomedical applications since its invention several centuries ago. Ability to non-destructively observe very fine details of biological objects in real time enabled to answer many important questions about their structures and functions. Unfortunately, most of these advance microscopes are complex, bulky, expensive, and/or hard to operate, so they could not reach beyond the walls of well-equipped laboratories. Recent improvements in optoelectronic components and computational methods allow creating imaging systems that better fulfill the specific needs of clinics or research related biomedical applications. In this respect, lensfree computational microscopy aims to replace bulky and expensive optical components with compact and cost-effective alternatives through the use of computation, which can be particularly useful for lab-on-a-chip platforms as well as imaging applications in low-resource settings. Several high-throughput on-chip platforms are built with this approach for applications including, but not limited to, cytometry, micro-array imaging, rare cell analysis, telemedicine, and water quality screening. The lack of optical complexity in these lensfree on-chip imaging platforms is compensated by using computational techniques. These computational methods are utilized for various purposes in coherent, incoherent and fluorescent on-chip imaging platforms e.g. improving the spatial resolution, to undo the light diffraction without using lenses, localization of objects in a large volume and retrieval of the phase or the color/spectral content of the objects. For instance, pixel super resolution approaches based on source shifting are used in lensfree imaging platforms to prevent under sampling, Bayer pattern, and aliasing artifacts. Another method, iterative phase retrieval, is utilized to compensate the lack of lenses by undoing the diffraction and removing the twin image noise of in-line holograms. This technique enables recovering the complex optical field from its intensity measurement(s) by using additional constraints in iterations, such as spatial boundaries and other known properties of objects. Another computational tool employed in lensfree imaging is compressive sensing (or decoding), which is a novel method taking advantage of the fact that natural signals/objects are mostly sparse or compressible in known bases. This inherent property of objects enables better signal recovery when the number of measurement is low, even below the Nyquist rate, and increases the additive noise immunity of the system.

Clinically translatable nanotheranostic platforms for peripheral nerve regeneration: design with outcome in mind

NASA Astrophysics Data System (ADS)

Janjic, Jelena M.; Gorantla, Vijay S.

2018-02-01

Neuroinflammation is a dynamic immune phenomenon that changes in severity with time after neurotrauma and has a profound impact on neuroregeneration, tissue healing and neuropathic pain, which is a common consequence of peripheral nerve injury (PNI). Macrophages are key cellular mediators of neuroinflammation. Macrophage-targeted nanotherapies, such as complex (perfluorocarbon/hydrocarbon) multimodal nanoemulsions (NEs) provide highly specific imaging signatures of neuroinflammation and hence indirect surrogate metrics of regeneration. We present a novel strategy where these NEs incorporating multiple imaging modalities and biosensors are delivered locally to directly target key cellular players of neuroregeneration. Two representative formulations of a nanotheranostic platform for local delivery of cell targeted NEs are presented: 1) A dual (macrophage and neuronal) targeted nanoparticle laden hydrogel for synergistic modulation of neuroinflammation and analgesia following PNI; and 2) neurotherapeutic loaded nanoparticles with extended release profile for sustained support of neuroregeneration. Each platform is capable of dual imaging payloads (NIRF, MRI and/or PET) and/or cell specific targeting moieties for controlled drug release. In vitro and pilot in vivo results will be presented. Theranostic nanosystem based platforms offer a unique opportunity to sequentially monitor cellular and molecular events at the site of neuronal injury, enabling dynamic, in-vivo mechanistic insights rather than static, ex-vivo histopathologic evaluation. Given their targeted capabilities, these platforms can help achieve personalized treatments that are customized and optimized for patients with PNI.

Integrated nanotechnology platform for tumor-targeted multimodal imaging and therapeutic cargo release

PubMed Central

Hosoya, Hitomi; Dobroff, Andrey S.; Driessen, Wouter H. P.; Cristini, Vittorio; Brinker, Lina M.; Staquicini, Fernanda I.; Cardó-Vila, Marina; D’Angelo, Sara; Ferrara, Fortunato; Proneth, Bettina; Lin, Yu-Shen; Dunphy, Darren R.; Dogra, Prashant; Melancon, Marites P.; Stafford, R. Jason; Miyazono, Kohei; Gelovani, Juri G.; Kataoka, Kazunori; Brinker, C. Jeffrey; Sidman, Richard L.; Arap, Wadih; Pasqualini, Renata

2016-01-01

A major challenge of targeted molecular imaging and drug delivery in cancer is establishing a functional combination of ligand-directed cargo with a triggered release system. Here we develop a hydrogel-based nanotechnology platform that integrates tumor targeting, photon-to-heat conversion, and triggered drug delivery within a single nanostructure to enable multimodal imaging and controlled release of therapeutic cargo. In proof-of-concept experiments, we show a broad range of ligand peptide-based applications with phage particles, heat-sensitive liposomes, or mesoporous silica nanoparticles that self-assemble into a hydrogel for tumor-targeted drug delivery. Because nanoparticles pack densely within the nanocarrier, their surface plasmon resonance shifts to near-infrared, thereby enabling a laser-mediated photothermal mechanism of cargo release. We demonstrate both noninvasive imaging and targeted drug delivery in preclinical mouse models of breast and prostate cancer. Finally, we applied mathematical modeling to predict and confirm tumor targeting and drug delivery. These results are meaningful steps toward the design and initial translation of an enabling nanotechnology platform with potential for broad clinical applications. PMID:26839407

Cloud-enabled microscopy and droplet microfluidic platform for specific detection of Escherichia coli in water.

PubMed

Golberg, Alexander; Linshiz, Gregory; Kravets, Ilia; Stawski, Nina; Hillson, Nathan J; Yarmush, Martin L; Marks, Robert S; Konry, Tania

2014-01-01

We report an all-in-one platform - ScanDrop - for the rapid and specific capture, detection, and identification of bacteria in drinking water. The ScanDrop platform integrates droplet microfluidics, a portable imaging system, and cloud-based control software and data storage. The cloud-based control software and data storage enables robotic image acquisition, remote image processing, and rapid data sharing. These features form a "cloud" network for water quality monitoring. We have demonstrated the capability of ScanDrop to perform water quality monitoring via the detection of an indicator coliform bacterium, Escherichia coli, in drinking water contaminated with feces. Magnetic beads conjugated with antibodies to E. coli antigen were used to selectively capture and isolate specific bacteria from water samples. The bead-captured bacteria were co-encapsulated in pico-liter droplets with fluorescently-labeled anti-E. coli antibodies, and imaged with an automated custom designed fluorescence microscope. The entire water quality diagnostic process required 8 hours from sample collection to online-accessible results compared with 2-4 days for other currently available standard detection methods.

Integrated nanotechnology platform for tumor-targeted multimodal imaging and therapeutic cargo release.

PubMed

Hosoya, Hitomi; Dobroff, Andrey S; Driessen, Wouter H P; Cristini, Vittorio; Brinker, Lina M; Staquicini, Fernanda I; Cardó-Vila, Marina; D'Angelo, Sara; Ferrara, Fortunato; Proneth, Bettina; Lin, Yu-Shen; Dunphy, Darren R; Dogra, Prashant; Melancon, Marites P; Stafford, R Jason; Miyazono, Kohei; Gelovani, Juri G; Kataoka, Kazunori; Brinker, C Jeffrey; Sidman, Richard L; Arap, Wadih; Pasqualini, Renata

2016-02-16

A major challenge of targeted molecular imaging and drug delivery in cancer is establishing a functional combination of ligand-directed cargo with a triggered release system. Here we develop a hydrogel-based nanotechnology platform that integrates tumor targeting, photon-to-heat conversion, and triggered drug delivery within a single nanostructure to enable multimodal imaging and controlled release of therapeutic cargo. In proof-of-concept experiments, we show a broad range of ligand peptide-based applications with phage particles, heat-sensitive liposomes, or mesoporous silica nanoparticles that self-assemble into a hydrogel for tumor-targeted drug delivery. Because nanoparticles pack densely within the nanocarrier, their surface plasmon resonance shifts to near-infrared, thereby enabling a laser-mediated photothermal mechanism of cargo release. We demonstrate both noninvasive imaging and targeted drug delivery in preclinical mouse models of breast and prostate cancer. Finally, we applied mathematical modeling to predict and confirm tumor targeting and drug delivery. These results are meaningful steps toward the design and initial translation of an enabling nanotechnology platform with potential for broad clinical applications.

X-ray Diffraction and Multi-Frame Phase Contrast Imaging Diagnostics for IMPULSE at the Advanced Photon Source

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

Iverson, Adam; Carlson, Carl; Young, Jason

2013-07-08

The diagnostic needs of any dynamic loading platform present unique technical challenges that must be addressed in order to accurately measure in situ material properties in an extreme environment. The IMPULSE platform (IMPact system for Ultrafast Synchrotron Experiments) at the Advanced Photon Source (APS) is no exception and, in fact, may be more challenging, as the imaging diagnostics must be synchronized to both the experiment and the 60 ps wide x-ray bunches produced at APS. The technical challenges of time-resolved x-ray diffraction imaging and high-resolution multi-frame phase contrast imaging (PCI) are described in this paper. Example data from recent IMPULSEmore » experiments are shown to illustrate the advances and evolution of these diagnostics with a focus on comparing the performance of two intensified CCD cameras and their suitability for multi-frame PCI. The continued development of these diagnostics is fundamentally important to IMPULSE and many other loading platforms and will benefit future facilities such as the Dynamic Compression Sector at APS and MaRIE at Los Alamos National Laboratory.« less

Cloud-Enabled Microscopy and Droplet Microfluidic Platform for Specific Detection of Escherichia coli in Water

PubMed Central

Kravets, Ilia; Stawski, Nina; Hillson, Nathan J.; Yarmush, Martin L.; Marks, Robert S.; Konry, Tania

2014-01-01

We report an all-in-one platform – ScanDrop – for the rapid and specific capture, detection, and identification of bacteria in drinking water. The ScanDrop platform integrates droplet microfluidics, a portable imaging system, and cloud-based control software and data storage. The cloud-based control software and data storage enables robotic image acquisition, remote image processing, and rapid data sharing. These features form a “cloud” network for water quality monitoring. We have demonstrated the capability of ScanDrop to perform water quality monitoring via the detection of an indicator coliform bacterium, Escherichia coli, in drinking water contaminated with feces. Magnetic beads conjugated with antibodies to E. coli antigen were used to selectively capture and isolate specific bacteria from water samples. The bead-captured bacteria were co-encapsulated in pico-liter droplets with fluorescently-labeled anti-E. coli antibodies, and imaged with an automated custom designed fluorescence microscope. The entire water quality diagnostic process required 8 hours from sample collection to online-accessible results compared with 2–4 days for other currently available standard detection methods. PMID:24475107

Integrated nanotechnology platform for tumor-targeted multimodal imaging and therapeutic cargo release

DOE PAGES

Hosoya, Hitomi; Dobroff, Andrey S.; Driessen, Wouter H. P.; ...

2016-02-02

A major challenge of targeted molecular imaging and drug delivery in cancer is establishing a functional combination of ligand-directed cargo with a triggered release system. Here we develop a hydrogel-based nanotechnology platform that integrates tumor targeting, photon-to-heat conversion, and triggered drug delivery within a single nanostructure to enable multimodal imaging and controlled release of therapeutic cargo. In proof-of-concept experiments, we show a broad range of ligand peptide-based applications with phage particles, heat-sensitive liposomes, or mesoporous silica nanoparticles that self-assemble into a hydrogel for tumor-targeted drug delivery. Because nanoparticles pack densely within the nanocarrier, their surface plasmon resonance shifts to near-infrared,more » thereby enabling a laser-mediated photothermal mechanism of cargo release. We demonstrate both noninvasive imaging and targeted drug delivery in preclinical mouse models of breast and prostate cancer. Finally, we applied mathematical modeling to predict and confirm tumor targeting and drug delivery. We conclude that these results are meaningful steps toward the design and initial translation of an enabling nanotechnology platform with potential for broad clinical applications.« less

Integrated nanotechnology platform for tumor-targeted multimodal imaging and therapeutic cargo release

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

Hosoya, Hitomi; Dobroff, Andrey S.; Driessen, Wouter H. P.

A major challenge of targeted molecular imaging and drug delivery in cancer is establishing a functional combination of ligand-directed cargo with a triggered release system. Here we develop a hydrogel-based nanotechnology platform that integrates tumor targeting, photon-to-heat conversion, and triggered drug delivery within a single nanostructure to enable multimodal imaging and controlled release of therapeutic cargo. In proof-of-concept experiments, we show a broad range of ligand peptide-based applications with phage particles, heat-sensitive liposomes, or mesoporous silica nanoparticles that self-assemble into a hydrogel for tumor-targeted drug delivery. Because nanoparticles pack densely within the nanocarrier, their surface plasmon resonance shifts to near-infrared,more » thereby enabling a laser-mediated photothermal mechanism of cargo release. We demonstrate both noninvasive imaging and targeted drug delivery in preclinical mouse models of breast and prostate cancer. Finally, we applied mathematical modeling to predict and confirm tumor targeting and drug delivery. We conclude that these results are meaningful steps toward the design and initial translation of an enabling nanotechnology platform with potential for broad clinical applications.« less

Multi-angle lensless digital holography for depth resolved imaging on a chip.

PubMed

Su, Ting-Wei; Isikman, Serhan O; Bishara, Waheb; Tseng, Derek; Erlinger, Anthony; Ozcan, Aydogan

2010-04-26

A multi-angle lensfree holographic imaging platform that can accurately characterize both the axial and lateral positions of cells located within multi-layered micro-channels is introduced. In this platform, lensfree digital holograms of the micro-objects on the chip are recorded at different illumination angles using partially coherent illumination. These digital holograms start to shift laterally on the sensor plane as the illumination angle of the source is tilted. Since the exact amount of this lateral shift of each object hologram can be calculated with an accuracy that beats the diffraction limit of light, the height of each cell from the substrate can be determined over a large field of view without the use of any lenses. We demonstrate the proof of concept of this multi-angle lensless imaging platform by using light emitting diodes to characterize various sized microparticles located on a chip with sub-micron axial and lateral localization over approximately 60 mm(2) field of view. Furthermore, we successfully apply this lensless imaging approach to simultaneously characterize blood samples located at multi-layered micro-channels in terms of the counts, individual thicknesses and the volumes of the cells at each layer. Because this platform does not require any lenses, lasers or other bulky optical/mechanical components, it provides a compact and high-throughput alternative to conventional approaches for cytometry and diagnostics applications involving lab on a chip systems.

Small animal radiotherapy research platforms

NASA Astrophysics Data System (ADS)

Verhaegen, Frank; Granton, Patrick; Tryggestad, Erik

2011-06-01

Advances in conformal radiation therapy and advancements in pre-clinical radiotherapy research have recently stimulated the development of precise micro-irradiators for small animals such as mice and rats. These devices are often kilovolt x-ray radiation sources combined with high-resolution CT imaging equipment for image guidance, as the latter allows precise and accurate beam positioning. This is similar to modern human radiotherapy practice. These devices are considered a major step forward compared to the current standard of animal experimentation in cancer radiobiology research. The availability of this novel equipment enables a wide variety of pre-clinical experiments on the synergy of radiation with other therapies, complex radiation schemes, sub-target boost studies, hypofractionated radiotherapy, contrast-enhanced radiotherapy and studies of relative biological effectiveness, to name just a few examples. In this review we discuss the required irradiation and imaging capabilities of small animal radiation research platforms. We describe the need for improved small animal radiotherapy research and highlight pioneering efforts, some of which led recently to commercially available prototypes. From this, it will be clear that much further development is still needed, on both the irradiation side and imaging side. We discuss at length the need for improved treatment planning tools for small animal platforms, and the current lack of a standard therein. Finally, we mention some recent experimental work using the early animal radiation research platforms, and the potential they offer for advancing radiobiology research.

An Airborne Infrared Spectrometer for Solar Eclipse Observations

NASA Astrophysics Data System (ADS)

Samra, Jenna; DeLuca, Edward E.; Golub, Leon; Cheimets, Peter; Philip, Judge

2016-05-01

The airborne infrared spectrometer (AIR-Spec) is an innovative solar spectrometer that will observe the 2017 solar eclipse from the NSF/NCAR High-Performance Instrumented Airborne Platform for Environmental Research (HIAPER). AIR-Spec will image five infrared coronal emission lines to determine whether they may be useful probes of coronal magnetism.The solar magnetic field provides the free energy that controls coronal heating, structure, and dynamics. Energy stored in coronal magnetic fields is released in flares and coronal mass ejections and ultimately drives space weather. Therefore, direct coronal field measurements have significant potential to enhance understanding of coronal dynamics and improve solar forecasting models. Of particular interest are observations of field lines in the transitional region between closed and open flux systems, providing important information on the origin of the slow solar wind.While current instruments routinely observe only the photospheric and chromospheric magnetic fields, AIR-Spec will take a step toward the direct observation of coronal fields by measuring plasma emission in the infrared at high spatial and spectral resolution. During the total solar eclipse of 2017, AIR-Spec will observe five magnetically sensitive coronal emission lines between 1.4 and 4 µm from the HIAPER Gulfstream V at an altitude above 14.9 km. The instrument will measure emission line intensity, width, and Doppler shift, map the spatial distribution of infrared emitting plasma, and search for waves in the emission line velocities.AIR-Spec consists of an optical system (feed telescope, grating spectrometer, and infrared detector) and an image stabilization system, which uses a fast steering mirror to correct the line-of-sight for platform perturbations. To ensure that the instrument meets its research goals, both systems are undergoing extensive performance modeling and testing. These results are shown with reference to the science requirements.

EOS Terra Validation Program

NASA Technical Reports Server (NTRS)

Starr, David

2000-01-01

The EOS Terra mission will be launched in July 1999. This mission has great relevance to the atmospheric radiation community and global change issues. Terra instruments include Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER), Clouds and Earth's Radiant Energy System (CERES), Multi-Angle Imaging Spectroradiometer (MISR), Moderate Resolution Imaging Spectroradiometer (MODIS) and Measurements of Pollution in the Troposphere (MOPITT). In addition to the fundamental radiance data sets, numerous global science data products will be generated, including various Earth radiation budget, cloud and aerosol parameters, as well as land surface, terrestrial ecology, ocean color, and atmospheric chemistry parameters. Significant investments have been made in on-board calibration to ensure the quality of the radiance observations. A key component of the Terra mission is the validation of the science data products. This is essential for a mission focused on global change issues and the underlying processes. The Terra algorithms have been subject to extensive pre-launch testing with field data whenever possible. Intensive efforts will be made to validate the Terra data products after launch. These include validation of instrument calibration (vicarious calibration) experiments, instrument and cross-platform comparisons, routine collection of high quality correlative data from ground-based networks, such as AERONET, and intensive sites, such as the SGP ARM site, as well as a variety field experiments, cruises, etc. Airborne simulator instruments have been developed for the field experiment and underflight activities including the MODIS Airborne Simulator (MAS) AirMISR, MASTER (MODIS-ASTER), and MOPITT-A. All are integrated on the NASA ER-2 though low altitude platforms are more typically used for MASTER. MATR is an additional sensor used for MOPITT algorithm development and validation. The intensive validation activities planned for the first year of the Terra mission will be described with emphasis on derived geophysical parameters of most relevance to the atmospheric radiation community.

TestDose: A nuclear medicine software based on Monte Carlo modeling for generating gamma camera acquisitions and dosimetry

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

Garcia, Marie-Paule, E-mail: marie-paule.garcia@univ-brest.fr; Villoing, Daphnée; McKay, Erin

Purpose: The TestDose platform was developed to generate scintigraphic imaging protocols and associated dosimetry by Monte Carlo modeling. TestDose is part of a broader project (www.dositest.com) whose aim is to identify the biases induced by different clinical dosimetry protocols. Methods: The TestDose software allows handling the whole pipeline from virtual patient generation to resulting planar and SPECT images and dosimetry calculations. The originality of their approach relies on the implementation of functional segmentation for the anthropomorphic model representing a virtual patient. Two anthropomorphic models are currently available: 4D XCAT and ICRP 110. A pharmacokinetic model describes the biodistribution of amore » given radiopharmaceutical in each defined compartment at various time-points. The Monte Carlo simulation toolkit GATE offers the possibility to accurately simulate scintigraphic images and absorbed doses in volumes of interest. The TestDose platform relies on GATE to reproduce precisely any imaging protocol and to provide reference dosimetry. For image generation, TestDose stores user’s imaging requirements and generates automatically command files used as input for GATE. Each compartment is simulated only once and the resulting output is weighted using pharmacokinetic data. Resulting compartment projections are aggregated to obtain the final image. For dosimetry computation, emission data are stored in the platform database and relevant GATE input files are generated for the virtual patient model and associated pharmacokinetics. Results: Two samples of software runs are given to demonstrate the potential of TestDose. A clinical imaging protocol for the Octreoscan™ therapeutical treatment was implemented using the 4D XCAT model. Whole-body “step and shoot” acquisitions at different times postinjection and one SPECT acquisition were generated within reasonable computation times. Based on the same Octreoscan™ kinetics, a dosimetry computation performed on the ICRP 110 model is also presented. Conclusions: The proposed platform offers a generic framework to implement any scintigraphic imaging protocols and voxel/organ-based dosimetry computation. Thanks to the modular nature of TestDose, other imaging modalities could be supported in the future such as positron emission tomography.« less

TestDose: A nuclear medicine software based on Monte Carlo modeling for generating gamma camera acquisitions and dosimetry.

PubMed

Garcia, Marie-Paule; Villoing, Daphnée; McKay, Erin; Ferrer, Ludovic; Cremonesi, Marta; Botta, Francesca; Ferrari, Mahila; Bardiès, Manuel

2015-12-01

The TestDose platform was developed to generate scintigraphic imaging protocols and associated dosimetry by Monte Carlo modeling. TestDose is part of a broader project (www.dositest.com) whose aim is to identify the biases induced by different clinical dosimetry protocols. The TestDose software allows handling the whole pipeline from virtual patient generation to resulting planar and SPECT images and dosimetry calculations. The originality of their approach relies on the implementation of functional segmentation for the anthropomorphic model representing a virtual patient. Two anthropomorphic models are currently available: 4D XCAT and ICRP 110. A pharmacokinetic model describes the biodistribution of a given radiopharmaceutical in each defined compartment at various time-points. The Monte Carlo simulation toolkit gate offers the possibility to accurately simulate scintigraphic images and absorbed doses in volumes of interest. The TestDose platform relies on gate to reproduce precisely any imaging protocol and to provide reference dosimetry. For image generation, TestDose stores user's imaging requirements and generates automatically command files used as input for gate. Each compartment is simulated only once and the resulting output is weighted using pharmacokinetic data. Resulting compartment projections are aggregated to obtain the final image. For dosimetry computation, emission data are stored in the platform database and relevant gate input files are generated for the virtual patient model and associated pharmacokinetics. Two samples of software runs are given to demonstrate the potential of TestDose. A clinical imaging protocol for the Octreoscan™ therapeutical treatment was implemented using the 4D XCAT model. Whole-body "step and shoot" acquisitions at different times postinjection and one SPECT acquisition were generated within reasonable computation times. Based on the same Octreoscan™ kinetics, a dosimetry computation performed on the ICRP 110 model is also presented. The proposed platform offers a generic framework to implement any scintigraphic imaging protocols and voxel/organ-based dosimetry computation. Thanks to the modular nature of TestDose, other imaging modalities could be supported in the future such as positron emission tomography.

A technique for multi-dimensional optimization of radiation dose, contrast dose, and image quality in CT imaging

NASA Astrophysics Data System (ADS)

Sahbaee, Pooyan; Abadi, Ehsan; Sanders, Jeremiah; Becchetti, Marc; Zhang, Yakun; Agasthya, Greeshma; Segars, Paul; Samei, Ehsan

2016-03-01

The purpose of this study was to substantiate the interdependency of image quality, radiation dose, and contrast material dose in CT towards the patient-specific optimization of the imaging protocols. The study deployed two phantom platforms. First, a variable sized phantom containing an iodinated insert was imaged on a representative CT scanner at multiple CTDI values. The contrast and noise were measured from the reconstructed images for each phantom diameter. Linearly related to iodine-concentration, contrast to noise ratio (CNR), was calculated for different iodine-concentration levels. Second, the analysis was extended to a recently developed suit of 58 virtual human models (5D-XCAT) with added contrast dynamics. Emulating a contrast-enhanced abdominal image procedure and targeting a peak-enhancement in aorta, each XCAT phantom was "imaged" using a CT simulation platform. 3D surfaces for each patient/size established the relationship between iodine-concentration, dose, and CNR. The Sensitivity of Ratio (SR), defined as ratio of change in iodine-concentration versus dose to yield a constant change in CNR was calculated and compared at high and low radiation dose for both phantom platforms. The results show that sensitivity of CNR to iodine concentration is larger at high radiation dose (up to 73%). The SR results were highly affected by radiation dose metric; CTDI or organ dose. Furthermore, results showed that the presence of contrast material could have a profound impact on optimization results (up to 45%).

BREAST: a novel method to improve the diagnostic efficacy of mammography

NASA Astrophysics Data System (ADS)

Brennan, P. C.; Tapia, K.; Ryan, J.; Lee, W.

2013-03-01

High quality breast imaging and accurate image assessment are critical to the early diagnoses, treatment and management of women with breast cancer. Breast Screen Reader Assessment Strategy (BREAST) provides a platform, accessible by researchers and clinicians world-wide, which will contain image data bases, algorithms to assess reader performance and on-line systems for image evaluation. The platform will contribute to the diagnostic efficacy of breast imaging in Australia and beyond on two fronts: reducing errors in mammography, and transforming our assessment of novel technologies and techniques. Mammography is the primary diagnostic tool for detecting breast cancer with over 800,000 women X-rayed each year in Australia, however, it fails to detect 30% of breast cancers with a number of missed cancers being visible on the image [1-6]. BREAST will monitor the mistakes, identify reasons for mammographic errors, and facilitate innovative solutions to reduce error rates. The BREAST platform has the potential to enable expert assessment of breast imaging innovations, anywhere in the world where experts or innovations are located. Currently, innovations are often being assessed by limited numbers of individuals who happen to be geographically located close to the innovation, resulting in equivocal studies with low statistical power. BREAST will transform this current paradigm by enabling large numbers of experts to assess any new method or technology using our embedded evaluation methods. We are confident that this world-first system will play an important part in the future efficacy of breast imaging.

Nearshore Measurements From a Small UAV.

NASA Astrophysics Data System (ADS)

Holman, R. A.; Brodie, K. L.; Spore, N.

2016-02-01

Traditional measurements of nearshore hydrodynamics and evolving bathymetry are expensive and dangerous and must be frequently repeated to track the rapid changes of typical ocean beaches. However, extensive research into remote sensing methods using cameras or radars mounted on fixed towers has resulted in increasingly mature algorithms for estimating bathymetry, currents and wave characteristics. This naturally raises questions about how easily and effectively these algorithms can be applied to optical data from low-cost, easily-available UAV platforms. This paper will address the characteristics and quality of data taken from a small, low-cost UAV, the DJI Phantom. In particular, we will study the stability of imagery from a vehicle `parked' at 300 feet altitude, methods to stabilize remaining wander, and the quality of nearshore bathymetry estimates from the resulting image time series, computed using the cBathy algorithm. Estimates will be compared to ground truth surveys collected at the Field Research Facility at Duck, NC.

Synthetic Botany.

PubMed

Boehm, Christian R; Pollak, Bernardo; Purswani, Nuri; Patron, Nicola; Haseloff, Jim

2017-07-05

Plants are attractive platforms for synthetic biology and metabolic engineering. Plants' modular and plastic body plans, capacity for photosynthesis, extensive secondary metabolism, and agronomic systems for large-scale production make them ideal targets for genetic reprogramming. However, efforts in this area have been constrained by slow growth, long life cycles, the requirement for specialized facilities, a paucity of efficient tools for genetic manipulation, and the complexity of multicellularity. There is a need for better experimental and theoretical frameworks to understand the way genetic networks, cellular populations, and tissue-wide physical processes interact at different scales. We highlight new approaches to the DNA-based manipulation of plants and the use of advanced quantitative imaging techniques in simple plant models such as Marchantia polymorpha. These offer the prospects of improved understanding of plant dynamics and new approaches to rational engineering of plant traits. Copyright © 2017 Cold Spring Harbor Laboratory Press; all rights reserved.

An SPM12 extension for multiple sclerosis lesion segmentation

NASA Astrophysics Data System (ADS)

Roura, Eloy; Oliver, Arnau; Cabezas, Mariano; Valverde, Sergi; Pareto, Deborah; Vilanova, Joan C.; Ramió-Torrentà, Lluís.; Rovira, Àlex; Lladó, Xavier

2016-03-01

Purpose: Magnetic resonance imaging is nowadays the hallmark to diagnose multiple sclerosis (MS), characterized by white matter lesions. Several approaches have been recently presented to tackle the lesion segmentation problem, but none of them have been accepted as a standard tool in the daily clinical practice. In this work we present yet another tool able to automatically segment white matter lesions outperforming the current-state-of-the-art approaches. Methods: This work is an extension of Roura et al. [1], where external and platform dependent pre-processing libraries (brain extraction, noise reduction and intensity normalization) were required to achieve an optimal performance. Here we have updated and included all these required pre-processing steps into a single framework (SPM software). Therefore, there is no need of external tools to achieve the desired segmentation results. Besides, we have changed the working space from T1w to FLAIR, reducing interpolation errors produced in the registration process from FLAIR to T1w space. Finally a post-processing constraint based on shape and location has been added to reduce false positive detections. Results: The evaluation of the tool has been done on 24 MS patients. Qualitative and quantitative results are shown with both approaches in terms of lesion detection and segmentation. Conclusion: We have simplified both installation and implementation of the approach, providing a multiplatform tool1 integrated into the SPM software, which relies only on using T1w and FLAIR images. We have reduced with this new version the computation time of the previous approach while maintaining the performance.

Performance Evaluation of Cots Uav for Architectural Heritage Documentation. a Test on S.GIULIANO Chapel in Savigliano (cn) - Italy

NASA Astrophysics Data System (ADS)

Chiabrando, F.; Teppati Losè, L.

2017-08-01

Even more the use of UAV platforms is a standard for images or videos acquisitions from an aerial point of view. According to the enormous growth of requests, we are assisting to an increasing of the production of COTS (Commercial off the Shelf) platforms and systems to answer to the market requirements. In this last years, different platforms have been developed and sell at low-medium cost and nowadays the offer of interesting systems is very large. One of the most important company that produce UAV and other imaging systems is the DJI (Dà-Jiāng Innovations Science and Technology Co., Ltd) founded in 2006 headquartered in Shenzhen - China. The platforms realized by the company range from low cost systems up to professional equipment, tailored for high resolution acquisitions useful for film maker purposes. According to the characteristics of the last developed low cost DJI platforms, the onboard sensors and the performance of the modern photogrammetric software based on Structure from Motion (SfM) algorithms, those systems are nowadays employed for performing 3D surveys starting from the small up to the large scale. The present paper is aimed to test the characteristic in terms of image quality, flight operations, flight planning and accuracy evaluation of the final products of three COTS platforms realized by DJI: the Mavic Pro, the Phantom 4 and the Phantom 4 PRO. The test site chosen was the Chapel of San Giuliano in the municipality of Savigliano (Cuneo-Italy), a small church with two aisles dating back to the early eleventh century.

Concepts for a geostationary-like polar mission

NASA Astrophysics Data System (ADS)

Macdonald, Malcolm; Anderson, Pamela; Carrea, Laura; Dobke, Benjamin; Embury, Owen; Merchant, Chris; Bensi, Paolo

2014-10-01

An evidence-led scientific case for development of a space-based polar remote sensing platform at geostationary-like (GEO-like) altitudes is developed through methods including a data user survey. Whilst a GEO platform provides a nearstatic perspective, multiple platforms are required to provide circumferential coverage. Systems for achieving GEO-like polar observation likewise require multiple platforms however the perspective is non-stationery. A key choice is between designs that provide complete polar view from a single platform at any given instant, and designs where this is obtained by compositing partial views from multiple sensors. Users foresee an increased challenge in extracting geophysical information from composite images and consider the use of non-composited images advantageous. Users also find the placement of apogee over the pole to be preferable to the alternative scenarios. Thus, a clear majority of data users find the "Taranis" orbit concept to be better than a critical inclination orbit, due to the improved perspective offered. The geophysical products that would benefit from a GEO-like polar platform are mainly estimated from radiances in the visible/near infrared and thermal parts of the electromagnetic spectrum, which is consistent with currently proven technologies from GEO. Based on the survey results, needs analysis, and current technology proven from GEO, scientific and observation requirements are developed along with two instrument concepts with eight and four channels, based on Flexible Combined Imager heritage. It is found that an operational system could, mostly likely, be deployed from an Ariane 5 ES to a 16-hour orbit, while a proof-of-concept system could be deployed from a Soyuz launch to the same orbit.

The Contribution of Social Media to Body Dissatisfaction, Eating Disorder Symptoms, and Anabolic Steroid Use Among Sexual Minority Men.

PubMed

Griffiths, Scott; Murray, Stuart B; Krug, Isabel; McLean, Siân A

2018-03-01

Social media has been associated with body dissatisfaction and eating disorder symptoms among young women and adolescent girls. However, despite notable evidence of susceptibility to body image pressures, it remains unknown whether these associations generalize to sexual minority men. A nationwide sample of 2,733 sexual minority men completed an online survey advertised to Australian and New Zealand users of a popular dating app. Participants answered questions about how frequently they used 11 different social media platforms in addition to questions about their dating app use, body image, eating disorder symptoms, and anabolic steroids. Facebook, Youtube, Instagram, and Snapchat were the most frequently used social media platforms. A pattern of small-sized and positive associations emerged between social media use and body dissatisfaction, eating disorder symptoms, and thoughts about using anabolic steroids. Facebook, Instagram, and Snapchat evidenced the strongest associations. The associations of social media use with both muscularity dissatisfaction and eating disorder symptoms were stronger for image-centric social media platforms (e.g., Instagram) than nonimage-centric platforms (e.g., Wordpress); no differences were observed for body fat dissatisfaction, height dissatisfaction, or thoughts about using anabolic steroids. Previously documented associations of social media use with body dissatisfaction and related variables among women and girls appear to generalize to sexual minority men. Social media platforms that more centrally involve imagery may be of greater concern than nonimage-centric platforms. Additional research with sexual minority men is needed to elucidate the distinctions between adaptive and maladaptive social media use in the context of body dissatisfaction, eating disorders, and anabolic steroid use.

Towards multi-platform software architecture for Collaborative Teleoperation

NASA Astrophysics Data System (ADS)

Domingues, Christophe; Otmane, Samir; Davesne, Frederic; Mallem, Malik

2009-03-01

Augmented Reality (AR) can provide to a Human Operator (HO) a real help in achieving complex tasks, such as remote control of robots and cooperative teleassistance. Using appropriate augmentations, the HO can interact faster, safer and easier with the remote real world. In this paper, we present an extension of an existing distributed software and network architecture for collaborative teleoperation based on networked human-scaled mixed reality and mobile platform. The first teleoperation system was composed by a VR application and a Web application. However the 2 systems cannot be used together and it is impossible to control a distant robot simultaneously. Our goal is to update the teleoperation system to permit a heterogeneous collaborative teleoperation between the 2 platforms. An important feature of this interface is based on the use of different Virtual Reality platforms and different Mobile platforms to control one or many robots.

Towards multi-platform software architecture for Collaborative Teleoperation

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

Domingues, Christophe; Otmane, Samir; Davesne, Frederic

2009-03-05

Augmented Reality (AR) can provide to a Human Operator (HO) a real help in achieving complex tasks, such as remote control of robots and cooperative teleassistance. Using appropriate augmentations, the HO can interact faster, safer and easier with the remote real world. In this paper, we present an extension of an existing distributed software and network architecture for collaborative teleoperation based on networked human-scaled mixed reality and mobile platform. The first teleoperation system was composed by a VR application and a Web application. However the 2 systems cannot be used together and it is impossible to control a distant robotmore » simultaneously. Our goal is to update the teleoperation system to permit a heterogeneous collaborative teleoperation between the 2 platforms. An important feature of this interface is based on the use of different Virtual Reality platforms and different Mobile platforms to control one or many robots.« less

Compressive hyperspectral time-resolved wide-field fluorescence lifetime imaging

NASA Astrophysics Data System (ADS)

Pian, Qi; Yao, Ruoyang; Sinsuebphon, Nattawut; Intes, Xavier

2017-07-01

Spectrally resolved fluorescence lifetime imaging and spatial multiplexing have offered information content and collection-efficiency boosts in microscopy, but efficient implementations for macroscopic applications are still lacking. An imaging platform based on time-resolved structured light and hyperspectral single-pixel detection has been developed to perform quantitative macroscopic fluorescence lifetime imaging (MFLI) over a large field of view (FOV) and multiple spectral bands simultaneously. The system makes use of three digital micromirror device (DMD)-based spatial light modulators (SLMs) to generate spatial optical bases and reconstruct N by N images over 16 spectral channels with a time-resolved capability (∼40 ps temporal resolution) using fewer than N2 optical measurements. We demonstrate the potential of this new imaging platform by quantitatively imaging near-infrared (NIR) Förster resonance energy transfer (FRET) both in vitro and in vivo. The technique is well suited for quantitative hyperspectral lifetime imaging with a high sensitivity and paves the way for many important biomedical applications.

Internet (WWW) based system of ultrasonic image processing tools for remote image analysis.

PubMed

Zeng, Hong; Fei, Ding-Yu; Fu, Cai-Ting; Kraft, Kenneth A

2003-07-01

Ultrasonic Doppler color imaging can provide anatomic information and simultaneously render flow information within blood vessels for diagnostic purpose. Many researchers are currently developing ultrasound image processing algorithms in order to provide physicians with accurate clinical parameters from the images. Because researchers use a variety of computer languages and work on different computer platforms to implement their algorithms, it is difficult for other researchers and physicians to access those programs. A system has been developed using World Wide Web (WWW) technologies and HTTP communication protocols to publish our ultrasonic Angle Independent Doppler Color Image (AIDCI) processing algorithm and several general measurement tools on the Internet, where authorized researchers and physicians can easily access the program using web browsers to carry out remote analysis of their local ultrasonic images or images provided from the database. In order to overcome potential incompatibility between programs and users' computer platforms, ActiveX technology was used in this project. The technique developed may also be used for other research fields.

High-throughput two-dimensional root system phenotyping platform facilitates genetic analysis of root growth and development.

PubMed

Clark, Randy T; Famoso, Adam N; Zhao, Keyan; Shaff, Jon E; Craft, Eric J; Bustamante, Carlos D; McCouch, Susan R; Aneshansley, Daniel J; Kochian, Leon V

2013-02-01

High-throughput phenotyping of root systems requires a combination of specialized techniques and adaptable plant growth, root imaging and software tools. A custom phenotyping platform was designed to capture images of whole root systems, and novel software tools were developed to process and analyse these images. The platform and its components are adaptable to a wide range root phenotyping studies using diverse growth systems (hydroponics, paper pouches, gel and soil) involving several plant species, including, but not limited to, rice, maize, sorghum, tomato and Arabidopsis. The RootReader2D software tool is free and publicly available and was designed with both user-guided and automated features that increase flexibility and enhance efficiency when measuring root growth traits from specific roots or entire root systems during large-scale phenotyping studies. To demonstrate the unique capabilities and high-throughput capacity of this phenotyping platform for studying root systems, genome-wide association studies on rice (Oryza sativa) and maize (Zea mays) root growth were performed and root traits related to aluminium (Al) tolerance were analysed on the parents of the maize nested association mapping (NAM) population. © 2012 Blackwell Publishing Ltd.

Near-infrared fluorescence imaging platform for quantifying in vivo nanoparticle diffusion from drug loaded implants.

PubMed

Markovic, Stacey; Belz, Jodi; Kumar, Rajiv; Cormack, Robert A; Sridhar, Srinivas; Niedre, Mark

2016-01-01

Drug loaded implants are a new, versatile technology platform to deliver a localized payload of drugs for various disease models. One example is the implantable nanoplatform for chemo-radiation therapy where inert brachytherapy spacers are replaced by spacers doped with nanoparticles (NPs) loaded with chemotherapeutics and placed directly at the disease site for long-term localized drug delivery. However, it is difficult to directly validate and optimize the diffusion of these doped NPs in in vivo systems. To better study this drug release and diffusion, we developed a custom macroscopic fluorescence imaging system to visualize and quantify fluorescent NP diffusion from spacers in vivo. To validate the platform, we studied the release of free fluorophores, and 30 nm and 200 nm NPs conjugated with the same fluorophores as a model drug, in agar gel phantoms in vitro and in mice in vivo. Our data verified that the diffusion volume was NP size-dependent in all cases. Our near-infrared imaging system provides a method by which NP diffusion from implantable nanoplatform for chemo-radiation therapy spacers can be systematically optimized (eg, particle size or charge) thereby improving treatment efficacy of the platform.

Passive millimetre wave imaging for ballistic missile launch detection

NASA Astrophysics Data System (ADS)

Higgins, Christopher J.; Salmon, Neil A.

2008-10-01

QinetiQ has used a suite of modelling tools to predict the millimetric plume signatures from a range of ballistic missile types, based on the accepted theory that Bremsstrahlung emission, generated by the collision of free electrons with neutral species in a rocket motor plume, is the dominant signature mechanism. Plume signatures in terms of radiation temperatures varied from a few hundred Kelvin to over one thousand Kelvin, and were predicted to be dependent on emission frequency, propellant type and missile thrust. Two types of platform were considered for the passive mmw imager launch detection system; a High Altitude Platform Station (HAPS) and a satellite based platform in low, mid and geosynchronous earth orbits. It was concluded that the optimum operating frequency for a HAPS based imager would be 35GHz with a 4.5m aperture and a sensitivity of 20mK providing visibility through 500 vertical feet of cloud. For a satellite based platform with a nadir view, the optimum frequency is 220 GHz. With such a system, in a low earth orbit at an altitude of 320km, with a sensitivity of 20mK, a 29cm aperture would be desirable.

Intraoperative optical coherence tomography: past, present, and future

PubMed Central

Ehlers, J P

2016-01-01

To provide an overview of the current state of intraoperative optical coherence tomography (OCT). Literature review of studies pertaining to intraoperative OCT examining both the technology aspects of the imaging platform and the current evidence for patient care. Over the last several years, there have been significant advances in integrative technology for intraoperative OCT. This has resulted in the development of multiple microscope-integrated systems and a rapidly expanding field of image-guided surgical care. Multiple studies have demonstrated the potential role for intraoperative OCT in facilitating surgeon understanding of the surgical environment, tissue configuration, and overall changes to anatomy. In fact, the PIONEER and DISCOVER studies, both demonstrated a potential significant percentage of cases that intraoperative OCT alters surgical decision-making in both anterior and posterior segment surgery. Current areas of exploration and development include OCT-compatible instrumentation, automated tracking, intraoperative OCT software platforms, and surgeon feedback/visualization platforms. Intraoperative OCT is an emerging technology that holds promise for enhancing the surgical care of both anterior segment and posterior segment conditions. Hurdles remain for adoption and widespread utilization, including cost, optimized feedback platforms, and more definitive value for individualized surgical care with image guidance. PMID:26681147

A Big-Data-based platform of workers' behavior: Observations from the field.

PubMed

Guo, S Y; Ding, L Y; Luo, H B; Jiang, X Y

2016-08-01

Behavior-Based Safety (BBS) has been used in construction to observe, analyze and modify workers' behavior. However, studies have identified that BBS has several limitations, which have hindered its effective implementation. To mitigate the negative impact of BBS, this paper uses a case study approach to develop a Big-Data-based platform to classify, collect and store data about workers' unsafe behavior that is derived from a metro construction project. In developing the platform, three processes were undertaken: (1) a behavioral risk knowledge base was established; (2) images reflecting workers' unsafe behavior were collected from intelligent video surveillance and mobile application; and (3) images with semantic information were stored via a Hadoop Distributed File System (HDFS). The platform was implemented during the construction of the metro-system and it is demonstrated that it can effectively analyze semantic information contained in images, automatically extract workers' unsafe behavior and quickly retrieve on HDFS as well. The research presented in this paper can enable construction organizations with the ability to visualize unsafe acts in real-time and further identify patterns of behavior that can jeopardize safety outcomes. Copyright © 2015 Elsevier Ltd. All rights reserved.

Small animal imaging platform for quantitative assessment of short-wave infrared-emitting contrast agents

NASA Astrophysics Data System (ADS)

Hu, Philip; Mingozzi, Marco; Higgins, Laura M.; Ganapathy, Vidya; Zevon, Margot; Riman, Richard E.; Roth, Charles M.; Moghe, Prabhas V.; Pierce, Mark C.

2015-03-01

We report the design, calibration, and testing of a pre-clinical small animal imaging platform for use with short-wave infrared (SWIR) emitting contrast agents. Unlike materials emitting at visible or near-infrared wavelengths, SWIR-emitting agents require detection systems with sensitivity in the 1-2 μm wavelength region, beyond the range of commercially available small animal imagers. We used a collimated 980 nm laser beam to excite rare-earth-doped NaYF4:Er,Yb nanocomposites, as an example of a SWIR emitting material under development for biomedical imaging applications. This beam was raster scanned across the animal, with fluorescence in the 1550 nm wavelength region detected by an InGaAs area camera. Background adjustment and intensity non-uniformity corrections were applied in software. The final SWIR fluorescence image was overlaid onto a standard white-light image for registration of contrast agent uptake with respect to anatomical features.

Design Tools for Accelerating Development and Usage of Multi-Core Computing Platforms

DTIC Science & Technology

2014-04-01

Government formulated or supplied the drawings, specifications, or other data does not license the holder or any other person or corporation ; or convey...multicore PDSP platforms. The GPU- based capabilities of TDIF are currently oriented towards NVIDIA GPUs, based on the Compute Unified Device Architecture...CUDA) programming language [ NVIDIA 2007], which can be viewed as an extension of C. The multicore PDSP capabilities currently in TDIF are oriented

Detecting ordered small molecule drug aggregates in live macrophages: a multi-parameter microscope image data acquisition and analysis strategy

PubMed Central

Rzeczycki, Phillip; Yoon, Gi Sang; Keswani, Rahul K.; Sud, Sudha; Stringer, Kathleen A.; Rosania, Gus R.

2017-01-01

Following prolonged administration, certain orally bioavailable but poorly soluble small molecule drugs are prone to precipitate out and form crystal-like drug inclusions (CLDIs) within the cells of living organisms. In this research, we present a quantitative multi-parameter imaging platform for measuring the fluorescence and polarization diattenuation signals of cells harboring intracellular CLDIs. To validate the imaging system, the FDA-approved drug clofazimine (CFZ) was used as a model compound. Our results demonstrated that a quantitative multi-parameter microscopy image analysis platform can be used to study drug sequestering macrophages, and to detect the formation of ordered molecular aggregates formed by poorly soluble small molecule drugs in animals. PMID:28270989

Detecting ordered small molecule drug aggregates in live macrophages: a multi-parameter microscope image data acquisition and analysis strategy.

PubMed

Rzeczycki, Phillip; Yoon, Gi Sang; Keswani, Rahul K; Sud, Sudha; Stringer, Kathleen A; Rosania, Gus R

2017-02-01

Following prolonged administration, certain orally bioavailable but poorly soluble small molecule drugs are prone to precipitate out and form crystal-like drug inclusions (CLDIs) within the cells of living organisms. In this research, we present a quantitative multi-parameter imaging platform for measuring the fluorescence and polarization diattenuation signals of cells harboring intracellular CLDIs. To validate the imaging system, the FDA-approved drug clofazimine (CFZ) was used as a model compound. Our results demonstrated that a quantitative multi-parameter microscopy image analysis platform can be used to study drug sequestering macrophages, and to detect the formation of ordered molecular aggregates formed by poorly soluble small molecule drugs in animals.

Reconfigurable, Intelligently-Adaptive, Communication System, an SDR Platform

NASA Technical Reports Server (NTRS)

Roche, Rigoberto

2016-01-01

The Space Telecommunications Radio System (STRS) provides a common, consistent framework to abstract the application software from the radio platform hardware. STRS aims to reduce the cost and risk of using complex, configurable and reprogrammable radio systems across NASA missions. The Glenn Research Center (GRC) team made a software-defined radio (SDR) platform STRS compliant by adding an STRS operating environment and a field programmable gate array (FPGA) wrapper, capable of implementing each of the platforms interfaces, as well as a test waveform to exercise those interfaces. This effort serves to provide a framework toward waveform development on an STRS compliant platform to support future space communication systems for advanced exploration missions. Validated STRS compliant applications provided tested code with extensive documentation to potentially reduce risk, cost and efforts in development of space-deployable SDRs. This paper discusses the advantages of STRS, the integration of STRS onto a Reconfigurable, Intelligently-Adaptive, Communication System (RIACS) SDR platform, the sample waveform, and wrapper development efforts. The paper emphasizes the infusion of the STRS Architecture onto the RIACS platform for potential use in next generation SDRs for advance exploration missions.

Data Mining and Knowledge Discovery tools for exploiting big Earth-Observation data

NASA Astrophysics Data System (ADS)

Espinoza Molina, D.; Datcu, M.

2015-04-01

The continuous increase in the size of the archives and in the variety and complexity of Earth-Observation (EO) sensors require new methodologies and tools that allow the end-user to access a large image repository, to extract and to infer knowledge about the patterns hidden in the images, to retrieve dynamically a collection of relevant images, and to support the creation of emerging applications (e.g.: change detection, global monitoring, disaster and risk management, image time series, etc.). In this context, we are concerned with providing a platform for data mining and knowledge discovery content from EO archives. The platform's goal is to implement a communication channel between Payload Ground Segments and the end-user who receives the content of the data coded in an understandable format associated with semantics that is ready for immediate exploitation. It will provide the user with automated tools to explore and understand the content of highly complex images archives. The challenge lies in the extraction of meaningful information and understanding observations of large extended areas, over long periods of time, with a broad variety of EO imaging sensors in synergy with other related measurements and data. The platform is composed of several components such as 1.) ingestion of EO images and related data providing basic features for image analysis, 2.) query engine based on metadata, semantics and image content, 3.) data mining and knowledge discovery tools for supporting the interpretation and understanding of image content, 4.) semantic definition of the image content via machine learning methods. All these components are integrated and supported by a relational database management system, ensuring the integrity and consistency of Terabytes of Earth Observation data.

Optimization of image processing algorithms on mobile platforms

NASA Astrophysics Data System (ADS)

Poudel, Pramod; Shirvaikar, Mukul

2011-03-01

This work presents a technique to optimize popular image processing algorithms on mobile platforms such as cell phones, net-books and personal digital assistants (PDAs). The increasing demand for video applications like context-aware computing on mobile embedded systems requires the use of computationally intensive image processing algorithms. The system engineer has a mandate to optimize them so as to meet real-time deadlines. A methodology to take advantage of the asymmetric dual-core processor, which includes an ARM and a DSP core supported by shared memory, is presented with implementation details. The target platform chosen is the popular OMAP 3530 processor for embedded media systems. It has an asymmetric dual-core architecture with an ARM Cortex-A8 and a TMS320C64x Digital Signal Processor (DSP). The development platform was the BeagleBoard with 256 MB of NAND RAM and 256 MB SDRAM memory. The basic image correlation algorithm is chosen for benchmarking as it finds widespread application for various template matching tasks such as face-recognition. The basic algorithm prototypes conform to OpenCV, a popular computer vision library. OpenCV algorithms can be easily ported to the ARM core which runs a popular operating system such as Linux or Windows CE. However, the DSP is architecturally more efficient at handling DFT algorithms. The algorithms are tested on a variety of images and performance results are presented measuring the speedup obtained due to dual-core implementation. A major advantage of this approach is that it allows the ARM processor to perform important real-time tasks, while the DSP addresses performance-hungry algorithms.

Clinically Approved Nanoparticle Imaging Agents

PubMed Central

Thakor, Avnesh S.; Jokerst, Jesse V.; Ghanouni, Pejman; Campbell, Jos L.; Mittra, Erik

2016-01-01

Nanoparticles are a new class of imaging agent used for both anatomic and molecular imaging. Nanoparticle-based imaging exploits the signal intensity, stability, and biodistribution behavior of submicron-diameter molecular imaging agents. This review focuses on nanoparticles used in human medical imaging, with an emphasis on radionuclide imaging and MRI. Newer nanoparticle platforms are also discussed in relation to theranostic and multimodal uses. PMID:27738007

Secure public cloud platform for medical images sharing.

PubMed

Pan, Wei; Coatrieux, Gouenou; Bouslimi, Dalel; Prigent, Nicolas

2015-01-01

Cloud computing promises medical imaging services offering large storage and computing capabilities for limited costs. In this data outsourcing framework, one of the greatest issues to deal with is data security. To do so, we propose to secure a public cloud platform devoted to medical image sharing by defining and deploying a security policy so as to control various security mechanisms. This policy stands on a risk assessment we conducted so as to identify security objectives with a special interest for digital content protection. These objectives are addressed by means of different security mechanisms like access and usage control policy, partial-encryption and watermarking.

An approach of point cloud denoising based on improved bilateral filtering

NASA Astrophysics Data System (ADS)

Zheng, Zeling; Jia, Songmin; Zhang, Guoliang; Li, Xiuzhi; Zhang, Xiangyin

2018-04-01

An omnidirectional mobile platform is designed for building point cloud based on an improved filtering algorithm which is employed to handle the depth image. First, the mobile platform can move flexibly and the control interface is convenient to control. Then, because the traditional bilateral filtering algorithm is time-consuming and inefficient, a novel method is proposed which called local bilateral filtering (LBF). LBF is applied to process depth image obtained by the Kinect sensor. The results show that the effect of removing noise is improved comparing with the bilateral filtering. In the condition of off-line, the color images and processed images are used to build point clouds. Finally, experimental results demonstrate that our method improves the speed of processing time of depth image and the effect of point cloud which has been built.

SU-D-206-01: Employing a Novel Consensus Optimization Strategy to Achieve Iterative Cone Beam CT Reconstruction On a Multi-GPU Platform

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

Li, B; Southern Medical University, Guangzhou, Guangdong; Tian, Z

Purpose: While compressed sensing-based cone-beam CT (CBCT) iterative reconstruction techniques have demonstrated tremendous capability of reconstructing high-quality images from undersampled noisy data, its long computation time still hinders wide application in routine clinic. The purpose of this study is to develop a reconstruction framework that employs modern consensus optimization techniques to achieve CBCT reconstruction on a multi-GPU platform for improved computational efficiency. Methods: Total projection data were evenly distributed to multiple GPUs. Each GPU performed reconstruction using its own projection data with a conventional total variation regularization approach to ensure image quality. In addition, the solutions from GPUs were subjectmore » to a consistency constraint that they should be identical. We solved the optimization problem with all the constraints considered rigorously using an alternating direction method of multipliers (ADMM) algorithm. The reconstruction framework was implemented using OpenCL on a platform with two Nvidia GTX590 GPU cards, each with two GPUs. We studied the performance of our method and demonstrated its advantages through a simulation case with a NCAT phantom and an experimental case with a Catphan phantom. Result: Compared with the CBCT images reconstructed using conventional FDK method with full projection datasets, our proposed method achieved comparable image quality with about one third projection numbers. The computation time on the multi-GPU platform was ∼55 s and ∼ 35 s in the two cases respectively, achieving a speedup factor of ∼ 3.0 compared with single GPU reconstruction. Conclusion: We have developed a consensus ADMM-based CBCT reconstruction method which enabled performing reconstruction on a multi-GPU platform. The achieved efficiency made this method clinically attractive.« less

Development of a WDM platform for charged-particle stopping experiments

DOE PAGES

Zylstra, A. B.; Frenje, J. A.; Grabowski, P. E.; ...

2016-05-26

A platform has been developed for generating large and relatively quiescent plasmas in the warm-dense matter (WDM) regime on the OMEGA laser facility. A cylindrical geometry is used to allow charged-particle probing along the axis. The plasma heating is radiative by L-shell emission generated on the outside of the cylinder. The cylinder drive is characterized with x-ray diagnostics. Possibilities for direct characterization of the plasma temperature are discussed. Lastly, the unimportance of electromagnetic fields around the target is demonstrated with proton radiography. We expect this platform to be used extensively in future experiments studying charged-particle stopping in this regime.

A contact-force regulated photoplethysmography (PPG) platform

NASA Astrophysics Data System (ADS)

Sim, Jai Kyoung; Ahn, Bongyoung; Doh, Il

2018-04-01

A photoplethysmography (PPG) platform integrated with a miniaturized force-regulator is proposed in this study. Because a thermo-pneumatic type regulator maintains a consistent contact-force between the PPG probe and the measuring site, a consistent and stable PPG signal can be obtained. We designed and fabricated a watch-type PPG platform with an overall size of 35 mm × 19 mm. In the PPG measurement on the radial artery wrist while posture of the wrist is changed to extension, neutral, or flexion, regulation of the contact-force provides consistent PPG measurements for which the variations in the PPG amplitude (PPGA) was 7.2 %. The proposed PPG platform can be applied to biosignal measurements in various fields such as PPG-based ANS monitoring to estimate nociception, sleep apnea syndrome, and psychological stress.

Global Magnetospheric Imaging from the Deep Space Gateway in Lunar Orbit

NASA Astrophysics Data System (ADS)

Chua, D. H.; Socker, D. G.; Englert, C. R.; Carter, M. T.; Plunkett, S. P.; Korendyke, C. M.; Meier, R. R.

2018-02-01

We propose to use the Deep Space Gateway as an observing platform for a magnetospheric imager that will capture the first direct global images of the interface between the incident solar wind and the Earth's magnetosphere.

Peripheral nerve regeneration using a microporous polylactic acid asymmetric conduit in a rabbit long-gap sciatic nerve transection model.

PubMed

Hsu, Shan-Hui; Chan, Shan-Ho; Chiang, Chih-Ming; Chen, Clayton Chi-Chang; Jiang, Ching-Fen

2011-05-01

The performance of an asymmetric conduit made of microporous polylactic acid (PLA) in promoting the long-term peripheral nerve regeneration across a 20-mm-long sciatic nerve gap was evaluated by a rabbit sciatic nerve transection model. Magnetic resonance imaging (MRI) was employed to monitor the nerve regeneration process. The extents of nerve regeneration and conduit degradation were quantified by image analysis. Functional and histological analyses were followed to assess nerve reinnervation. MR images showed that the transected nerve was connected at about 4 months. The diameter of the regenerated nerve continued to increase while the conduit was gradually degraded. The conduit was completely degraded in 18 months. The degradation kinetics in vivo was estimated based on MR images. The functional recovery after 18 months was ∼82% based on electrophysiology. The extension range of the operated limb was slowly recuperated to ∼81% at 18 months. Histology showed that nerve bundles were self-assembled after 16-18 months, but the morphologies were still different from those of normal sciatic nerve. This was the first work on the long-term evaluation of peripheral nerve regeneration in a rabbit model, and the first to report the use of MRI to obtain the real-time images of regenerated nerve in a biomaterial conduit as well as to define the degradation rate of the conduit in vivo. The platform established in this study serves to evaluate the regeneration of larger-diameter (>3-mm) nerve across a long-gap bridged by a conduit. Copyright © 2011 Elsevier Ltd. All rights reserved.

JHelioviewer: Open-Source Software for Discovery and Image Access in the Petabyte Age (Invited)

NASA Astrophysics Data System (ADS)

Mueller, D.; Dimitoglou, G.; Langenberg, M.; Pagel, S.; Dau, A.; Nuhn, M.; Garcia Ortiz, J. P.; Dietert, H.; Schmidt, L.; Hughitt, V. K.; Ireland, J.; Fleck, B.

2010-12-01

The unprecedented torrent of data returned by the Solar Dynamics Observatory is both a blessing and a barrier: a blessing for making available data with significantly higher spatial and temporal resolution, but a barrier for scientists to access, browse and analyze them. With such staggering data volume, the data is bound to be accessible only from a few repositories and users will have to deal with data sets effectively immobile and practically difficult to download. From a scientist's perspective this poses three challenges: accessing, browsing and finding interesting data while avoiding the proverbial search for a needle in a haystack. To address these challenges, we have developed JHelioviewer, an open-source visualization software that lets users browse large data volumes both as still images and movies. We did so by deploying an efficient image encoding, storage, and dissemination solution using the JPEG 2000 standard. This solution enables users to access remote images at different resolution levels as a single data stream. Users can view, manipulate, pan, zoom, and overlay JPEG 2000 compressed data quickly, without severe network bandwidth penalties. Besides viewing data, the browser provides third-party metadata and event catalog integration to quickly locate data of interest, as well as an interface to the Virtual Solar Observatory to download science-quality data. As part of the Helioviewer Project, JHelioviewer offers intuitive ways to browse large amounts of heterogeneous data remotely and provides an extensible and customizable open-source platform for the scientific community.

Aerolian erosion, transport, and deposition of volcaniclastic sands among the shifting sand dunes, Christmas Lake Valley, Oregon: TIMS image analysis

NASA Technical Reports Server (NTRS)

Edgett, Kenneth S.; Ramsey, Michael S.; Christensen, Philip R.

1995-01-01

Remote sensing is a tool that, in the context of aeolian studies, offers a synoptic view of a dune field, sand sea, or entire desert region. Blount et al. (1990) presented one of the first studies demonstrating the power of multispectral images for interpreting the dynamic history of an aeolian sand sea. Blount's work on the Gran Desierto of Mexico used a Landsat TM scene and a linear spectral mixing model to show where different sand populations occur and along what paths these sands may have traveled before becoming incorporated into dunes. Interpretation of sand transport paths and sources in the Gran Desierto led to an improved understanding of the origin and Holocene history of the dunes. With the anticipated advent of the EOS-A platform and ASTER thermal infrared capability in 1998, it will become possible to look at continental sand seas and map sand transport paths using 8-12 mu m bands that are well-suited to tracking silicate sediments. A logical extension of Blount's work is to attempt a similar study using thermal infrared images. One such study has already begun by looking at feldspar, quartz, magnetite, and clay distributions in the Kelso Dunes of southern California. This paper describes the geology and application of TIMS image analysis of a less-well known Holocene dune field in south central Oregon using TIMS data obtained in 1991.

MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data

PubMed Central

Moore, Eider B; Poliakov, Andrew V; Lincoln, Peter; Brinkley, James F

2007-01-01

Background Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system. Results We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: . Conclusion MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine. PMID:17937818

MindSeer: a portable and extensible tool for visualization of structural and functional neuroimaging data.

PubMed

Moore, Eider B; Poliakov, Andrew V; Lincoln, Peter; Brinkley, James F

2007-10-15

Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that include some aspect of 3-D visualization, including both free and commercial products. These applications range from highly specific programs for a single modality, to general purpose toolkits that include many image processing functions in addition to visualization. However, few if any of these combine both stand-alone and remote multi-modality visualization in an open source, portable and extensible tool that is easy to install and use, yet can be included as a component of a larger information system. We have developed a new open source multimodality 3-D visualization application, called MindSeer, that has these features: integrated and interactive 3-D volume and surface visualization, Java and Java3D for true cross-platform portability, one-click installation and startup, integrated data management to help organize large studies, extensibility through plugins, transparent remote visualization, and the ability to be integrated into larger information management systems. We describe the design and implementation of the system, as well as several case studies that demonstrate its utility. These case studies are available as tutorials or demos on the associated website: http://sig.biostr.washington.edu/projects/MindSeer. MindSeer provides a powerful visualization tool for multimodality neuroimaging data. Its architecture and unique features also allow it to be extended into other visualization domains within biomedicine.

Computerized tomography platform using beta rays

NASA Astrophysics Data System (ADS)

Paetkau, Owen; Parsons, Zachary; Paetkau, Mark

2017-12-01

A computerized tomography (CT) system using a 0.1 μCi Sr-90 beta source, Geiger counter, and low density foam samples was developed. A simple algorithm was used to construct images from the data collected with the beta CT scanner. The beta CT system is analogous to X-ray CT as both types of radiation are sensitive to density variations. This system offers a platform for learning opportunities in an undergraduate laboratory, covering topics such as image reconstruction algorithms, radiation exposure, and the energy dependence of absorption.

Assessment of the cPAS-based BGISEQ-500 platform for metagenomic sequencing.

PubMed

Fang, Chao; Zhong, Huanzi; Lin, Yuxiang; Chen, Bing; Han, Mo; Ren, Huahui; Lu, Haorong; Luber, Jacob M; Xia, Min; Li, Wangsheng; Stein, Shayna; Xu, Xun; Zhang, Wenwei; Drmanac, Radoje; Wang, Jian; Yang, Huanming; Hammarström, Lennart; Kostic, Aleksandar D; Kristiansen, Karsten; Li, Junhua

2018-03-01

More extensive use of metagenomic shotgun sequencing in microbiome research relies on the development of high-throughput, cost-effective sequencing. Here we present a comprehensive evaluation of the performance of the new high-throughput sequencing platform BGISEQ-500 for metagenomic shotgun sequencing and compare its performance with that of 2 Illumina platforms. Using fecal samples from 20 healthy individuals, we evaluated the intra-platform reproducibility for metagenomic sequencing on the BGISEQ-500 platform in a setup comprising 8 library replicates and 8 sequencing replicates. Cross-platform consistency was evaluated by comparing 20 pairwise replicates on the BGISEQ-500 platform vs the Illumina HiSeq 2000 platform and the Illumina HiSeq 4000 platform. In addition, we compared the performance of the 2 Illumina platforms against each other. By a newly developed overall accuracy quality control method, an average of 82.45 million high-quality reads (96.06% of raw reads) per sample, with 90.56% of bases scoring Q30 and above, was obtained using the BGISEQ-500 platform. Quantitative analyses revealed extremely high reproducibility between BGISEQ-500 intra-platform replicates. Cross-platform replicates differed slightly more than intra-platform replicates, yet a high consistency was observed. Only a low percentage (2.02%-3.25%) of genes exhibited significant differences in relative abundance comparing the BGISEQ-500 and HiSeq platforms, with a bias toward genes with higher GC content being enriched on the HiSeq platforms. Our study provides the first set of performance metrics for human gut metagenomic sequencing data using BGISEQ-500. The high accuracy and technical reproducibility confirm the applicability of the new platform for metagenomic studies, though caution is still warranted when combining metagenomic data from different platforms.

Helioviewer.org: Simple Solar and Heliospheric Data Visualization

NASA Astrophysics Data System (ADS)

Hughitt, V. K.; Ireland, J.; Mueller, D.

2011-12-01

Helioviewer.org is a free and open-source web application for exploring solar physics data in a simple and intuitive manner. Over the past several years, Helioviewer.org has enabled thousands of users from across the globe to explore the inner heliosphere, providing access to over ten million images from the SOHO, SDO, and STEREO missions. While Helioviewer.org has seen a surge in use by the public in recent months, it is still ultimately a science tool. The newest version of Helioviewer.org provides access to science-quality data for all available images through the Virtual Solar Observatory (VSO). In addition to providing a powerful platform for browsing heterogeneous sets of solar data, Helioviewer.org also seeks to be as flexible and extensible as possible, providing access to much of its functionality via a simple Application Programming Interface (API). Recently, the Helioviewer.org API was used for two such applications: a Wordpress plugin, and a Python library for solar physics data analysis (SunPy). These applications are discussed and examples of API usage are provided. Finally, Helioviewer.org is undergoing continual development, with new features being added on a regular basis. Recent updates to Helioviewer.org are discussed, along with a preview of things to come.

Accelerating object detection via a visual-feature-directed search cascade: algorithm and field programmable gate array implementation

NASA Astrophysics Data System (ADS)

Kyrkou, Christos; Theocharides, Theocharis

2016-07-01

Object detection is a major step in several computer vision applications and a requirement for most smart camera systems. Recent advances in hardware acceleration for real-time object detection feature extensive use of reconfigurable hardware [field programmable gate arrays (FPGAs)], and relevant research has produced quite fascinating results, in both the accuracy of the detection algorithms as well as the performance in terms of frames per second (fps) for use in embedded smart camera systems. Detecting objects in images, however, is a daunting task and often involves hardware-inefficient steps, both in terms of the datapath design and in terms of input/output and memory access patterns. We present how a visual-feature-directed search cascade composed of motion detection, depth computation, and edge detection, can have a significant impact in reducing the data that needs to be examined by the classification engine for the presence of an object of interest. Experimental results on a Spartan 6 FPGA platform for face detection indicate data search reduction of up to 95%, which results in the system being able to process up to 50 1024×768 pixels images per second with a significantly reduced number of false positives.

Carrington-L5: The UK/US Space Weather Operational Mission.

NASA Astrophysics Data System (ADS)

Bisi, M. M.; Trichas, M.

2015-12-01

Airbus Defence and Space (UK) have carried out a study for an operational L5 space weather mission, in collaboration with RAL, the UK Met Office, UCL and Imperial College London. The study looked at the user requirements for an operational mission, a model instrument payload, and a mission/spacecraft concept. A particular focus is cost effectiveness and timelineness of the data, suitable for operational forecasting needs. The study focussed on a mission at L5 assuming that a US mission to L1 will already occur, on the basis that L5 offers the greatest benefit for SWE predictions. The baseline payload has been selected to address all MOSWOC/SWPC priorities using UK/US instruments, consisting of: a heliospheric imager, coronagraph, EUV imager, magnetograph, magnetometer, solar wind analyser and radiation monitor. The platform is based on extensive re-use from Airbus' past missions to minimize the cost and a Falcon-9 launcher has been selected on the same basis. A schedule analysis shows that the earliest launch could occur in 2020, assuming Phase A KO in 2015. The study team have selected the name "Carrington" for the mission, reflecting the UK's proud history in this domain.

The Image Data Resource: A Bioimage Data Integration and Publication Platform.

PubMed

Williams, Eleanor; Moore, Josh; Li, Simon W; Rustici, Gabriella; Tarkowska, Aleksandra; Chessel, Anatole; Leo, Simone; Antal, Bálint; Ferguson, Richard K; Sarkans, Ugis; Brazma, Alvis; Salas, Rafael E Carazo; Swedlow, Jason R

2017-08-01

Access to primary research data is vital for the advancement of science. To extend the data types supported by community repositories, we built a prototype Image Data Resource (IDR) that collects and integrates imaging data acquired across many different imaging modalities. IDR links data from several imaging modalities, including high-content screening, super-resolution and time-lapse microscopy, digital pathology, public genetic or chemical databases, and cell and tissue phenotypes expressed using controlled ontologies. Using this integration, IDR facilitates the analysis of gene networks and reveals functional interactions that are inaccessible to individual studies. To enable re-analysis, we also established a computational resource based on Jupyter notebooks that allows remote access to the entire IDR. IDR is also an open source platform that others can use to publish their own image data. Thus IDR provides both a novel on-line resource and a software infrastructure that promotes and extends publication and re-analysis of scientific image data.

Light-Directed Ranging System Implementing Single Camera System for Telerobotics Applications

NASA Technical Reports Server (NTRS)

Wells, Dennis L. (Inventor); Li, Larry C. (Inventor); Cox, Brian J. (Inventor)

1997-01-01

A laser-directed ranging system has utility for use in various fields, such as telerobotics applications and other applications involving physically handicapped individuals. The ranging system includes a single video camera and a directional light source such as a laser mounted on a camera platform, and a remotely positioned operator. In one embodiment, the position of the camera platform is controlled by three servo motors to orient the roll axis, pitch axis and yaw axis of the video cameras, based upon an operator input such as head motion. The laser is offset vertically and horizontally from the camera, and the laser/camera platform is directed by the user to point the laser and the camera toward a target device. The image produced by the video camera is processed to eliminate all background images except for the spot created by the laser. This processing is performed by creating a digital image of the target prior to illumination by the laser, and then eliminating common pixels from the subsequent digital image which includes the laser spot. A reference point is defined at a point in the video frame, which may be located outside of the image area of the camera. The disparity between the digital image of the laser spot and the reference point is calculated for use in a ranging analysis to determine range to the target.

The implementation of depth measurement and related algorithms based on binocular vision in embedded AM5728

NASA Astrophysics Data System (ADS)

Deng, Zhiwei; Li, Xicai; Shi, Junsheng; Huang, Xiaoqiao; Li, Feiyan

2018-01-01

Depth measurement is the most basic measurement in various machine vision, such as automatic driving, unmanned aerial vehicle (UAV), robot and so on. And it has a wide range of use. With the development of image processing technology and the improvement of hardware miniaturization and processing speed, real-time depth measurement using dual cameras has become a reality. In this paper, an embedded AM5728 and the ordinary low-cost dual camera is used as the hardware platform. The related algorithms of dual camera calibration, image matching and depth calculation have been studied and implemented on the hardware platform, and hardware design and the rationality of the related algorithms of the system are tested. The experimental results show that the system can realize simultaneous acquisition of binocular images, switching of left and right video sources, display of depth image and depth range. For images with a resolution of 640 × 480, the processing speed of the system can be up to 25 fps. The experimental results show that the optimal measurement range of the system is from 0.5 to 1.5 meter, and the relative error of the distance measurement is less than 5%. Compared with the PC, ARM11 and DMCU hardware platforms, the embedded AM5728 hardware is good at meeting real-time depth measurement requirements in ensuring the image resolution.

Tectonic framework of Turkish sedimentary basins

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

Yilmaz, P.O.

1988-08-01

Turkey's exploration potential primarily exists in seven onshore (Southeast Turkey platform, Tauride platform, Pontide platform, East Anatolian platform, Interior, Trace, and Adana) basins and four offshore (Black Sea, Marmara Sea, Aegean Sea, and Mediterranean Sea) regional basins formed during the Mesozoic and Tertiary. The Mesozoic basins are the onshore basins: Southeast Turkey, Tauride, Pontide, East Anatolian, and Interior basins. Due to their common tectonic heritage, the southeast Turkey and Tauride basins have similar source rocks, structural growth, trap size, and structural styles. In the north, another Mesozoic basin, the Pontide platform, has a much more complex history and very littlemore » in common with the southerly basins. The Pontide has two distinct parts; the west has Paleozoic continental basement and the east is underlain by island-arc basement of Jurassic age. The plays are in the upper Mesozoic rocks in the west Pontide. The remaining Mesozoic basins of the onshore Interior and East Anatolian basins are poorly known and very complex. Their source, reservoir, and seal are not clearly defined. The basins formed during several orogenic phases in mesozoic and Tertiary. The Cenozoic basins are the onshore Thrace and Adana basins, and all offshore regional basins formed during Miocene extension. Further complicating the onshore basins evolution is the superposition of Cenozoic basins and Mesozoic basins. The Thrace basin in the northwest and Adana basin in the south both originate from Tertiary extension over Tethyan basement and result in a similar source, reservoir, and seal. Local strike-slip movement along the North Anatolian fault modifies the Thrace basin structures, influencing its hydrocarbon potential.« less

Development of estimation system of knee extension strength using image features in ultrasound images of rectus femoris

NASA Astrophysics Data System (ADS)

Murakami, Hiroki; Watanabe, Tsuneo; Fukuoka, Daisuke; Terabayashi, Nobuo; Hara, Takeshi; Muramatsu, Chisako; Fujita, Hiroshi

2016-04-01

The word "Locomotive syndrome" has been proposed to describe the state of requiring care by musculoskeletal disorders and its high-risk condition. Reduction of the knee extension strength is cited as one of the risk factors, and the accurate measurement of the strength is needed for the evaluation. The measurement of knee extension strength using a dynamometer is one of the most direct and quantitative methods. This study aims to develop a system for measuring the knee extension strength using the ultrasound images of the rectus femoris muscles obtained with non-invasive ultrasonic diagnostic equipment. First, we extract the muscle area from the ultrasound images and determine the image features, such as the thickness of the muscle. We combine these features and physical features, such as the patient's height, and build a regression model of the knee extension strength from training data. We have developed a system for estimating the knee extension strength by applying the regression model to the features obtained from test data. Using the test data of 168 cases, correlation coefficient value between the measured values and estimated values was 0.82. This result suggests that this system can estimate knee extension strength with high accuracy.

A simple and low-cost biofilm quantification method using LED and CMOS image sensor.

PubMed

Kwak, Yeon Hwa; Lee, Junhee; Lee, Junghoon; Kwak, Soo Hwan; Oh, Sangwoo; Paek, Se-Hwan; Ha, Un-Hwan; Seo, Sungkyu

2014-12-01

A novel biofilm detection platform, which consists of a cost-effective red, green, and blue light-emitting diode (RGB LED) as a light source and a lens-free CMOS image sensor as a detector, is designed. This system can measure the diffraction patterns of cells from their shadow images, and gather light absorbance information according to the concentration of biofilms through a simple image processing procedure. Compared to a bulky and expensive commercial spectrophotometer, this platform can provide accurate and reproducible biofilm concentration detection and is simple, compact, and inexpensive. Biofilms originating from various bacterial strains, including Pseudomonas aeruginosa (P. aeruginosa), were tested to demonstrate the efficacy of this new biofilm detection approach. The results were compared with the results obtained from a commercial spectrophotometer. To utilize a cost-effective light source (i.e., an LED) for biofilm detection, the illumination conditions were optimized. For accurate and reproducible biofilm detection, a simple, custom-coded image processing algorithm was developed and applied to a five-megapixel CMOS image sensor, which is a cost-effective detector. The concentration of biofilms formed by P. aeruginosa was detected and quantified by varying the indole concentration, and the results were compared with the results obtained from a commercial spectrophotometer. The correlation value of the results from those two systems was 0.981 (N = 9, P < 0.01) and the coefficients of variation (CVs) were approximately threefold lower at the CMOS image-sensor platform. Copyright © 2014 Elsevier B.V. All rights reserved.

A Supporting Platform for Semi-Automatic Hyoid Bone Tracking and Parameter Extraction from Videofluoroscopic Images for the Diagnosis of Dysphagia Patients.

PubMed

Lee, Jun Chang; Nam, Kyoung Won; Jang, Dong Pyo; Paik, Nam Jong; Ryu, Ju Seok; Kim, In Young

2017-04-01

Conventional kinematic analysis of videofluoroscopic (VF) swallowing image, most popular for dysphagia diagnosis, requires time-consuming and repetitive manual extraction of diagnostic information from multiple images representing one swallowing period, which results in a heavy work load for clinicians and excessive hospital visits for patients to receive counseling and prescriptions. In this study, a software platform was developed that can assist in the VF diagnosis of dysphagia by automatically extracting a two-dimensional moving trajectory of the hyoid bone as well as 11 temporal and kinematic parameters. Fifty VF swallowing videos containing both non-mandible-overlapped and mandible-overlapped cases from eight patients with dysphagia of various etiologies and 19 videos from ten healthy controls were utilized for performance verification. Percent errors of hyoid bone tracking were 1.7 ± 2.1% for non-overlapped images and 4.2 ± 4.8% for overlapped images. Correlation coefficients between manually extracted and automatically extracted moving trajectories of the hyoid bone were 0.986 ± 0.017 (X-axis) and 0.992 ± 0.006 (Y-axis) for non-overlapped images, and 0.988 ± 0.009 (X-axis) and 0.991 ± 0.006 (Y-axis) for overlapped images. Based on the experimental results, we believe that the proposed platform has the potential to improve the satisfaction of both clinicians and patients with dysphagia.

Constructing Cost-Effective and Targetable ICS Honeypots Suited for Production Networks

DTIC Science & Technology

2015-03-26

introducing Honeyd+ has a marginal impact on performance. Notable findings are that the Raspberry Pi is the preferred hosting platform for the EtherNet/IP... Raspberry Pi or Gumstix, which is a low-cost approach to replicating multiple decoys. One hidden drawback to low- interaction honeypots is the extensive time...EtherNet/IP industrial protocol. Honeyd+ is hosted on a low-cost computing platform ( Raspberry Pi running Raspbian, approximately $50) and a high-cost

Teachable, high-content analytics for live-cell, phase contrast movies.

PubMed

Alworth, Samuel V; Watanabe, Hirotada; Lee, James S J

2010-09-01

CL-Quant is a new solution platform for broad, high-content, live-cell image analysis. Powered by novel machine learning technologies and teach-by-example interfaces, CL-Quant provides a platform for the rapid development and application of scalable, high-performance, and fully automated analytics for a broad range of live-cell microscopy imaging applications, including label-free phase contrast imaging. The authors used CL-Quant to teach off-the-shelf universal analytics, called standard recipes, for cell proliferation, wound healing, cell counting, and cell motility assays using phase contrast movies collected on the BioStation CT and BioStation IM platforms. Similar to application modules, standard recipes are intended to work robustly across a wide range of imaging conditions without requiring customization by the end user. The authors validated the performance of the standard recipes by comparing their performance with truth created manually, or by custom analytics optimized for each individual movie (and therefore yielding the best possible result for the image), and validated by independent review. The validation data show that the standard recipes' performance is comparable with the validated truth with low variation. The data validate that the CL-Quant standard recipes can provide robust results without customization for live-cell assays in broad cell types and laboratory settings.

MSiReader: an open-source interface to view and analyze high resolving power MS imaging files on Matlab platform.

PubMed

Robichaud, Guillaume; Garrard, Kenneth P; Barry, Jeremy A; Muddiman, David C

2013-05-01

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

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

MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform

NASA Astrophysics Data System (ADS)

Robichaud, Guillaume; Garrard, Kenneth P.; Barry, Jeremy A.; Muddiman, David C.

2013-05-01

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.

Mechanically latchable tiltable platform for forming micromirrors and micromirror arrays

DOEpatents

Garcia, Ernest J [Albuquerque, NM; Polosky, Marc A [Tijeras, NM; Sleefe, Gerard E [Cedar Crest, NM

2006-12-12

A microelectromechanical (MEM) apparatus is disclosed which includes a platform that can be electrostatically tilted from being parallel to a substrate on which the platform to being tilted at an angle of 1 20 degrees with respect to the substrate. Once the platform has been tilted to a maximum angle of tilt, the platform can be locked in position using an electrostatically-operable latching mechanism which engages a tab protruding below the platform. The platform has a light-reflective upper surface which can be optionally coated to provide an enhanced reflectivity and form a micromirror. An array of such micromirrors can be formed on a common substrate for applications including optical switching (e.g. for fiber optic communications), optical information processing, image projection displays or non-volatile optical memories.

Genomics Portals: integrative web-platform for mining genomics data.

PubMed

Shinde, Kaustubh; Phatak, Mukta; Johannes, Freudenberg M; Chen, Jing; Li, Qian; Vineet, Joshi K; Hu, Zhen; Ghosh, Krishnendu; Meller, Jaroslaw; Medvedovic, Mario

2010-01-13

A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org.

Genomics Portals: integrative web-platform for mining genomics data

PubMed Central

2010-01-01

Background A large amount of experimental data generated by modern high-throughput technologies is available through various public repositories. Our knowledge about molecular interaction networks, functional biological pathways and transcriptional regulatory modules is rapidly expanding, and is being organized in lists of functionally related genes. Jointly, these two sources of information hold a tremendous potential for gaining new insights into functioning of living systems. Results Genomics Portals platform integrates access to an extensive knowledge base and a large database of human, mouse, and rat genomics data with basic analytical visualization tools. It provides the context for analyzing and interpreting new experimental data and the tool for effective mining of a large number of publicly available genomics datasets stored in the back-end databases. The uniqueness of this platform lies in the volume and the diversity of genomics data that can be accessed and analyzed (gene expression, ChIP-chip, ChIP-seq, epigenomics, computationally predicted binding sites, etc), and the integration with an extensive knowledge base that can be used in such analysis. Conclusion The integrated access to primary genomics data, functional knowledge and analytical tools makes Genomics Portals platform a unique tool for interpreting results of new genomics experiments and for mining the vast amount of data stored in the Genomics Portals backend databases. Genomics Portals can be accessed and used freely at http://GenomicsPortals.org. PMID:20070909

Sedimentological evolution of the Cretaceous carbonate platform of Chiapas (Mexico)

NASA Astrophysics Data System (ADS)

Cros, Pierre; Michaud, François; Fourcade, Eric; Fleury, Jean-Jacques

1998-07-01

The Cretaceous epicontinental carbonate platform of Chiapas (south-east of Mexico) extends along a 200 km NW-SE narrow strip, north of the Sierra Madre basement, from Ocozocoautla to Comitan. In the western and central domain, three stratigraphic sections of the Sierra Madre Formation (late Aptian to early Senonian) display well exposed facies sequences enabling broad facies correlations about: (1) The successive transgressive-regressive stages, (2) the different subsidence rates controlling the outer to inner platform environmental evolution, (3) the conditions of tectonically controlled partial platform drowning during Campanian-Maastrichtian. Three other sections through the eastern Maastrichtian carbonate platform area record the changes from limestone to dolomite during the Angostura Maastrichtian platform stage. This evolution of thickness and facies in the occidental domain of Piedra Parada and in the central domain of Guadalupe Victoria and Julian Grajales illustrates the settlement process of the carbonate platform and the general decreasing of the thickness of the Sierra Madre Formation from west to east. The eastern platform domain (Comitan) crops out extensively and enables new correlations along a south-north transect. The Sierra Madre Formation and Angostura Formation documents continuous carbonate platform sedimentation with foraminifers, rudists and dasycladacean algae during Campanian and Maastrichtian. These sections permit palaeogeographical comparisons of depositional conditions of the Mexican margin of the Maya block.

Advanced Forensic Format: an Open Extensible Format for Disk Imaging

NASA Astrophysics Data System (ADS)

Garfinkel, Simson; Malan, David; Dubec, Karl-Alexander; Stevens, Christopher; Pham, Cecile

This paper describes the Advanced Forensic Format (AFF), which is designed as an alternative to current proprietary disk image formats. AFF offers two significant benefits. First, it is more flexible because it allows extensive metadata to be stored with images. Second, AFF images consume less disk space than images in other formats (e.g., EnCase images). This paper also describes the Advanced Disk Imager, a new program for acquiring disk images that compares favorably with existing alternatives.

Flexible imaging payload for real-time fluorescent biological imaging in parabolic, suborbital and space analog environments

NASA Astrophysics Data System (ADS)

Bamsey, Matthew T.; Paul, Anna-Lisa; Graham, Thomas; Ferl, Robert J.

2014-10-01

Fluorescent imaging offers the ability to monitor biological functions, in this case biological responses to space-related environments. For plants, fluorescent imaging can include general health indicators such as chlorophyll fluorescence as well as specific metabolic indicators such as engineered fluorescent reporters. This paper describes the Flex Imager a fluorescent imaging payload designed for Middeck Locker deployment and now tested on multiple flight and flight-related platforms. The Flex Imager and associated payload elements have been developed with a focus on 'flexibility' allowing for multiple imaging modalities and change-out of individual imaging or control components in the field. The imaging platform is contained within the standard Middeck Locker spaceflight form factor, with components affixed to a baseplate that permits easy rearrangement and fine adjustment of components. The Flex Imager utilizes standard software packages to simplify operation, operator training, and evaluation by flight provider flight test engineers, or by researchers processing the raw data. Images are obtained using a commercial cooled CCD image sensor, with light-emitting diodes for excitation and a suite of filters that allow biological samples to be imaged over wavelength bands of interest. Although baselined for the monitoring of green fluorescent protein and chlorophyll fluorescence from Arabidopsis samples, the Flex Imager payload permits imaging of any biological sample contained within a standard 10 cm by 10 cm square Petri plate. A sample holder was developed to secure sample plates under different flight profiles while permitting sample change-out should crewed operations be possible. In addition to crew-directed imaging, autonomous or telemetric operation of the payload is also a viable operational mode. An infrared camera has also been integrated into the Flex Imager payload to allow concurrent fluorescent and thermal imaging of samples. The Flex Imager has been utilized to assess, in real-time, the response of plants to novel environments including various spaceflight analogs, including several parabolic flight environments as well as hypobaric plant growth chambers. Basic performance results obtained under these operational environments, as well as laboratory-based tests are described. The Flex Imager has also been designed to be compatible with emerging suborbital platforms.

A coral-on-a-chip microfluidic platform enabling live-imaging microscopy of reef-building corals

PubMed Central

Shapiro, Orr H.; Kramarsky-Winter, Esti; Gavish, Assaf R.; Stocker, Roman; Vardi, Assaf

2016-01-01

Coral reefs, and the unique ecosystems they support, are facing severe threats by human activities and climate change. Our understanding of these threats is hampered by the lack of robust approaches for studying the micro-scale interactions between corals and their environment. Here we present an experimental platform, coral-on-a-chip, combining micropropagation and microfluidics to allow direct microscopic study of live coral polyps. The small and transparent coral micropropagates are ideally suited for live-imaging microscopy, while the microfluidic platform facilitates long-term visualization under controlled environmental conditions. We demonstrate the usefulness of this approach by imaging coral micropropagates at previously unattainable spatio-temporal resolutions, providing new insights into several micro-scale processes including coral calcification, coral–pathogen interaction and the loss of algal symbionts (coral bleaching). Coral-on-a-chip thus provides a powerful method for studying coral physiology in vivo at the micro-scale, opening new vistas in coral biology. PMID:26940983

A coral-on-a-chip microfluidic platform enabling live-imaging microscopy of reef-building corals.

PubMed

Shapiro, Orr H; Kramarsky-Winter, Esti; Gavish, Assaf R; Stocker, Roman; Vardi, Assaf

2016-03-04

Coral reefs, and the unique ecosystems they support, are facing severe threats by human activities and climate change. Our understanding of these threats is hampered by the lack of robust approaches for studying the micro-scale interactions between corals and their environment. Here we present an experimental platform, coral-on-a-chip, combining micropropagation and microfluidics to allow direct microscopic study of live coral polyps. The small and transparent coral micropropagates are ideally suited for live-imaging microscopy, while the microfluidic platform facilitates long-term visualization under controlled environmental conditions. We demonstrate the usefulness of this approach by imaging coral micropropagates at previously unattainable spatio-temporal resolutions, providing new insights into several micro-scale processes including coral calcification, coral-pathogen interaction and the loss of algal symbionts (coral bleaching). Coral-on-a-chip thus provides a powerful method for studying coral physiology in vivo at the micro-scale, opening new vistas in coral biology.

A Platform to Monitor Tumor Cellular and Vascular Response to Radiation Therapy by Optical Coherence Tomography and Fluorescence Microscopy in vivo

NASA Astrophysics Data System (ADS)

Leung, Michael Ka Kit

Radiotherapy plays a significant role in cancer treatment, and is thought to be curative by mainly killing tumor cells through damage to their genetic material. However, recent findings indicate that the tumor's vascular blood supply is also a major determinant of radiation response. The goals of this thesis are to: (1) develop an experimental platform for small animals to deliver ionizing radiation and perform high-resolution optical imaging to treatment targets, and (2) use this toolkit to longitudinally monitor the response of tumors and the associated vasculature. The thesis has achieved: (1) customization of a novel micro-irradiator for mice, (2) technical development of an improved optical coherence tomography imaging system, (3) comprehensive experimental protocol and imaging optimization for optical microscopy in a specialized animal model, and (4) completion of a feasibility study to demonstrate the capabilities of the experimental platform in monitoring the response of tumor and vasculature to radiotherapy.

Design method of ARM based embedded iris recognition system

NASA Astrophysics Data System (ADS)

Wang, Yuanbo; He, Yuqing; Hou, Yushi; Liu, Ting

2008-03-01

With the advantages of non-invasiveness, uniqueness, stability and low false recognition rate, iris recognition has been successfully applied in many fields. Up to now, most of the iris recognition systems are based on PC. However, a PC is not portable and it needs more power. In this paper, we proposed an embedded iris recognition system based on ARM. Considering the requirements of iris image acquisition and recognition algorithm, we analyzed the design method of the iris image acquisition module, designed the ARM processing module and its peripherals, studied the Linux platform and the recognition algorithm based on this platform, finally actualized the design method of ARM-based iris imaging and recognition system. Experimental results show that the ARM platform we used is fast enough to run the iris recognition algorithm, and the data stream can flow smoothly between the camera and the ARM chip based on the embedded Linux system. It's an effective method of using ARM to actualize portable embedded iris recognition system.

History and Generality of Aquatox

EPA Pesticide Factsheets

Aquatic fate, toxicology, and ecosystem submodels were coupled to “close the loop,” representing both direct and indirecteffects. the model is also a platform to which other environmental stressors may be added for extensive analysis.

Space platforms - A cost effective evolution of Spacelab operation

NASA Technical Reports Server (NTRS)

Stofan, A. J.

1981-01-01

The capabilities added to the Shuttle/Spacelab configuration by the addition of the Power Extension Package (PEP), the Power System (PS), and the Science and Applications Space Platforms (SASP) are reviewed with an emphasis on SASP. SASP are intended for placement in orbit by the Shuttle to test new instruments and systems, for clustering of instrumentation, and for servicing, refurbishment, repair, or augmentation by the Shuttle. The PEP permits extended stays in orbit (30 days), and the PS is an orbital solar array and energy storage system acting as a free flying spacecraft. The Shuttle can deliver payloads to the PS or attach to it for extension of the Spacelab operations. Applications of SASP for long term space-based biological experiments are outlined, and the fact that SASP do not increase the required Shuttle in-orbit time is stressed.

Gadolinium-doped hollow CeO2-ZrO2 nanoplatform as multifunctional MRI/CT dual-modal imaging agent and drug delivery vehicle.

PubMed

Wei, Zuwu; Wu, Ming; Li, Zuanfang; Lin, Zhan; Zeng, Jinhua; Sun, Haiyan; Liu, Xiaolong; Liu, Jingfeng; Li, Buhong; Zeng, Yongyi

2018-11-01

Developing multifunctional nanoparticle-based theranostic platform for cancer diagnosis and treatment is highly desirable, however, most of the present theranostic platforms are fabricated via complicated structure/composition design and time-consuming synthesis procedures. Herein, the multifunctional Gd/CeO 2 -ZrO 2 /DOX-PEG nanoplatform with single nano-structure was fabricated through a facile route, which possessed MR/CT dual-model imaging and chemotherapy ability. The nanoplatform not only exhibited well-defined shapes, tunable compositions and narrow size distributions, but also presented a well anti-cancer effect and MR/CT imaging ability. Therefore, the Gd/CeO 2 -ZrO 2 /DOX-PEG nanoplatform could be applied for chemotherapy as well as dual-model MR/CT imaging.

Algorithm for automatic image dodging of unmanned aerial vehicle images using two-dimensional radiometric spatial attributes

NASA Astrophysics Data System (ADS)

Li, Wenzhuo; Sun, Kaimin; Li, Deren; Bai, Ting

2016-07-01

Unmanned aerial vehicle (UAV) remote sensing technology has come into wide use in recent years. The poor stability of the UAV platform, however, produces more inconsistencies in hue and illumination among UAV images than other more stable platforms. Image dodging is a process used to reduce these inconsistencies caused by different imaging conditions. We propose an algorithm for automatic image dodging of UAV images using two-dimensional radiometric spatial attributes. We use object-level image smoothing to smooth foreground objects in images and acquire an overall reference background image by relative radiometric correction. We apply the Contourlet transform to separate high- and low-frequency sections for every single image, and replace the low-frequency section with the low-frequency section extracted from the corresponding region in the overall reference background image. We apply the inverse Contourlet transform to reconstruct the final dodged images. In this process, a single image must be split into reasonable block sizes with overlaps due to large pixel size. Experimental mosaic results show that our proposed method reduces the uneven distribution of hue and illumination. Moreover, it effectively eliminates dark-bright interstrip effects caused by shadows and vignetting in UAV images while maximally protecting image texture information.

A New Parallel Approach for Accelerating the GPU-Based Execution of Edge Detection Algorithms

PubMed Central

Emrani, Zahra; Bateni, Soroosh; Rabbani, Hossein

2017-01-01

Real-time image processing is used in a wide variety of applications like those in medical care and industrial processes. This technique in medical care has the ability to display important patient information graphi graphically, which can supplement and help the treatment process. Medical decisions made based on real-time images are more accurate and reliable. According to the recent researches, graphic processing unit (GPU) programming is a useful method for improving the speed and quality of medical image processing and is one of the ways of real-time image processing. Edge detection is an early stage in most of the image processing methods for the extraction of features and object segments from a raw image. The Canny method, Sobel and Prewitt filters, and the Roberts’ Cross technique are some examples of edge detection algorithms that are widely used in image processing and machine vision. In this work, these algorithms are implemented using the Compute Unified Device Architecture (CUDA), Open Source Computer Vision (OpenCV), and Matrix Laboratory (MATLAB) platforms. An existing parallel method for Canny approach has been modified further to run in a fully parallel manner. This has been achieved by replacing the breadth- first search procedure with a parallel method. These algorithms have been compared by testing them on a database of optical coherence tomography images. The comparison of results shows that the proposed implementation of the Canny method on GPU using the CUDA platform improves the speed of execution by 2–100× compared to the central processing unit-based implementation using the OpenCV and MATLAB platforms. PMID:28487831

A New Parallel Approach for Accelerating the GPU-Based Execution of Edge Detection Algorithms.

PubMed

Emrani, Zahra; Bateni, Soroosh; Rabbani, Hossein

2017-01-01

Real-time image processing is used in a wide variety of applications like those in medical care and industrial processes. This technique in medical care has the ability to display important patient information graphi graphically, which can supplement and help the treatment process. Medical decisions made based on real-time images are more accurate and reliable. According to the recent researches, graphic processing unit (GPU) programming is a useful method for improving the speed and quality of medical image processing and is one of the ways of real-time image processing. Edge detection is an early stage in most of the image processing methods for the extraction of features and object segments from a raw image. The Canny method, Sobel and Prewitt filters, and the Roberts' Cross technique are some examples of edge detection algorithms that are widely used in image processing and machine vision. In this work, these algorithms are implemented using the Compute Unified Device Architecture (CUDA), Open Source Computer Vision (OpenCV), and Matrix Laboratory (MATLAB) platforms. An existing parallel method for Canny approach has been modified further to run in a fully parallel manner. This has been achieved by replacing the breadth- first search procedure with a parallel method. These algorithms have been compared by testing them on a database of optical coherence tomography images. The comparison of results shows that the proposed implementation of the Canny method on GPU using the CUDA platform improves the speed of execution by 2-100× compared to the central processing unit-based implementation using the OpenCV and MATLAB platforms.

SU-G-BRA-01: A Real-Time Tumor Localization and Guidance Platform for Radiotherapy Using US and MRI

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

Bednarz, B; Culberson, W; Bassetti, M

Purpose: To develop and validate a real-time motion management platform for radiotherapy that directly tracks tumor motion using ultrasound and MRI. This will be a cost-effective and non-invasive real-time platform combining the excellent temporal resolution of ultrasound with the excellent soft-tissue contrast of MRI. Methods: A 4D planar ultrasound acquisition during the treatment that is coupled to a pre-treatment calibration training image set consisting of a simultaneous 4D ultrasound and 4D MRI acquisition. The image sets will be rapidly matched using advanced image and signal processing algorithms, allowing the display of virtual MR images of the tumor/organ motion in real-timemore » from an ultrasound acquisition. Results: The completion of this work will result in several innovations including: a (2D) patch-like, MR and LINAC compatible 4D planar ultrasound transducer that is electronically steerable for hands-free operation to provide real-time virtual MR and ultrasound imaging for motion management during radiation therapy; a multi- modal tumor localization strategy that uses ultrasound and MRI; and fast and accurate image processing algorithms that provide real-time information about the motion and location of tumor or related soft-tissue structures within the patient. Conclusion: If successful, the proposed approach will provide real-time guidance for radiation therapy without degrading image or treatment plan quality. The approach would be equally suitable for image-guided proton beam or heavy ion-beam therapy. This work is partially funded by NIH grant R01CA190298.« less

The Contribution of Social Media to Body Dissatisfaction, Eating Disorder Symptoms, and Anabolic Steroid Use Among Sexual Minority Men

PubMed Central

Murray, Stuart B.; Krug, Isabel; McLean, Siân A.

2018-01-01

Abstract Social media has been associated with body dissatisfaction and eating disorder symptoms among young women and adolescent girls. However, despite notable evidence of susceptibility to body image pressures, it remains unknown whether these associations generalize to sexual minority men. A nationwide sample of 2,733 sexual minority men completed an online survey advertised to Australian and New Zealand users of a popular dating app. Participants answered questions about how frequently they used 11 different social media platforms in addition to questions about their dating app use, body image, eating disorder symptoms, and anabolic steroids. Facebook, Youtube, Instagram, and Snapchat were the most frequently used social media platforms. A pattern of small-sized and positive associations emerged between social media use and body dissatisfaction, eating disorder symptoms, and thoughts about using anabolic steroids. Facebook, Instagram, and Snapchat evidenced the strongest associations. The associations of social media use with both muscularity dissatisfaction and eating disorder symptoms were stronger for image-centric social media platforms (e.g., Instagram) than nonimage-centric platforms (e.g., Wordpress); no differences were observed for body fat dissatisfaction, height dissatisfaction, or thoughts about using anabolic steroids. Previously documented associations of social media use with body dissatisfaction and related variables among women and girls appear to generalize to sexual minority men. Social media platforms that more centrally involve imagery may be of greater concern than nonimage-centric platforms. Additional research with sexual minority men is needed to elucidate the distinctions between adaptive and maladaptive social media use in the context of body dissatisfaction, eating disorders, and anabolic steroid use. PMID:29363993

Integrated Rapid-Diagnostic-Test Reader Platform on a Cellphone

PubMed Central

Mudanyali, Onur; Dimitrov, Stoyan; Sikora, Uzair; Padmanabhan, Swati; Navruz, Isa; Ozcan, Aydogan

2012-01-01

We demonstrate a cellphone based Rapid-Diagnostic-Test (RDT) reader platform that can work with various lateral flow immuno-chromatographic assays and similar tests to sense the presence of a target analyte in a sample. This compact and cost-effective digital RDT reader, weighing only ~65 grams, mechanically attaches to the existing camera unit of a cellphone, where various types of RDTs can be inserted to be imaged in reflection or transmission modes under light-emitting-diode (LED) based illumination. Captured raw images of these tests are then digitally processed (within less than 0.2 sec/image) through a smart application running on the cellphone for validation of the RDT as well as for automated reading of its diagnostic result. The same smart application running on the cellphone then transmits the resulting data, together with the RDT images and other related information (e.g., demographic data) to a central server, which presents the diagnostic results on a world-map through geo-tagging. This dynamic spatio-temporal map of various RDT results can then be viewed and shared using internet browsers or through the same cellphone application. We tested this platform using malaria, tuberculosis (TB) as well as HIV RDTs by installing it on both Android based smart-phones as well as an iPhone. Providing real-time spatio-temporal statistics for the prevalence of various infectious diseases, this smart RDT reader platform running on cellphones might assist health-care professionals and policy makers to track emerging epidemics worldwide and help epidemic preparedness. PMID:22596243

The Evolving MCART Multimodal Imaging Core: Establishing a protocol for Computed Tomography and Echocardiography in the Rhesus macaque to perform longitudinal analysis of radiation-induced organ injury

PubMed Central

de Faria, Eduardo B.; Barrow, Kory R.; Ruehle, Bradley T.; Parker, Jordan T.; Swartz, Elisa; Taylor-Howell, Cheryl; Kieta, Kaitlyn M.; Lees, Cynthia J.; Sleeper, Meg M.; Dobbin, Travis; Baron, Adam D.; Mohindra, Pranshu; MacVittie, Thomas J.

2015-01-01

Computed Tomography (CT) and Echocardiography (EC) are two imaging modalities that produce critical longitudinal data that can be analyzed for radiation-induced organ-specific injury to the lung and heart. The Medical Countermeasures Against Radiological Threats (MCART) consortium has a well-established animal model research platform that includes nonhuman primate (NHP) models of the acute radiation syndrome and the delayed effects of acute radiation exposure. These models call for a definition of the latency, incidence, severity, duration, and resolution of different organ-specific radiation-induced subsyndromes. The pulmonary subsyndromes and cardiac effects are a pair of inter-dependent syndromes impacted by exposure to potentially lethal doses of radiation. Establishing a connection between these will reveal important information about their interaction and progression of injury and recovery. Herein, we demonstrate the use of CT and EC data in the rhesus macaque models to define delayed organ injury thereby establishing: a) consistent and reliable methodology to assess radiation-induced damage to the lung and heart, b) an extensive database in normal age-matched NHP for key primary and secondary endpoints, c) identified problematic variables in imaging techniques and proposed solutions to maintain data integrity and d) initiated longitudinal analysis of potentially lethal radiation-induced damage to the lung and heart. PMID:26425907