Science.gov

Sample records for standard imaging software

  1. Emerging standards for still image compression: A software implementation and simulation study

    NASA Technical Reports Server (NTRS)

    Pollara, F.; Arnold, S.

    1991-01-01

    The software implementation is described of an emerging standard for the lossy compression of continuous tone still images. This software program can be used to compress planetary images and other 2-D instrument data. It provides a high compression image coding capability that preserves image fidelity at compression rates competitive or superior to most known techniques. This software implementation confirms the usefulness of such data compression and allows its performance to be compared with other schemes used in deep space missions and for data based storage.

  2. Software Formal Inspections Standard

    NASA Technical Reports Server (NTRS)

    1993-01-01

    This Software Formal Inspections Standard (hereinafter referred to as Standard) is applicable to NASA software. This Standard defines the requirements that shall be fulfilled by the software formal inspections process whenever this process is specified for NASA software. The objective of this Standard is to define the requirements for a process that inspects software products to detect and eliminate defects as early as possible in the software life cycle. The process also provides for the collection and analysis of inspection data to improve the inspection process as well as the quality of the software.

  3. Software assurance standard

    NASA Technical Reports Server (NTRS)

    1992-01-01

    This standard specifies the software assurance program for the provider of software. It also delineates the assurance activities for the provider and the assurance data that are to be furnished by the provider to the acquirer. In any software development effort, the provider is the entity or individual that actually designs, develops, and implements the software product, while the acquirer is the entity or individual who specifies the requirements and accepts the resulting products. This standard specifies at a high level an overall software assurance program for software developed for and by NASA. Assurance includes the disciplines of quality assurance, quality engineering, verification and validation, nonconformance reporting and corrective action, safety assurance, and security assurance. The application of these disciplines during a software development life cycle is called software assurance. Subsequent lower-level standards will specify the specific processes within these disciplines.

  4. NASA Software Documentation Standard

    NASA Technical Reports Server (NTRS)

    1991-01-01

    The NASA Software Documentation Standard (hereinafter referred to as "Standard") is designed to support the documentation of all software developed for NASA; its goal is to provide a framework and model for recording the essential information needed throughout the development life cycle and maintenance of a software system. The NASA Software Documentation Standard can be applied to the documentation of all NASA software. The Standard is limited to documentation format and content requirements. It does not mandate specific management, engineering, or assurance standards or techniques. This Standard defines the format and content of documentation for software acquisition, development, and sustaining engineering. Format requirements address where information shall be recorded and content requirements address what information shall be recorded. This Standard provides a framework to allow consistency of documentation across NASA and visibility into the completeness of project documentation. The basic framework consists of four major sections (or volumes). The Management Plan contains all planning and business aspects of a software project, including engineering and assurance planning. The Product Specification contains all technical engineering information, including software requirements and design. The Assurance and Test Procedures contains all technical assurance information, including Test, Quality Assurance (QA), and Verification and Validation (V&V). The Management, Engineering, and Assurance Reports is the library and/or listing of all project reports.

  5. NASA's Software Safety Standard

    NASA Technical Reports Server (NTRS)

    Ramsay, Christopher M.

    2007-01-01

    NASA relies more and more on software to control, monitor, and verify its safety critical systems, facilities and operations. Since the 1960's there has hardly been a spacecraft launched that does not have a computer on board that will provide command and control services. There have been recent incidents where software has played a role in high-profile mission failures and hazardous incidents. For example, the Mars Orbiter, Mars Polar Lander, the DART (Demonstration of Autonomous Rendezvous Technology), and MER (Mars Exploration Rover) Spirit anomalies were all caused or contributed to by software. The Mission Control Centers for the Shuttle, ISS, and unmanned programs are highly dependant on software for data displays, analysis, and mission planning. Despite this growing dependence on software control and monitoring, there has been little to no consistent application of software safety practices and methodology to NASA's projects with safety critical software. Meanwhile, academia and private industry have been stepping forward with procedures and standards for safety critical systems and software, for example Dr. Nancy Leveson's book Safeware: System Safety and Computers. The NASA Software Safety Standard, originally published in 1997, was widely ignored due to its complexity and poor organization. It also focused on concepts rather than definite procedural requirements organized around a software project lifecycle. Led by NASA Headquarters Office of Safety and Mission Assurance, the NASA Software Safety Standard has recently undergone a significant update. This new standard provides the procedures and guidelines for evaluating a project for safety criticality and then lays out the minimum project lifecycle requirements to assure the software is created, operated, and maintained in the safest possible manner. This update of the standard clearly delineates the minimum set of software safety requirements for a project without detailing the implementation for those

  6. NASA's Software Safety Standard

    NASA Technical Reports Server (NTRS)

    Ramsay, Christopher M.

    2005-01-01

    NASA (National Aeronautics and Space Administration) relies more and more on software to control, monitor, and verify its safety critical systems, facilities and operations. Since the 1960's there has hardly been a spacecraft (manned or unmanned) launched that did not have a computer on board that provided vital command and control services. Despite this growing dependence on software control and monitoring, there has been no consistent application of software safety practices and methodology to NASA's projects with safety critical software. Led by the NASA Headquarters Office of Safety and Mission Assurance, the NASA Software Safety Standard (STD-18l9.13B) has recently undergone a significant update in an attempt to provide that consistency. This paper will discuss the key features of the new NASA Software Safety Standard. It will start with a brief history of the use and development of software in safety critical applications at NASA. It will then give a brief overview of the NASA Software Working Group and the approach it took to revise the software engineering process across the Agency.

  7. Development of a viability standard curve for microencapsulated probiotic bacteria using confocal microscopy and image analysis software.

    PubMed

    Moore, Sarah; Kailasapathy, Kasipathy; Phillips, Michael; Jones, Mark R

    2015-07-01

    Microencapsulation is proposed to protect probiotic strains from food processing procedures and to maintain probiotic viability. Little research has described the in situ viability of microencapsulated probiotics. This study successfully developed a real-time viability standard curve for microencapsulated bacteria using confocal microscopy, fluorescent dyes and image analysis software.

  8. libdrdc: software standards library

    NASA Astrophysics Data System (ADS)

    Erickson, David; Peng, Tie

    2008-04-01

    This paper presents the libdrdc software standards library including internal nomenclature, definitions, units of measure, coordinate reference frames, and representations for use in autonomous systems research. This library is a configurable, portable C-function wrapped C++ / Object Oriented C library developed to be independent of software middleware, system architecture, processor, or operating system. It is designed to use the automatically-tuned linear algebra suite (ATLAS) and Basic Linear Algebra Suite (BLAS) and port to firmware and software. The library goal is to unify data collection and representation for various microcontrollers and Central Processing Unit (CPU) cores and to provide a common Application Binary Interface (ABI) for research projects at all scales. The library supports multi-platform development and currently works on Windows, Unix, GNU/Linux, and Real-Time Executive for Multiprocessor Systems (RTEMS). This library is made available under LGPL version 2.1 license.

  9. Image Processing Software

    NASA Astrophysics Data System (ADS)

    Bosio, M. A.

    1990-11-01

    ABSTRACT: A brief description of astronomical image software is presented. This software was developed in a Digital Micro Vax II Computer System. : St presenta una somera descripci6n del software para procesamiento de imagenes. Este software fue desarrollado en un equipo Digital Micro Vax II. : DATA ANALYSIS - IMAGE PROCESSING

  10. NASA software documentation standard software engineering program

    NASA Technical Reports Server (NTRS)

    1991-01-01

    The NASA Software Documentation Standard (hereinafter referred to as Standard) can be applied to the documentation of all NASA software. This Standard is limited to documentation format and content requirements. It does not mandate specific management, engineering, or assurance standards or techniques. This Standard defines the format and content of documentation for software acquisition, development, and sustaining engineering. Format requirements address where information shall be recorded and content requirements address what information shall be recorded. This Standard provides a framework to allow consistency of documentation across NASA and visibility into the completeness of project documentation. This basic framework consists of four major sections (or volumes). The Management Plan contains all planning and business aspects of a software project, including engineering and assurance planning. The Product Specification contains all technical engineering information, including software requirements and design. The Assurance and Test Procedures contains all technical assurance information, including Test, Quality Assurance (QA), and Verification and Validation (V&V). The Management, Engineering, and Assurance Reports is the library and/or listing of all project reports.

  11. Biological imaging software tools.

    PubMed

    Eliceiri, Kevin W; Berthold, Michael R; Goldberg, Ilya G; Ibáñez, Luis; Manjunath, B S; Martone, Maryann E; Murphy, Robert F; Peng, Hanchuan; Plant, Anne L; Roysam, Badrinath; Stuurman, Nico; Stuurmann, Nico; Swedlow, Jason R; Tomancak, Pavel; Carpenter, Anne E

    2012-06-28

    Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the inherent challenges and the overall status of available software for bioimage informatics, focusing on open-source options.

  12. Biological Imaging Software Tools

    PubMed Central

    Eliceiri, Kevin W.; Berthold, Michael R.; Goldberg, Ilya G.; Ibáñez, Luis; Manjunath, B.S.; Martone, Maryann E.; Murphy, Robert F.; Peng, Hanchuan; Plant, Anne L.; Roysam, Badrinath; Stuurman, Nico; Swedlow, Jason R.; Tomancak, Pavel; Carpenter, Anne E.

    2013-01-01

    Few technologies are more widespread in modern biological laboratories than imaging. Recent advances in optical technologies and instrumentation are providing hitherto unimagined capabilities. Almost all these advances have required the development of software to enable the acquisition, management, analysis, and visualization of the imaging data. We review each computational step that biologists encounter when dealing with digital images, the challenges in that domain, and the overall status of available software for bioimage informatics, focusing on open source options. PMID:22743775

  13. Future of Software Engineering Standards

    NASA Technical Reports Server (NTRS)

    Poon, Peter T.

    1997-01-01

    In the new millennium, software engineering standards are expected to continue to influence the process of producing software-intensive systems which are cost-effetive and of high quality. These sytems may range from ground and flight systems used for planetary exploration to educational support systems used in schools as well as consumer-oriented systems.

  14. Image Processing Software

    NASA Technical Reports Server (NTRS)

    1992-01-01

    To convert raw data into environmental products, the National Weather Service and other organizations use the Global 9000 image processing system marketed by Global Imaging, Inc. The company's GAE software package is an enhanced version of the TAE, developed by Goddard Space Flight Center to support remote sensing and image processing applications. The system can be operated in three modes and is combined with HP Apollo workstation hardware.

  15. Software Development Standard Processes (SDSP)

    NASA Technical Reports Server (NTRS)

    Lavin, Milton L.; Wang, James J.; Morillo, Ronald; Mayer, John T.; Jamshidian, Barzia; Shimizu, Kenneth J.; Wilkinson, Belinda M.; Hihn, Jairus M.; Borgen, Rosana B.; Meyer, Kenneth N.; Crean, Kathleen A.; Rinker, George C.; Smith, Thomas P.; Lum, Karen T.; Hanna, Robert A.; Erickson, Daniel E.; Gamble, Edward B., Jr.; Morgan, Scott C.; Kelsay, Michael G.; Newport, Brian J.; Lewicki, Scott A.; Stipanuk, Jeane G.; Cooper, Tonja M.; Meshkat, Leila

    2011-01-01

    A JPL-created set of standard processes is to be used throughout the lifecycle of software development. These SDSPs cover a range of activities, from management and engineering activities, to assurance and support activities. These processes must be applied to software tasks per a prescribed set of procedures. JPL s Software Quality Improvement Project is currently working at the behest of the JPL Software Process Owner to ensure that all applicable software tasks follow these procedures. The SDSPs are captured as a set of 22 standards in JPL s software process domain. They were developed in-house at JPL by a number of Subject Matter Experts (SMEs) residing primarily within the Engineering and Science Directorate, but also from the Business Operations Directorate and Safety and Mission Success Directorate. These practices include not only currently performed best practices, but also JPL-desired future practices in key thrust areas like software architecting and software reuse analysis. Additionally, these SDSPs conform to many standards and requirements to which JPL projects are beholden.

  16. NASA space station software standards issues

    NASA Technical Reports Server (NTRS)

    Tice, G. D., Jr.

    1985-01-01

    The selection and application of software standards present the NASA Space Station Program with the opportunity to serve as a pacesetter for the United States software in the area of software standards. The strengths and weaknesses of each of the NASA defined software standards issues are summerized and discussed. Several significant standards issues are offered for NASA consideration. A challenge is presented for the NASA Space Station Program to serve as a pacesetter for the U.S. Software Industry through: (1) Management commitment to software standards; (2) Overall program participation in software standards; and (3) Employment of the best available technology to support software standards

  17. Computed Tomography software and standards

    SciTech Connect

    Azevedo, S.G.; Martz, H.E.; Skeate, M.F.; Schneberk, D.J.; Roberson, G.P.

    1990-02-20

    This document establishes the software design, nomenclature, and conventions for industrial Computed Tomography (CT) used in the Nondestructive Evaluation Section at Lawrence Livermore National Laboratory. It is mainly a users guide to the technical use of the CT computer codes, but also presents a proposed standard for describing CT experiments and reconstructions. Each part of this document specifies different aspects of the CT software organization. A set of tables at the end describes the CT parameters of interest in our project. 4 refs., 6 figs., 1 tab.

  18. Confined Space Imager (CSI) Software

    SciTech Connect

    Karelilz, David

    2013-07-03

    The software provides real-time image capture, enhancement, and display, and sensor control for the Confined Space Imager (CSI) sensor system The software captures images over a Cameralink connection and provides the following image enhancements: camera pixel to pixel non-uniformity correction, optical distortion correction, image registration and averaging, and illumination non-uniformity correction. The software communicates with the custom CSI hardware over USB to control sensor parameters and is capable of saving enhanced sensor images to an external USB drive. The software provides sensor control, image capture, enhancement, and display for the CSI sensor system. It is designed to work with the custom hardware.

  19. SOFT-1: Imaging Processing Software

    NASA Technical Reports Server (NTRS)

    1984-01-01

    Five levels of image processing software are enumerated and discussed: (1) logging and formatting; (2) radiometric correction; (3) correction for geometric camera distortion; (4) geometric/navigational corrections; and (5) general software tools. Specific concerns about access to and analysis of digital imaging data within the Planetary Data System are listed.

  20. Standardized development of computer software. Part 2: Standards

    NASA Technical Reports Server (NTRS)

    Tausworthe, R. C.

    1978-01-01

    This monograph contains standards for software development and engineering. The book sets forth rules for design, specification, coding, testing, documentation, and quality assurance audits of software; it also contains detailed outlines for the documentation to be produced.

  1. Standard Leak Calibration Facility software system

    SciTech Connect

    McClain, S.K.

    1989-06-01

    A Standard Leak Calibration Facility Software System has been developed and implemented for controlling, and running a standard Leak Calibration Facility. Primary capabilities provided by the software system include computer control of the vacuum system, automatic leak calibration, and data acquisition, manipulation, and storage.

  2. Software for Managing an Archive of Images

    NASA Technical Reports Server (NTRS)

    Hallai, Charles; Jones, Helene; Callac, Chris

    2003-01-01

    This is a revised draft by Innovators concerning the report on Software for Managing and Archive of Images.The SSC Multimedia Archive is an automated electronic system to manage images, acquired both by film and digital cameras, for the Public Affairs Office (PAO) at Stennis Space Center (SSC). Previously, the image archive was based on film photography and utilized a manual system that, by todays standards, had become inefficient and expensive. Now, the SSC Multimedia Archive, based on a server at SSC, contains both catalogs and images for pictures taken both digitally and with a traditional film-based camera, along with metadata about each image.

  3. Diversification and Challenges of Software Engineering Standards

    NASA Technical Reports Server (NTRS)

    Poon, Peter T.

    1994-01-01

    The author poses certain questions in this paper: 'In the future, should there be just one software engineering standards set? If so, how can we work towards that goal? What are the challenges of internationalizing standards?' Based on the author's personal view, the statement of his position is as follows: 'There should NOT be just one set of software engineering standards in the future. At the same time, there should NOT be the proliferation of standards, and the number of sets of standards should be kept to a minimum.It is important to understand the diversification of the areas which are spanned by the software engineering standards.' The author goes on to describe the diversification of processes, the diversification in the national and international character of standards organizations, the diversification of the professional organizations producing standards, the diversification of the types of businesses and industries, and the challenges of internationalizing standards.

  4. Standard classification of software documentation

    NASA Technical Reports Server (NTRS)

    Tausworthe, R. C.

    1976-01-01

    General conceptual requirements for standard levels of documentation and for application of these requirements to intended usages. These standards encourage the policy to produce only those forms of documentation that are needed and adequate for the purpose. Documentation standards are defined with respect to detail and format quality. Classes A through D range, in order, from the most definitive down to the least definitive, and categories 1 through 4 range, in order, from high-quality typeset down to handwritten material. Criteria for each of the classes and categories, as well as suggested selection guidelines for each are given.

  5. Image processing software for imaging spectrometry

    NASA Technical Reports Server (NTRS)

    Mazer, Alan S.; Martin, Miki; Lee, Meemong; Solomon, Jerry E.

    1988-01-01

    The paper presents a software system, Spectral Analysis Manager (SPAM), which has been specifically designed and implemented to provide the exploratory analysis tools necessary for imaging spectrometer data, using only modest computational resources. The basic design objectives are described as well as the major algorithms designed or adapted for high-dimensional images. Included in a discussion of system implementation are interactive data display, statistical analysis, image segmentation and spectral matching, and mixture analysis.

  6. Software Development Standard for Mission Critical Systems

    DTIC Science & Technology

    2014-03-17

    applied on contracts for mission critical systems . This report provides a full lifecycle software development process standard. This version includes an...integration and test environments. 5.3 Updated requirements for system requirements analysis . v Issue Date Sections Changes 5.4 Updated...requirements for system architectural design. 5.5 Updated requirements for software requirements analysis . 5.6 Major update to software

  7. 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.

  8. FITS Liberator: Image processing software

    NASA Astrophysics Data System (ADS)

    Lindberg Christensen, Lars; Nielsen, Lars Holm; Nielsen, Kaspar K.; Johansen, Teis; Hurt, Robert; de Martin, David

    2012-06-01

    The ESA/ESO/NASA FITS Liberator makes it possible to process and edit astronomical science data in the FITS format to produce stunning images of the universe. Formerly a plugin for Adobe Photoshop, the current version of FITS Liberator is a stand-alone application and no longer requires Photoshop. This image processing software makes it possible to create color images using raw observations from a range of telescopes; the FITS Liberator continues to support the FITS and PDS formats, preferred by astronomers and planetary scientists respectively, which enables data to be processed from a wide range of telescopes and planetary probes, including ESO's Very Large Telescope, the NASA/ESA Hubble Space Telescope, NASA's Spitzer Space Telescope, ESA's XMM-Newton Telescope and Cassini-Huygens or Mars Reconnaissance Orbiter.

  9. Automatic AVHRR image navigation software

    NASA Technical Reports Server (NTRS)

    Baldwin, Dan; Emery, William

    1992-01-01

    This is the final report describing the work done on the project entitled Automatic AVHRR Image Navigation Software funded through NASA-Washington, award NAGW-3224, Account 153-7529. At the onset of this project, we had developed image navigation software capable of producing geo-registered images from AVHRR data. The registrations were highly accurate but required a priori knowledge of the spacecraft's axes alignment deviations, commonly known as attitude. The three angles needed to describe the attitude are called roll, pitch, and yaw, and are the components of the deviations in the along scan, along track and about center directions. The inclusion of the attitude corrections in the navigation software results in highly accurate georegistrations, however, the computation of the angles is very tedious and involves human interpretation for several steps. The technique also requires easily identifiable ground features which may not be available due to cloud cover or for ocean data. The current project was motivated by the need for a navigation system which was automatic and did not require human intervention or ground control points. The first step in creating such a system must be the ability to parameterize the spacecraft's attitude. The immediate goal of this project was to study the attitude fluctuations and determine if they displayed any systematic behavior which could be modeled or parameterized. We chose a period in 1991-1992 to study the attitude of the NOAA 11 spacecraft using data from the Tiros receiving station at the Colorado Center for Astrodynamic Research (CCAR) at the University of Colorado.

  10. Objective facial photograph analysis using imaging software.

    PubMed

    Pham, Annette M; Tollefson, Travis T

    2010-05-01

    Facial analysis is an integral part of the surgical planning process. Clinical photography has long been an invaluable tool in the surgeon's practice not only for accurate facial analysis but also for enhancing communication between the patient and surgeon, for evaluating postoperative results, for medicolegal documentation, and for educational and teaching opportunities. From 35-mm slide film to the digital technology of today, clinical photography has benefited greatly from technological advances. With the development of computer imaging software, objective facial analysis becomes easier to perform and less time consuming. Thus, while the original purpose of facial analysis remains the same, the process becomes much more efficient and allows for some objectivity. Although clinical judgment and artistry of technique is never compromised, the ability to perform objective facial photograph analysis using imaging software may become the standard in facial plastic surgery practices in the future.

  11. Salvo: Seismic imaging software for complex geologies

    SciTech Connect

    OBER,CURTIS C.; GJERTSEN,ROB; WOMBLE,DAVID E.

    2000-03-01

    This report describes Salvo, a three-dimensional seismic-imaging software for complex geologies. Regions of complex geology, such as overthrusts and salt structures, can cause difficulties for many seismic-imaging algorithms used in production today. The paraxial wave equation and finite-difference methods used within Salvo can produce high-quality seismic images in these difficult regions. However this approach comes with higher computational costs which have been too expensive for standard production. Salvo uses improved numerical algorithms and methods, along with parallel computing, to produce high-quality images and to reduce the computational and the data input/output (I/O) costs. This report documents the numerical algorithms implemented for the paraxial wave equation, including absorbing boundary conditions, phase corrections, imaging conditions, phase encoding, and reduced-source migration. This report also describes I/O algorithms for large seismic data sets and images and parallelization methods used to obtain high efficiencies for both the computations and the I/O of seismic data sets. Finally, this report describes the required steps to compile, port and optimize the Salvo software, and describes the validation data sets used to help verify a working copy of Salvo.

  12. Automated computer software development standards enforcement

    SciTech Connect

    Yule, H.P.; Formento, J.W.

    1991-01-01

    The Uniform Development Environment (UDE) is being investigated as a means of enforcing software engineering standards. For the programmer, it provides an environment containing the tools and utilities necessary for orderly and controlled development and maintenance of code according to requirements. In addition, it provides DoD management and developer management the tools needed for all phases of software life cycle management and control, from project planning and management, to code development, configuration management, version control, and change control. This paper reports the status of UDE development and field testing. 5 refs.

  13. Easy and Accessible Imaging Software

    NASA Technical Reports Server (NTRS)

    2003-01-01

    DATASTAR, Inc., of Picayune, Mississippi, has taken NASA s award-winning Earth Resources Laboratory Applications Software (ELAS) program and evolved it into a user-friendly desktop application and Internet service to perform processing, analysis, and manipulation of remotely sensed imagery data. NASA s Stennis Space Center developed ELAS in the early 1980s to process satellite and airborne sensor imagery data of the Earth s surface into readable and accessible information. Since then, ELAS information has been applied worldwide to determine soil content, rainfall levels, and numerous other variances of topographical information. However, end-users customarily had to depend on scientific or computer experts to provide the results, because the imaging processing system was intricate and labor intensive.

  14. Software for Automated Image-to-Image Co-registration

    NASA Technical Reports Server (NTRS)

    Benkelman, Cody A.; Hughes, Heidi

    2007-01-01

    The project objectives are: a) Develop software to fine-tune image-to-image co-registration, presuming images are orthorectified prior to input; b) Create a reusable software development kit (SDK) to enable incorporation of these tools into other software; d) provide automated testing for quantitative analysis; and e) Develop software that applies multiple techniques to achieve subpixel precision in the co-registration of image pairs.

  15. Sandia software guidelines. Volume 3. Standards, practices, and conventions

    SciTech Connect

    Not Available

    1986-07-01

    This volume is one in a series of Sandia Software Guidelines intended for use in producing quality software within Sandia National Laboratories. In consonance with the IEEE Standard for Software Quality Assurance Plans, this volume identifies software standards, conventions, and practices. These guidelines are the result of a collective effort within Sandia National Laboratories to define recommended deliverables and to document standards, practices, and conventions which will help ensure quality software. 66 refs., 5 figs., 6 tabs.

  16. Software For Computing Image Ratios

    NASA Technical Reports Server (NTRS)

    Yates, Gigi L.

    1993-01-01

    RATIO_TOOL is interactive computer program for viewing and analyzing large sets of multispectral image data created by imaging spectrometer. Uses ratios between intensities in different spectral bands in order to spot significant areas of interest within multispectral image. Each image band viewed iteratively, or selected image band of set of data requested and displayed. When image ratios computed, result displayed as grayscale image. Written in C Language.

  17. OSIRIX: open source multimodality image navigation software

    NASA Astrophysics Data System (ADS)

    Rosset, Antoine; Pysher, Lance; Spadola, Luca; Ratib, Osman

    2005-04-01

    The goal of our project is to develop a completely new software platform that will allow users to efficiently and conveniently navigate through large sets of multidimensional data without the need of high-end expensive hardware or software. We also elected to develop our system on new open source software libraries allowing other institutions and developers to contribute to this project. OsiriX is a free and open-source imaging software designed manipulate and visualize large sets of medical images: http://homepage.mac.com/rossetantoine/osirix/

  18. Identifying Image Manipulation Software from Image Features

    DTIC Science & Technology

    2015-03-26

    6 2.1 Mathematical Image Definition , Image Formats, and Interpolation Algorithms...6 2.1.1 Mathematical Image Definition ...Farid [9]. The following section defines the mathematical definition of an image, discusses two image formats, and three interpolation algo- rithms. 2.1

  19. Image analysis library software development

    NASA Technical Reports Server (NTRS)

    Guseman, L. F., Jr.; Bryant, J.

    1977-01-01

    The Image Analysis Library consists of a collection of general purpose mathematical/statistical routines and special purpose data analysis/pattern recognition routines basic to the development of image analysis techniques for support of current and future Earth Resources Programs. Work was done to provide a collection of computer routines and associated documentation which form a part of the Image Analysis Library.

  20. A Software Package For Biomedical Image Processing And Analysis

    NASA Astrophysics Data System (ADS)

    Goncalves, Joao G. M.; Mealha, Oscar

    1988-06-01

    The decreasing cost of computing power and the introduction of low cost imaging boards justifies the increasing number of applications of digital image processing techniques in the area of biomedicine. There is however a large software gap to be fulfilled, between the application and the equipment. The requirements to bridge this gap are twofold: good knowledge of the hardware provided and its interface to the host computer, and expertise in digital image processing and analysis techniques. A software package incorporating these two requirements was developped using the C programming language, in order to create a user friendly image processing programming environment. The software package can be considered in two different ways: as a data structure adapted to image processing and analysis, which acts as the backbone and the standard of communication for all the software; and as a set of routines implementing the basic algorithms used in image processing and analysis. Hardware dependency is restricted to a single module upon which all hardware calls are based. The data structure that was built has four main features: hierchical, open, object oriented, and object dependent dimensions. Considering the vast amount of memory needed by imaging applications and the memory available in small imaging systems, an effective image memory management scheme was implemented. This software package is being used for more than one and a half years by users with different applications. It proved to be an efficient tool for helping people to get adapted into the system, and for standardizing and exchanging software, yet preserving flexibility allowing for users' specific implementations. The philosophy of the software package is discussed and the data structure that was built is described in detail.

  1. Infrared Imaging Data Reduction Software and Techniques

    NASA Astrophysics Data System (ADS)

    Sabbey, C. N.; McMahon, R. G.; Lewis, J. R.; Irwin, M. J.

    Developed to satisfy certain design requirements not met in existing packages (e.g., full weight map handling) and to optimize the software for large data sets (non-interactive tasks that are CPU and disk efficient), the InfraRed Data Reduction software package is a small ANSI C library of fast image processing routines for automated pipeline reduction of infrared (dithered) observations. The software includes stand-alone C programs for tasks such as running sky frame subtraction with object masking, image registration and co-addition with weight maps, dither offset measurement using cross-correlation, and object mask dilation. Although currently used for near-IR mosaic images, the modular software is concise and readily adaptable for reuse in other work. IRDR, available via anonymous ftp at ftp.ast.cam.ac.uk in pub/sabbey

  2. Space and Missile Systems Center Standard: Software Development

    DTIC Science & Technology

    2015-01-16

    SPACE AND MISSILE SYSTEMS CENTER STANDARD SOFTWARE DEVELOPMENT APPROVED FOR PUBLIC RELEASE; DISTRIBUTION IS UNLIMITED Report...REPORT TYPE N/A 3. DATES COVERED - 4. TITLE AND SUBTITLE Space and Missile Systems Center Standard: Software Development 5a. CONTRACT...technology developments . 2. This revised SMC standard comprises the text of The Aerospace Corporation report number TR-RS-2015-00012, entitled

  3. Standard practices for the implementation of computer software

    NASA Technical Reports Server (NTRS)

    Irvine, A. P. (Editor)

    1978-01-01

    A standard approach to the development of computer program is provided that covers the file cycle of software development from the planning and requirements phase through the software acceptance testing phase. All documents necessary to provide the required visibility into the software life cycle process are discussed in detail.

  4. Video Image Stabilization and Registration (VISAR) Software

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Two scientists at NASA's Marshall Space Flight Center, atmospheric scientist Paul Meyer and solar physicist Dr. David Hathaway, developed promising new software, called Video Image Stabilization and Registration (VISAR), which is illustrated in this Quick Time movie. VISAR is a computer algorithm that stabilizes camera motion in the horizontal and vertical as well as rotation and zoom effects producing clearer images of moving objects, smoothes jagged edges, enhances still images, and reduces video noise or snow. It could steady images of ultrasounds, which are infamous for their grainy, blurred quality. VISAR could also have applications in law enforcement, medical, and meteorological imaging. The software can be used for defense application by improving reconnaissance video imagery made by military vehicles, aircraft, and ships traveling in harsh, rugged environments.

  5. Video Image Stabilization and Registration (VISAR) Software

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Two scientists at NASA's Marshall Space Flight Center,atmospheric scientist Paul Meyer and solar physicist Dr. David Hathaway, developed promising new software, called Video Image stabilization and Registration (VISAR), which is illustrated in this Quick Time movie. VISAR is a computer algorithm that stabilizes camera motion in the horizontal and vertical as well as rotation and zoom effects producing clearer images of moving objects, smoothes jagged edges, enhances still images, and reduces video noise or snow. It could steady images of ultrasounds, which are infamous for their grainy, blurred quality. VISAR could also have applications in law enforcement, medical, and meteorological imaging. The software can be used for defense application by improving reconnaissance video imagery made by military vehicles, aircraft, and ships traveling in harsh, rugged environments.

  6. Video Image Stabilization and Registration (VISAR) Software

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Two scientists at NASA's Marshall Space Flight Center,atmospheric scientist Paul Meyer and solar physicist Dr. David Hathaway, developed promising new software, called Video Image Stabilization and Registration (VISAR). VISAR may help law enforcement agencies catch criminals by improving the quality of video recorded at crime scenes. In this photograph, the single frame at left, taken at night, was brightened in order to enhance details and reduce noise or snow. To further overcome the video defects in one frame, Law enforcement officials can use VISAR software to add information from multiple frames to reveal a person. Images from less than a second of videotape were added together to create the clarified image at right. VISAR stabilizes camera motion in the horizontal and vertical as well as rotation and zoom effects producing clearer images of moving objects, smoothes jagged edges, enhances still images, and reduces video noise or snow. VISAR could also have applications in medical and meteorological imaging. It could steady images of ultrasounds, which are infamous for their grainy, blurred quality. The software can be used for defense application by improving recornaissance video imagery made by military vehicles, aircraft, and ships traveling in harsh, rugged environments.

  7. A study of software standards used in the avionics industry

    NASA Technical Reports Server (NTRS)

    Hayhurst, Kelly J.

    1994-01-01

    Within the past decade, software has become an increasingly common element in computing systems. In particular, the role of software used in the aerospace industry, especially in life- or safety-critical applications, is rapidly expanding. This intensifies the need to use effective techniques for achieving and verifying the reliability of avionics software. Although certain software development processes and techniques are mandated by government regulating agencies, no one methodology has been shown to consistently produce reliable software. The knowledge base for designing reliable software simply has not reached the maturity of its hardware counterpart. In an effort to increase our understanding of software, the Langley Research Center conducted a series of experiments over 15 years with the goal of understanding why and how software fails. As part of this program, the effectiveness of current industry standards for the development of avionics is being investigated. This study involves the generation of a controlled environment to conduct scientific experiments on software processes.

  8. Video Image Stabilization and Registration (VISAR) Software

    NASA Technical Reports Server (NTRS)

    1999-01-01

    Two scientists at NASA Marshall Space Flight Center, atmospheric scientist Paul Meyer (left) and solar physicist Dr. David Hathaway, have developed promising new software, called Video Image Stabilization and Registration (VISAR), that may help law enforcement agencies to catch criminals by improving the quality of video recorded at crime scenes, VISAR stabilizes camera motion in the horizontal and vertical as well as rotation and zoom effects; produces clearer images of moving objects; smoothes jagged edges; enhances still images; and reduces video noise of snow. VISAR could also have applications in medical and meteorological imaging. It could steady images of Ultrasounds which are infamous for their grainy, blurred quality. It would be especially useful for tornadoes, tracking whirling objects and helping to determine the tornado's wind speed. This image shows two scientists reviewing an enhanced video image of a license plate taken from a moving automobile.

  9. Contracting for Computer Software in Standardized Computer Languages

    PubMed Central

    Brannigan, Vincent M.; Dayhoff, Ruth E.

    1982-01-01

    The interaction between standardized computer languages and contracts for programs which use these languages is important to the buyer or seller of software. The rationale for standardization, the problems in standardizing computer languages, and the difficulties of determining whether the product conforms to the standard are issues which must be understood. The contract law processes of delivery, acceptance testing, acceptance, rejection, and revocation of acceptance are applicable to the contracting process for standard language software. Appropriate contract language is suggested for requiring strict compliance with a standard, and an overview of remedies is given for failure to comply.

  10. Awake Animal Imaging Motion Tracking Software

    SciTech Connect

    Goddard, James

    2010-03-15

    The Awake Animal Motion Tracking Software code calculates the 3D movement of the head motion of a live, awake animal during a medical imaging scan. In conjunction with markers attached to the head, images acquired from multiple cameras are processed and marker locations precisely determined. Using off-line camera calibration data, the 3D positions of the markers are calculated along with a 6 degree of freedom position and orientation (pose) relative to a fixed initial position. This calculation is performed in real time at frame rates up to 30 frames per second. A time stamp with microsecond accuracy from a time base source is attached to each pose measurement.

  11. Imaging Sensor Flight and Test Equipment Software

    NASA Technical Reports Server (NTRS)

    Freestone, Kathleen; Simeone, Louis; Robertson, Byran; Frankford, Maytha; Trice, David; Wallace, Kevin; Wilkerson, DeLisa

    2007-01-01

    The Lightning Imaging Sensor (LIS) is one of the components onboard the Tropical Rainfall Measuring Mission (TRMM) satellite, and was designed to detect and locate lightning over the tropics. The LIS flight code was developed to run on a single onboard digital signal processor, and has operated the LIS instrument since 1997 when the TRMM satellite was launched. The software provides controller functions to the LIS Real-Time Event Processor (RTEP) and onboard heaters, collects the lightning event data from the RTEP, compresses and formats the data for downlink to the satellite, collects housekeeping data and formats the data for downlink to the satellite, provides command processing and interface to the spacecraft communications and data bus, and provides watchdog functions for error detection. The Special Test Equipment (STE) software was designed to operate specific test equipment used to support the LIS hardware through development, calibration, qualification, and integration with the TRMM spacecraft. The STE software provides the capability to control instrument activation, commanding (including both data formatting and user interfacing), data collection, decompression, and display and image simulation. The LIS STE code was developed for the DOS operating system in the C programming language. Because of the many unique data formats implemented by the flight instrument, the STE software was required to comprehend the same formats, and translate them for the test operator. The hardware interfaces to the LIS instrument using both commercial and custom computer boards, requiring that the STE code integrate this variety into a working system. In addition, the requirement to provide RTEP test capability dictated the need to provide simulations of background image data with short-duration lightning transients superimposed. This led to the development of unique code used to control the location, intensity, and variation above background for simulated lightning strikes

  12. Terahertz/mm wave imaging simulation software

    NASA Astrophysics Data System (ADS)

    Fetterman, M. R.; Dougherty, J.; Kiser, W. L., Jr.

    2006-10-01

    We have developed a mm wave/terahertz imaging simulation package from COTS graphic software and custom MATLAB code. In this scheme, a commercial ray-tracing package was used to simulate the emission and reflections of radiation from scenes incorporating highly realistic imagery. Accurate material properties were assigned to objects in the scenes, with values obtained from the literature, and from our own terahertz spectroscopy measurements. The images were then post-processed with custom Matlab code to include the blur introduced by the imaging system and noise levels arising from system electronics and detector noise. The Matlab code was also used to simulate the effect of fog, an important aspect for mm wave imaging systems. Several types of image scenes were evaluated, including bar targets, contrast detail targets, a person in a portal screening situation, and a sailboat on the open ocean. The images produced by this simulation are currently being used as guidance for a 94 GHz passive mm wave imaging system, but have broad applicability for frequencies extending into the terahertz region.

  13. ICER-3D Hyperspectral Image Compression Software

    NASA Technical Reports Server (NTRS)

    Xie, Hua; Kiely, Aaron; Klimesh, matthew; Aranki, Nazeeh

    2010-01-01

    Software has been developed to implement the ICER-3D algorithm. ICER-3D effects progressive, three-dimensional (3D), wavelet-based compression of hyperspectral images. If a compressed data stream is truncated, the progressive nature of the algorithm enables reconstruction of hyperspectral data at fidelity commensurate with the given data volume. The ICER-3D software is capable of providing either lossless or lossy compression, and incorporates an error-containment scheme to limit the effects of data loss during transmission. The compression algorithm, which was derived from the ICER image compression algorithm, includes wavelet-transform, context-modeling, and entropy coding subalgorithms. The 3D wavelet decomposition structure used by ICER-3D exploits correlations in all three dimensions of sets of hyperspectral image data, while facilitating elimination of spectral ringing artifacts, using a technique summarized in "Improving 3D Wavelet-Based Compression of Spectral Images" (NPO-41381), NASA Tech Briefs, Vol. 33, No. 3 (March 2009), page 7a. Correlation is further exploited by a context-modeling subalgorithm, which exploits spectral dependencies in the wavelet-transformed hyperspectral data, using an algorithm that is summarized in "Context Modeler for Wavelet Compression of Hyperspectral Images" (NPO-43239), which follows this article. An important feature of ICER-3D is a scheme for limiting the adverse effects of loss of data during transmission. In this scheme, as in the similar scheme used by ICER, the spatial-frequency domain is partitioned into rectangular error-containment regions. In ICER-3D, the partitions extend through all the wavelength bands. The data in each partition are compressed independently of those in the other partitions, so that loss or corruption of data from any partition does not affect the other partitions. Furthermore, because compression is progressive within each partition, when data are lost, any data from that partition received

  14. Sine-Fitting Software for IEEE Standard 1057

    SciTech Connect

    Blair, Jerome

    1999-05-01

    Software application that performs the calculations related to the sine-fit tests of IEEE Standard 1057/94. Example outputs and explainations of these outputs to determine the important characteristics of the device under test. This application performs the calculations related to sine-fit tests and uses 4-parameter sine fit from IEEE Standard 1057-1994.

  15. Data to Pictures to Data: Outreach Imaging Software and Metadata

    NASA Astrophysics Data System (ADS)

    Levay, Z.

    2011-07-01

    A convergence between astronomy science and digital photography has enabled a steady stream of visually rich imagery from state-of-the-art data. The accessibility of hardware and software has facilitated an explosion of astronomical images for outreach, from space-based observatories, ground-based professional facilities and among the vibrant amateur astrophotography community. Producing imagery from science data involves a combination of custom software to understand FITS data (FITS Liberator), off-the-shelf, industry-standard software to composite multi-wavelength data and edit digital photographs (Adobe Photoshop), and application of photo/image-processing techniques. Some additional effort is needed to close the loop and enable this imagery to be conveniently available for various purposes beyond web and print publication. The metadata paradigms in digital photography are now complying with FITS and science software to carry information such as keyword tags and world coordinates, enabling these images to be usable in more sophisticated, imaginative ways exemplified by Sky in Google Earth and World Wide Telescope.

  16. Standardized development of computer software. Part 1: Methods

    NASA Technical Reports Server (NTRS)

    Tausworthe, R. C.

    1976-01-01

    This work is a two-volume set on standards for modern software engineering methodology. This volume presents a tutorial and practical guide to the efficient development of reliable computer software, a unified and coordinated discipline for design, coding, testing, documentation, and project organization and management. The aim of the monograph is to provide formal disciplines for increasing the probability of securing software that is characterized by high degrees of initial correctness, readability, and maintainability, and to promote practices which aid in the consistent and orderly development of a total software system within schedule and budgetary constraints. These disciplines are set forth as a set of rules to be applied during software development to drastically reduce the time traditionally spent in debugging, to increase documentation quality, to foster understandability among those who must come in contact with it, and to facilitate operations and alterations of the program as requirements on the program environment change.

  17. Image processing software for imaging spectrometry data analysis

    NASA Technical Reports Server (NTRS)

    Mazer, Alan; Martin, Miki; Lee, Meemong; Solomon, Jerry E.

    1988-01-01

    Imaging spectrometers simultaneously collect image data in hundreds of spectral channels, from the near-UV to the IR, and can thereby provide direct surface materials identification by means resembling laboratory reflectance spectroscopy. Attention is presently given to a software system, the Spectral Analysis Manager (SPAM) for the analysis of imaging spectrometer data. SPAM requires only modest computational resources and is composed of one main routine and a set of subroutine libraries. Additions and modifications are relatively easy, and special-purpose algorithms have been incorporated that are tailored to geological applications.

  18. Image processing software for imaging spectrometry data analysis

    NASA Astrophysics Data System (ADS)

    Mazer, Alan; Martin, Miki; Lee, Meemong; Solomon, Jerry E.

    1988-02-01

    Imaging spectrometers simultaneously collect image data in hundreds of spectral channels, from the near-UV to the IR, and can thereby provide direct surface materials identification by means resembling laboratory reflectance spectroscopy. Attention is presently given to a software system, the Spectral Analysis Manager (SPAM) for the analysis of imaging spectrometer data. SPAM requires only modest computational resources and is composed of one main routine and a set of subroutine libraries. Additions and modifications are relatively easy, and special-purpose algorithms have been incorporated that are tailored to geological applications.

  19. Standardization: Hardware and Software Standardization Can Reduce Costs and Save Time

    ERIC Educational Resources Information Center

    Brooks-Young, Susan

    2005-01-01

    Sadly, technical support doesn't come cheap. One money-saving strategy that's gained popularity among school technicians is equipment and software standardization. When it works, standardization can be very effective. However, standardization has its drawbacks. This article discusses the advantages and disadvantages of standardization.

  20. Software for Viewing Landsat Mosaic Images

    NASA Technical Reports Server (NTRS)

    Watts, Zack; Farve, Catharine L.; Harvey, Craig

    2003-01-01

    A Windows-based computer program has been written to enable novice users (especially educators and students) to view images of large areas of the Earth (e.g., the continental United States) generated from image data acquired in the Landsat observations performed circa the year 1990. The large-area images are constructed as mosaics from the original Landsat images, which were acquired in several wavelength bands and each of which spans an area (in effect, one tile of a mosaic) of .5 in latitude by .6 in longitude. Whereas the original Landsat data are registered on a universal transverse Mercator (UTM) grid, the program converts the UTM coordinates of a mouse pointer in the image to latitude and longitude, which are continuously updated and displayed as the pointer is moved. The mosaic image currently on display can be exported as a Windows bitmap file. Other images (e.g., of state boundaries or interstate highways) can be overlaid on Landsat mosaics. The program interacts with the user via standard toolbar, keyboard, and mouse user interfaces. The program is supplied on a compact disk along with tutorial and educational information.

  1. Electrophoretic gel image analysis software for the molecular biology laboratory.

    PubMed

    Redman, T; Jacobs, T

    1991-06-01

    We present GelReader 1.0, a microcomputer program designed to make precision, digital analysis of one-dimensional electrophoretic gels accessible to the molecular biology laboratory of modest means. Images of electrophoretic gels are digitized via a desktop flatbed scanner from instant photographs, autoradiograms or chromogenically stained blotting media. GelReader is then invoked to locate lanes and bands and generate a report of molecular weights of unknowns, based on specified sets of standards. Frequently used standards can be stored in the program. Lanes and bands can be added or removed, based upon users' subjective preferences. A unique lane histogram feature facilitates precise manual addition of bands missed by the software. Image enhancement features include palette manipulation, histogram equalization, shadowing and magnification. The user interface strikes a balance between program autonomy and user intervention, in recognition of the variability in electrophoretic gel quality and users' analytical needs.

  2. Standards guide for space and earth sciences computer software

    NASA Technical Reports Server (NTRS)

    Mason, G.; Chapman, R.; Klinglesmith, D.; Linnekin, J.; Putney, W.; Shaffer, F.; Dapice, R.

    1972-01-01

    Guidelines for the preparation of systems analysis and programming work statements are presented. The data is geared toward the efficient administration of available monetary and equipment resources. Language standards and the application of good management techniques to software development are emphasized.

  3. MRI/TRUS fusion software-based targeted biopsy: the new standard of care?

    PubMed

    Manfredi, M; Costa Moretti, T B; Emberton, M; Villers, A; Valerio, M

    2015-09-01

    The advent of multiparametric MRI has made it possible to change the way in which prostate biopsy is done, allowing to direct biopsies to suspicious lesions rather than randomly. The subject of this review relates to a computer-assisted strategy, the MRI/US fusion software-based targeted biopsy, and to its performance compared to the other sampling methods. Different devices with different methods to register MR images to live TRUS are currently in use to allow software-based targeted biopsy. Main clinical indications of MRI/US fusion software-based targeted biopsy are re-biopsy in men with persistent suspicious of prostate cancer after first negative standard biopsy and the follow-up of patients under active surveillance. Some studies have compared MRI/US fusion software-based targeted versus standard biopsy. In men at risk with MRI-suspicious lesion, targeted biopsy consistently detects more men with clinically significant disease as compared to standard biopsy; some studies have also shown decreased detection of insignificant disease. Only two studies directly compared MRI/US fusion software-based targeted biopsy with MRI/US fusion visual targeted biopsy, and the diagnostic ability seems to be in favor of the software approach. To date, no study comparing software-based targeted biopsy against in-bore MRI biopsy is available. The new software-based targeted approach seems to have the characteristics to be added in the standard pathway for achieving accurate risk stratification. Once reproducibility and cost-effectiveness will be verified, the actual issue will be to determine whether MRI/TRUS fusion software-based targeted biopsy represents anadd-on test or a replacement to standard TRUS biopsy.

  4. Introduction to color facsimile: hardware, software, and standards

    NASA Astrophysics Data System (ADS)

    Lee, Daniel T. L.

    1996-03-01

    The design of a color facsimile machine presents a number of unique challenges. From the technical side it requires a very efficient, seamless integration of algorithms and architectures in image scanning, compression, color processing, communications and printing. From the standardization side, it requires that agreements on the color representation space, negotiation protocols and coding methods must be reached through formal international standardization process. This paper presents an introduction to the overall development of color facsimile. An overview of the recent development of the international Color Facsimile Standard is first presented. The standard enables the transmission of continuous-tone colors and gray-scale images in Group 3 (over conventional telephone lines) and Group 4 (over digital lines) facsimile services, with backwards compatibility to current black and white facsimile. The standard provides specifications on color representation and color image encoding methods as well as extensions to current facsimile protocols to enable the transmission of color images. The technical challenges in implementing the color facsimile standard on existing facsimile machines are described next. The integration of algorithms and architectures in color scanning, compression, color processing, transmission and rendering of received hardcopy facsimile in a color imaging pipeline is described. Lastly, the current status on softcopy color facsimile standardization is reported.

  5. Software components for medical image visualization and surgical planning

    NASA Astrophysics Data System (ADS)

    Starreveld, Yves P.; Gobbi, David G.; Finnis, Kirk; Peters, Terence M.

    2001-05-01

    Purpose: The development of new applications in medical image visualization and surgical planning requires the completion of many common tasks such as image reading and re-sampling, segmentation, volume rendering, and surface display. Intra-operative use requires an interface to a tracking system and image registration, and the application requires basic, easy to understand user interface components. Rapid changes in computer and end-application hardware, as well as in operating systems and network environments make it desirable to have a hardware and operating system as an independent collection of reusable software components that can be assembled rapidly to prototype new applications. Methods: Using the OpenGL based Visualization Toolkit as a base, we have developed a set of components that implement the above mentioned tasks. The components are written in both C++ and Python, but all are accessible from Python, a byte compiled scripting language. The components have been used on the Red Hat Linux, Silicon Graphics Iris, Microsoft Windows, and Apple OS X platforms. Rigorous object-oriented software design methods have been applied to ensure hardware independence and a standard application programming interface (API). There are components to acquire, display, and register images from MRI, MRA, CT, Computed Rotational Angiography (CRA), Digital Subtraction Angiography (DSA), 2D and 3D ultrasound, video and physiological recordings. Interfaces to various tracking systems for intra-operative use have also been implemented. Results: The described components have been implemented and tested. To date they have been used to create image manipulation and viewing tools, a deep brain functional atlas, a 3D ultrasound acquisition and display platform, a prototype minimally invasive robotic coronary artery bypass graft planning system, a tracked neuro-endoscope guidance system and a frame-based stereotaxy neurosurgery planning tool. The frame-based stereotaxy module has been

  6. The role of open-source software in innovation and standardization in radiology.

    PubMed

    Erickson, Bradley J; Langer, Steve; Nagy, Paul

    2005-11-01

    The use of open-source software (OSS), in which developers release the source code to applications they have developed, is popular in the software industry. This is done to allow others to modify and improve software (which may or may not be shared back to the community) and to allow others to learn from the software. Radiology was an early participant in this model, supporting OSS that implemented the ACR-National Electrical Manufacturers Association (now Digital Imaging and Communications in Medicine) standard for medical image communications. In radiology and in other fields, OSS has promoted innovation and the adoption of standards. Popular OSS is of high quality because access to source code allows many people to identify and resolve errors. Open-source software is analogous to the peer-review scientific process: one must be able to see and reproduce results to understand and promote what is shared. The authors emphasize that support for OSS need not threaten vendors; most vendors embrace and benefit from standards. Open-source development does not replace vendors but more clearly defines their roles, typically focusing on areas in which proprietary differentiators benefit customers and on professional services such as implementation planning and service. Continued support for OSS is essential for the success of our field.

  7. Software Maintenance: Improvement through Better Development Standards and Documentation.

    DTIC Science & Technology

    1982-02-22

    criteria for achieving maintainability and evaluates Weapons Specification WS 8506 and MIL- STD 1679 against these criteria. Using these documents as...is Maintainability V. EVALUATION OF WEAPONS SPECIFICATION WS 8506 ---------- 19 VI. EVALUATION OF MILITARY STANDARD MIL- STD 1679 ------------ 27...techniques which were reviewed (e.g., MIL- STD 1679) were designed to be used for software development and not for maintenance, specifically. This

  8. Digital image processing software system using an array processor

    SciTech Connect

    Sherwood, R.J.; Portnoff, M.R.; Journeay, C.H.; Twogood, R.E.

    1981-03-10

    A versatile array processor-based system for general-purpose image processing was developed. At the heart of this system is an extensive, flexible software package that incorporates the array processor for effective interactive image processing. The software system is described in detail, and its application to a diverse set of applications at LLNL is briefly discussed. 4 figures, 1 table.

  9. Perspective automated inkless fingerprinting imaging software for fingerprint research.

    PubMed

    Nanakorn, Somsong; Poosankam, Pongsakorn; Mongconthawornchai, Paiboon

    2008-01-01

    Fingerprint collection using ink-and-paper image is a conventional method i.e. an ink-print, transparent-adhesive tape techniques which are slower and cumbersome. This is a pilot research for software development aimed at imaging an automated, inkless fingerprint using a fingerprint sensor, a development kit of the IT WORKS Company Limited, PC camera, and printer The development of software was performed to connect with the fingerprint sensor for collection of fingerprint images and recorded into a hard disk. It was also developed to connect with the PC camera for recording a face image of persons' fingerprints or identification card images. These images had been appropriately arranged in a PDF file prior to printing. This software is able to scan ten fingerprints and store high-quality electronics fingertip images with rapid, large, and clear images without dirt of ink or carbon. This fingerprint technology is helpful in a potential application in public health and clinical medicine research.

  10. Integration of CMM software standards for nanopositioning and nanomeasuring machines

    NASA Astrophysics Data System (ADS)

    Sparrer, E.; Machleidt, T.; Hausotte, T.; Manske, E.; Franke, K.-H.

    2011-06-01

    The paper focuses on the utilization of nanopositioning and nanomeasuring machines as a three dimensional coordinate measuring machine by means of the international harmonized communication protocol Inspection plus plus for Dimensional Measurement Equipment (abbreviated I++DME). I++DME was designed 1999 to enable the interoperability of different measuring hardware, like coordinate measuring machines, form tester, camshaft or crankshaft measuring machines, with a priori unknown third party controlling and analyzing software. Our recent work was focused on the implementation of a modular, standard conform command interpreter server for the Inspection plus plus protocol. This communication protocol enables the application of I++DME compliant graphical controlling software, which is easy to operate and less error prone than the currently used textural programming via MathWorks MATLab. The function and architecture of the I++DME command interpreter is discussed and the principle of operation is demonstrated by means of an example controlling a nanopositioning and nanomeasuring machine with Hexagon Metrology's controlling and analyzing software QUINDOS 7 via the I++DME command interpreter server.

  11. Software to model AXAF image quality

    NASA Technical Reports Server (NTRS)

    Ahmad, Anees

    1993-01-01

    This draft final report describes the work performed under this delivery order from May 1992 through June 1993. The purpose of this contract was to enhance and develop an integrated optical performance modeling software for complex x-ray optical systems such as AXAF. The GRAZTRACE program developed by the MSFC Optical Systems Branch for modeling VETA-I was used as the starting baseline program. The original program was a large single file program and, therefore, could not be modified very efficiently. The original source code has been reorganized, and a 'Make Utility' has been written to update the original program. The new version of the source code consists of 36 small source files to make it easier for the code developer to manage and modify the program. A user library has also been built and a 'Makelib' utility has been furnished to update the library. With the user library, the users can easily access the GRAZTRACE source files and build a custom library. A user manual for the new version of GRAZTRACE has been compiled. The plotting capability for the 3-D point spread functions and contour plots has been provided in the GRAZTRACE using the graphics package DISPLAY. The Graphics emulator over the network has been set up for programming the graphics routine. The point spread function and the contour plot routines have also been modified to display the plot centroid, and to allow the user to specify the plot range, and the viewing angle options. A Command Mode version of GRAZTRACE has also been developed. More than 60 commands have been implemented in a Code-V like format. The functions covered in this version include data manipulation, performance evaluation, and inquiry and setting of internal parameters. The user manual for these commands has been formatted as in Code-V, showing the command syntax, synopsis, and options. An interactive on-line help system for the command mode has also been accomplished to allow the user to find valid commands, command syntax

  12. Quantification of fungal infection of leaves with digital images and Scion Image software.

    PubMed

    Goodwin, Paul H; Hsiang, Tom

    2010-01-01

    Digital image analysis has been used to distinguish and quantify leaf color changes arising from a variety of factors. Its use to assess the percentage of leaf area with color differences caused by plant disease symptoms, such as necrosis, chlorosis, or sporulation, can provide a rigorous and quantitative means of assessing disease severity. A method is described for measuring symptoms of different fungal foliar infections that involves capturing the image with a standard flatbed scanner or digital camera followed by quantifying the area, where the color has been affected because of fungal infection. The method uses the freely available program, Scion Image for Windows or MAC, which is derived from the public domain software, NIH Image. The method has thus far been used to quantify the percentage of tissue with necrosis, chlorosis, or sporulation on leaves of variety of plants with several different diseases (anthracnose, apple scab, powdery mildew or rust).

  13. Survey of geographical information system and image processing software

    USGS Publications Warehouse

    Vanderzee, D.; Singh, A.

    1995-01-01

    The Global Resource Information Database—a part of the United Nations Environment Programme—conducts a bi-annual survey of geographical information system (GIS) and image processing (IP) software. This survey makes information about software products available in developing countries. The 1993 survey showed that the number of installations of GIS, IP, and related software products increased dramatically from 1991 to 1993, mostly in North America and Europe.

  14. Software Helps Extract Information From Astronomical Images

    NASA Technical Reports Server (NTRS)

    Hartley, Booth; Ebert, Rick; Laughlin, Gaylin

    1995-01-01

    PAC Skyview 2.0 is interactive program for display and analysis of astronomical images. Includes large set of functions for display, analysis and manipulation of images. "Man" pages with descriptions of functions and examples of usage included. Skyview used interactively or in "server" mode, in which another program calls Skyview and executes commands itself. Skyview capable of reading image data files of four types, including those in FITS, S, IRAF, and Z formats. Written in C.

  15. Earth Observation Services (Image Processing Software)

    NASA Technical Reports Server (NTRS)

    1992-01-01

    San Diego State University and Environmental Systems Research Institute, with other agencies, have applied satellite imaging and image processing techniques to geographic information systems (GIS) updating. The resulting images display land use and are used by a regional planning agency for applications like mapping vegetation distribution and preserving wildlife habitats. The EOCAP program provides government co-funding to encourage private investment in, and to broaden the use of NASA-developed technology for analyzing information about Earth and ocean resources.

  16. Software for Acquiring Image Data for PIV

    NASA Technical Reports Server (NTRS)

    Wernet, Mark P.; Cheung, H. M.; Kressler, Brian

    2003-01-01

    PIV Acquisition (PIVACQ) is a computer program for acquisition of data for particle-image velocimetry (PIV). In the PIV system for which PIVACQ was developed, small particles entrained in a flow are illuminated with a sheet of light from a pulsed laser. The illuminated region is monitored by a charge-coupled-device camera that operates in conjunction with a data-acquisition system that includes a frame grabber and a counter-timer board, both installed in a single computer. The camera operates in "frame-straddle" mode where a pair of images can be obtained closely spaced in time (on the order of microseconds). The frame grabber acquires image data from the camera and stores the data in the computer memory. The counter/timer board triggers the camera and synchronizes the pulsing of the laser with acquisition of data from the camera. PIVPROC coordinates all of these functions and provides a graphical user interface, through which the user can control the PIV data-acquisition system. PIVACQ enables the user to acquire a sequence of single-exposure images, display the images, process the images, and then save the images to the computer hard drive. PIVACQ works in conjunction with the PIVPROC program which processes the images of particles into the velocity field in the illuminated plane.

  17. Development and implementation of software systems for imaging spectroscopy

    USGS Publications Warehouse

    Boardman, J.W.; Clark, R.N.; Mazer, A.S.; Biehl, L.L.; Kruse, F.A.; Torson, J.; Staenz, K.

    2006-01-01

    Specialized software systems have played a crucial role throughout the twenty-five year course of the development of the new technology of imaging spectroscopy, or hyperspectral remote sensing. By their very nature, hyperspectral data place unique and demanding requirements on the computer software used to visualize, analyze, process and interpret them. Often described as a marriage of the two technologies of reflectance spectroscopy and airborne/spaceborne remote sensing, imaging spectroscopy, in fact, produces data sets with unique qualities, unlike previous remote sensing or spectrometer data. Because of these unique spatial and spectral properties hyperspectral data are not readily processed or exploited with legacy software systems inherited from either of the two parent fields of study. This paper provides brief reviews of seven important software systems developed specifically for imaging spectroscopy.

  18. Quantifying fungal infection of plant leaves by digital image analysis using Scion Image software.

    PubMed

    Wijekoon, C P; Goodwin, P H; Hsiang, T

    2008-08-01

    A digital image analysis method previously used to evaluate leaf color changes due to nutritional changes was modified to measure the severity of several foliar fungal diseases. Images captured with a flatbed scanner or digital camera were analyzed with a freely available software package, Scion Image, to measure changes in leaf color caused by fungal sporulation or tissue damage. High correlations were observed between the percent diseased leaf area estimated by Scion Image analysis and the percent diseased leaf area from leaf drawings. These drawings of various foliar diseases came from a disease key previously developed to aid in visual estimation of disease severity. For leaves of Nicotiana benthamiana inoculated with different spore concentrations of the anthracnose fungus Colletotrichum destructivum, a high correlation was found between the percent diseased tissue measured by Scion Image analysis and the number of leaf spots. The method was adapted to quantify percent diseased leaf area ranging from 0 to 90% for anthracnose of lily-of-the-valley, apple scab, powdery mildew of phlox and rust of golden rod. In some cases, the brightness and contrast of the images were adjusted and other modifications were made, but these were standardized for each disease. Detached leaves were used with the flatbed scanner, but a method using attached leaves with a digital camera was also developed to make serial measurements of individual leaves to quantify symptom progression. This was successfully applied to monitor anthracnose on N. benthamiana leaves. Digital image analysis using Scion Image software is a useful tool for quantifying a wide variety of fungal interactions with plant leaves.

  19. gr-MRI: A software package for magnetic resonance imaging using software defined radios

    NASA Astrophysics Data System (ADS)

    Hasselwander, Christopher J.; Cao, Zhipeng; Grissom, William A.

    2016-09-01

    The goal of this work is to develop software that enables the rapid implementation of custom MRI spectrometers using commercially-available software defined radios (SDRs). The developed gr-MRI software package comprises a set of Python scripts, flowgraphs, and signal generation and recording blocks for GNU Radio, an open-source SDR software package that is widely used in communications research. gr-MRI implements basic event sequencing functionality, and tools for system calibrations, multi-radio synchronization, and MR signal processing and image reconstruction. It includes four pulse sequences: a single-pulse sequence to record free induction signals, a gradient-recalled echo imaging sequence, a spin echo imaging sequence, and an inversion recovery spin echo imaging sequence. The sequences were used to perform phantom imaging scans with a 0.5 Tesla tabletop MRI scanner and two commercially-available SDRs. One SDR was used for RF excitation and reception, and the other for gradient pulse generation. The total SDR hardware cost was approximately 2000. The frequency of radio desynchronization events and the frequency with which the software recovered from those events was also measured, and the SDR's ability to generate frequency-swept RF waveforms was validated and compared to the scanner's commercial spectrometer. The spin echo images geometrically matched those acquired using the commercial spectrometer, with no unexpected distortions. Desynchronization events were more likely to occur at the very beginning of an imaging scan, but were nearly eliminated if the user invoked the sequence for a short period before beginning data recording. The SDR produced a 500 kHz bandwidth frequency-swept pulse with high fidelity, while the commercial spectrometer produced a waveform with large frequency spike errors. In conclusion, the developed gr-MRI software can be used to develop high-fidelity, low-cost custom MRI spectrometers using commercially-available SDRs.

  20. gr-MRI: A software package for magnetic resonance imaging using software defined radios.

    PubMed

    Hasselwander, Christopher J; Cao, Zhipeng; Grissom, William A

    2016-09-01

    The goal of this work is to develop software that enables the rapid implementation of custom MRI spectrometers using commercially-available software defined radios (SDRs). The developed gr-MRI software package comprises a set of Python scripts, flowgraphs, and signal generation and recording blocks for GNU Radio, an open-source SDR software package that is widely used in communications research. gr-MRI implements basic event sequencing functionality, and tools for system calibrations, multi-radio synchronization, and MR signal processing and image reconstruction. It includes four pulse sequences: a single-pulse sequence to record free induction signals, a gradient-recalled echo imaging sequence, a spin echo imaging sequence, and an inversion recovery spin echo imaging sequence. The sequences were used to perform phantom imaging scans with a 0.5Tesla tabletop MRI scanner and two commercially-available SDRs. One SDR was used for RF excitation and reception, and the other for gradient pulse generation. The total SDR hardware cost was approximately $2000. The frequency of radio desynchronization events and the frequency with which the software recovered from those events was also measured, and the SDR's ability to generate frequency-swept RF waveforms was validated and compared to the scanner's commercial spectrometer. The spin echo images geometrically matched those acquired using the commercial spectrometer, with no unexpected distortions. Desynchronization events were more likely to occur at the very beginning of an imaging scan, but were nearly eliminated if the user invoked the sequence for a short period before beginning data recording. The SDR produced a 500kHz bandwidth frequency-swept pulse with high fidelity, while the commercial spectrometer produced a waveform with large frequency spike errors. In conclusion, the developed gr-MRI software can be used to develop high-fidelity, low-cost custom MRI spectrometers using commercially-available SDRs.

  1. MOSAIC: Software for creating mosaics from collections of images

    NASA Technical Reports Server (NTRS)

    Varosi, F.; Gezari, D. Y.

    1992-01-01

    We have developed a powerful, versatile image processing and analysis software package called MOSAIC, designed specifically for the manipulation of digital astronomical image data obtained with (but not limited to) two-dimensional array detectors. The software package is implemented using the Interactive Data Language (IDL), and incorporates new methods for processing, calibration, analysis, and visualization of astronomical image data, stressing effective methods for the creation of mosaic images from collections of individual exposures, while at the same time preserving the photometric integrity of the original data. Since IDL is available on many computers, the MOSAIC software runs on most UNIX and VAX workstations with the X-Windows or Sun View graphics interface.

  2. The influence of software filtering in digital mammography image quality

    NASA Astrophysics Data System (ADS)

    Michail, C.; Spyropoulou, V.; Kalyvas, N.; Valais, I.; Dimitropoulos, N.; Fountos, G.; Kandarakis, I.; Panayiotakis, G.

    2009-05-01

    Breast cancer is one of the most frequently diagnosed cancers among women. Several techniques have been developed to help in the early detection of breast cancer such as conventional and digital x-ray mammography, positron and single-photon emission mammography, etc. A key advantage in digital mammography is that images can be manipulated as simple computer image files. Thus non-dedicated commercially available image manipulation software can be employed to process and store the images. The image processing tools of the Photoshop (CS 2) software usually incorporate digital filters which may be used to reduce image noise, enhance contrast and increase spatial resolution. However, improving an image quality parameter may result in degradation of another. The aim of this work was to investigate the influence of three sharpening filters, named hereafter sharpen, sharpen more and sharpen edges on image resolution and noise. Image resolution was assessed by means of the Modulation Transfer Function (MTF).In conclusion it was found that the correct use of commercial non-dedicated software on digital mammograms may improve some aspects of image quality.

  3. Colonoscopy tutorial software made with a cadaver's sectioned images.

    PubMed

    Chung, Beom Sun; Chung, Min Suk; Park, Hyung Seon; Shin, Byeong-Seok; Kwon, Koojoo

    2016-11-01

    Novice doctors may watch tutorial videos in training for actual or computed tomographic (CT) colonoscopy. The conventional learning videos can be complemented by virtual colonoscopy software made with a cadaver's sectioned images (SIs). The objective of this study was to assist colonoscopy trainees with the new interactive software. Submucosal segmentation on the SIs was carried out through the whole length of the large intestine. With the SIs and segmented images, a three dimensional model was reconstructed. Six-hundred seventy-one proximal colonoscopic views (conventional views) and corresponding distal colonoscopic views (simulating the retroflexion of a colonoscope) were produced. Not only navigation views showing the current location of the colonoscope tip and its course, but also, supplementary description views were elaborated. The four corresponding views were put into convenient browsing software to be downloaded free from the homepage (anatomy.co.kr). The SI colonoscopy software with the realistic images and supportive tools was available to anybody. Users could readily notice the position and direction of the virtual colonoscope tip and recognize meaningful structures in colonoscopic views. The software is expected to be an auxiliary learning tool to improve technique and related knowledge in actual and CT colonoscopies. Hopefully, the software will be updated using raw images from the Visible Korean project.

  4. Vertical bone measurements from cone beam computed tomography images using different software packages.

    PubMed

    Vasconcelos, Taruska Ventorini; Neves, Frederico Sampaio; Moraes, Lívia Almeida Bueno; Freitas, Deborah Queiroz

    2015-01-01

    This article aimed at comparing the accuracy of linear measurement tools of different commercial software packages. Eight fully edentulous dry mandibles were selected for this study. Incisor, canine, premolar, first molar and second molar regions were selected. Cone beam computed tomography (CBCT) images were obtained with i-CAT Next Generation. Linear bone measurements were performed by one observer on the cross-sectional images using three different software packages: XoranCat®, OnDemand3D® and KDIS3D®, all able to assess DICOM images. In addition, 25% of the sample was reevaluated for the purpose of reproducibility. The mandibles were sectioned to obtain the gold standard for each region. Intraclass coefficients (ICC) were calculated to examine the agreement between the two periods of evaluation; the one-way analysis of variance performed with the post-hoc Dunnett test was used to compare each of the software-derived measurements with the gold standard. The ICC values were excellent for all software packages. The least difference between the software-derived measurements and the gold standard was obtained with the OnDemand3D and KDIS3D (-0.11 and -0.14 mm, respectively), and the greatest, with the XoranCAT (+0.25 mm). However, there was no statistical significant difference between the measurements obtained with the different software packages and the gold standard (p> 0.05). In conclusion, linear bone measurements were not influenced by the software package used to reconstruct the image from CBCT DICOM data.

  5. Increasing software testability with standard access and control interfaces

    NASA Technical Reports Server (NTRS)

    Nikora, Allen P; Some, Raphael R.; Tamir, Yuval

    2003-01-01

    We describe an approach to improving the testability of complex software systems with software constructs modeled after the hardware JTAG bus, used to provide visibility and controlability in testing digital circuits.

  6. Image compression requirements and standards in PACS

    NASA Astrophysics Data System (ADS)

    Wilson, Dennis L.

    1995-05-01

    Cost effective telemedicine and storage create a need for medical image compression. Compression saves communication bandwidth and reduces the size of the stored images. After clinicians become acquainted with the quality of the images using some of the newer algorithms, they accept the idea of lossy compression. The older algorithms, JPEG and MPEG in particular, are generally not adequate for high quality compression of medical images. The requirements for compression for medical images center on diagnostic quality images after the restoration of the images. The compression artifacts should not interfere with the viewing of the images for diagnosis. New requirements for compression arise from the fact that the images will likely be viewed on a computer workstation, where the images may be manipulated in ways that would bring out the artifacts. A medical imaging compression standard must be applicable across a large variety of image types from CT and MR to CR and ultrasound. To have one or a very few compression algorithms that are effective across a broad range of image types is desirable. Related series of images as for CT, MR, or cardiology require inter-image processing as well as intra-image processing for effective compression. Two preferred decompositions of the medical images are lapped orthogonal transforms and wavelet transforms. These transforms decompose the images in frequency in two different ways. The lapped orthogonal transforms groups the data according to the area where the data originated, while the wavelet transforms group the data by the frequency band of the image. The compression realized depends on the similarity of close transform coefficients. Huffman coding or the coding of the RICE algorithm are a beginning for the encoding. To be really effective the coding must have an extension for the areas where there is little information, the low entropy extension. In these areas there are less than one bit per pixel and multiple pixels must be

  7. Uses of software in digital image analysis: a forensic report

    NASA Astrophysics Data System (ADS)

    Sharma, Mukesh; Jha, Shailendra

    2010-02-01

    Forensic image analysis is required an expertise to interpret the content of an image or the image itself in legal matters. Major sub-disciplines of forensic image analysis with law enforcement applications include photo-grammetry, photographic comparison, content analysis and image authentication. It has wide applications in forensic science range from documenting crime scenes to enhancing faint or indistinct patterns such as partial fingerprints. The process of forensic image analysis can involve several different tasks, regardless of the type of image analysis performed. Through this paper authors have tried to explain these tasks, which are described in to three categories: Image Compression, Image Enhancement & Restoration and Measurement Extraction. With the help of examples like signature comparison, counterfeit currency comparison and foot-wear sole impression using the software Canvas and Corel Draw.

  8. Approach to standardizing MR image intensity scale

    NASA Astrophysics Data System (ADS)

    Nyul, Laszlo G.; Udupa, Jayaram K.

    1999-05-01

    Despite the many advantages of MR images, they lack a standard image intensity scale. MR image intensity ranges and the meaning of intensity values vary even for the same protocol (P) and the same body region (D). This causes many difficulties in image display and analysis. We propose a two-step method for standardizing the intensity scale in such a way that for the same P and D, similar intensities will have similar meanings. In the first step, the parameters of the standardizing transformation are 'learned' from an image set. In the second step, for each MR study, these parameters are used to map their histogram into the standardized histogram. The method was tested quantitatively on 90 whole brain FSE T2, PD and T1 studies of MS patients and qualitatively on several other SE PD, T2 and SPGR studies of the grain and foot. Measurements using mean squared difference showed that the standardized image intensities have statistically significantly more consistent range and meaning than the originals. Fixed windows can be established for standardized imags and used for display without the need of per case adjustment. Preliminary results also indicate that the method facilitates improving the degree of automation of image segmentation.

  9. Accuracy of 3D Imaging Software in Cephalometric Analysis

    DTIC Science & Technology

    2013-06-21

    Imaging and Communication in Medicine ( DICOM ) files into personal computer-based software to enable 3D reconstruction of the craniofacial skeleton. These...tissue profile. CBCT data can be imported as DICOM files into personal computer–based software to provide 3D reconstruction of the craniofacial...been acquired for the three pig models. The CBCT data were exported into DICOM multi-file format. They will be imported into a proprietary

  10. Single-molecule localization software applied to photon counting imaging.

    PubMed

    Hirvonen, Liisa M; Kilfeather, Tiffany; Suhling, Klaus

    2015-06-01

    Centroiding in photon counting imaging has traditionally been accomplished by a single-step, noniterative algorithm, often implemented in hardware. Single-molecule localization techniques in superresolution fluorescence microscopy are conceptually similar, but use more sophisticated iterative software-based fitting algorithms to localize the fluorophore. Here, we discuss common features and differences between single-molecule localization and photon counting imaging and investigate the suitability of single-molecule localization software for photon event localization. We find that single-molecule localization software packages designed for superresolution microscopy-QuickPALM, rapidSTORM, and ThunderSTORM-can work well when applied to photon counting imaging with a microchannel-plate-based intensified camera system: photon event recognition can be excellent, fixed pattern noise can be low, and the microchannel plate pores can easily be resolved.

  11. Modified control software for imaging ultracold atomic clouds

    SciTech Connect

    Whitaker, D. L.; Sharma, A.; Brown, J. M.

    2006-12-15

    A charge-coupled device (CCD) camera capable of taking high-quality images of ultracold atomic samples can often represent a significant portion of the equipment costs in atom trapping experiment. We have modified the commercial control software of a CCD camera designed for astronomical imaging to take absorption images of ultracold rubidium clouds. This camera is sensitive at 780 nm and has been modified to take three successive 16-bit images at full resolution. The control software can be integrated into a Matlab graphical user interface with fitting routines written as Matlab functions. This camera is capable of recording high-quality images at a fraction of the cost of similar cameras typically used in atom trapping experiments.

  12. Computer Software Configuration Item-Specific Flight Software Image Transfer Script Generator

    NASA Technical Reports Server (NTRS)

    Bolen, Kenny; Greenlaw, Ronald

    2010-01-01

    A K-shell UNIX script enables the International Space Station (ISS) Flight Control Team (FCT) operators in NASA s Mission Control Center (MCC) in Houston to transfer an entire or partial computer software configuration item (CSCI) from a flight software compact disk (CD) to the onboard Portable Computer System (PCS). The tool is designed to read the content stored on a flight software CD and generate individual CSCI transfer scripts that are capable of transferring the flight software content in a given subdirectory on the CD to the scratch directory on the PCS. The flight control team can then transfer the flight software from the PCS scratch directory to the Electronically Erasable Programmable Read Only Memory (EEPROM) of an ISS Multiplexer/ Demultiplexer (MDM) via the Indirect File Transfer capability. The individual CSCI scripts and the CSCI Specific Flight Software Image Transfer Script Generator (CFITSG), when executed a second time, will remove all components from their original execution. The tool will identify errors in the transfer process and create logs of the transferred software for the purposes of configuration management.

  13. Cost Effectiveness Trade-Offs in Software Support Environment Standardization.

    DTIC Science & Technology

    1986-09-30

    investments in environments. USAF s cost fcr direct labor (in the form of USAF " spaces ," "faces" or "contract dollars") really dominates the economic...Researchers are exploring available systems, or are building their own improved versions, to relieve software developers of tedious or time-consuming tasks...Transactions on Software Engineeri, Vol. SE-lO, No. 5, Sept., 1984, pp. 494-497. Paper explores software reuse. It discusses briefly some economic

  14. Software Development for Ring Imaging Detector

    NASA Astrophysics Data System (ADS)

    Torisky, Benjamin

    2016-03-01

    Jefferson Lab (Jlab) is performing a large-scale upgrade to their Continuous Electron Beam Accelerator Facility (CEBAF) up to 12GeV beam. The Large Acceptance Spectrometer (CLAS12) in Hall B is being upgraded and a new Ring Imaging Cherenkov (RICH) detector is being developed to provide better kaon - pion separation throughout the 3 to 12 GeV range. With this addition, when the electron beam hits the target, the resulting pions, kaons, and other particles will pass through a wall of translucent aerogel tiles and create Cherenkov radiation. This light can then be accurately detected by a large array of Multi-Anode PhotoMultiplier Tubes (MA-PMT). I am presenting an update on my work on the implementation of Java based reconstruction programs for the RICH in the CLAS12 main analysis package.

  15. TANGO standard software to control the Nuclotron beam slow extraction

    NASA Astrophysics Data System (ADS)

    Andreev, V. A.; Volkov, V. I.; Gorbachev, E. V.; Isadov, V. A.; Kirichenko, A. E.; Romanov, S. V.; Sedykh, G. S.

    2016-09-01

    TANGO Controls is a basis of the NICA control system. The report describes the software which integrates the Nuclotron beam slow extraction subsystem into the TANGO system of NICA. Objects of control are power supplies for resonance lenses. The software consists of the subsystem device server, remote client and web-module for viewing the subsystem data.

  16. Non-Imaging Software/Data Analysis Requirements

    NASA Technical Reports Server (NTRS)

    1984-01-01

    The analysis software needs of the non-imaging planetary data user are discussed. Assumptions as to the nature of the planetary science data centers where the data are physically stored are advanced, the scope of the non-imaging data is outlined, and facilities that users are likely to need to define and access data are identified. Data manipulation and analysis needs and display graphics are discussed.

  17. Software to model AXAF-I image quality

    NASA Technical Reports Server (NTRS)

    Ahmad, Anees; Feng, Chen

    1995-01-01

    A modular user-friendly computer program for the modeling of grazing-incidence type x-ray optical systems has been developed. This comprehensive computer software GRAZTRACE covers the manipulation of input data, ray tracing with reflectivity and surface deformation effects, convolution with x-ray source shape, and x-ray scattering. The program also includes the capabilities for image analysis, detector scan modeling, and graphical presentation of the results. A number of utilities have been developed to interface the predicted Advanced X-ray Astrophysics Facility-Imaging (AXAF-I) mirror structural and thermal distortions with the ray-trace. This software is written in FORTRAN 77 and runs on a SUN/SPARC station. An interactive command mode version and a batch mode version of the software have been developed.

  18. Backhoe 3D "gold standard" image

    NASA Astrophysics Data System (ADS)

    Gorham, LeRoy; Naidu, Kiranmai D.; Majumder, Uttam; Minardi, Michael A.

    2005-05-01

    ViSUAl-D (VIsual Sar Using ALl Dimensions), a 2004 DARPA/IXO seedling effort, is developing a capability for reliable high confidence ID from standoff ranges. Recent conflicts have demonstrated that the warfighter would greatly benefit from the ability to ID targets beyond visual and electro-optical ranges[1]. Forming optical-quality SAR images while exploiting full polarization, wide angles, and large bandwidth would be key evidence such a capability is achievable. Using data generated by the Xpatch EM scattering code, ViSUAl-D investigates all degrees of freedom available to the radar designer, including 6 GHz bandwidth, full polarization and angle sampling over 2π steradians (upper hemisphere), in order to produce a "literal" image or representation of the target. This effort includes the generation of a "Gold Standard" image that can be produced at X-band utilizing all available target data. This "Gold Standard" image of the backhoe will serve as a test bed for future more relevant military targets and their image development. The seedling team produced a public release data which was released at the 2004 SPIE conference, as well as a 3D "Gold Standard" backhoe image using a 3D image formation algorithm. This paper describes the full backhoe data set, the image formation algorithm, the visualization process and the resulting image.

  19. Comparison of ISO 9000 and recent software life cycle standards to nuclear regulatory review guidance

    SciTech Connect

    Preckshot, G.G.; Scott, J.A.

    1998-01-20

    Lawrence Livermore National Laboratory is assisting the Nuclear Regulatory Commission with the assessment of certain quality and software life cycle standards to determine whether additional guidance for the U.S. nuclear regulatory context should be derived from the standards. This report describes the nature of the standards and compares the guidance of the standards to that of the recently updated Standard Review Plan.

  20. FBI compression standard for digitized fingerprint images

    NASA Astrophysics Data System (ADS)

    Brislawn, Christopher M.; Bradley, Jonathan N.; Onyshczak, Remigius J.; Hopper, Thomas

    1996-11-01

    The FBI has formulated national standards for digitization and compression of gray-scale fingerprint images. The compression algorithm for the digitized images is based on adaptive uniform scalar quantization of a discrete wavelet transform subband decomposition, a technique referred to as the wavelet/scalar quantization method. The algorithm produces archival-quality images at compression ratios of around 15 to 1 and will allow the current database of paper fingerprint cards to be replaced by digital imagery. A compliance testing program is also being implemented to ensure high standards of image quality and interchangeability of data between different implementations. We will review the current status of the FBI standard, including the compliance testing process and the details of the first-generation encoder.

  1. Stromatoporoid biometrics using image analysis software: A first order approach

    NASA Astrophysics Data System (ADS)

    Wolniewicz, Pawel

    2010-04-01

    Strommetric is a new image analysis computer program that performs morphometric measurements of stromatoporoid sponges. The program measures 15 features of skeletal elements (pillars and laminae) visible in both longitudinal and transverse thin sections. The software is implemented in C++, using the Open Computer Vision (OpenCV) library. The image analysis system distinguishes skeletal elements from sparry calcite using Otsu's method for image thresholding. More than 150 photos of thin sections were used as a test set, from which 36,159 measurements were obtained. The software provided about one hundred times more data than the current method applied until now. The data obtained are reproducible, even if the work is repeated by different workers. Thus the method makes the biometric studies of stromatoporoids objective.

  2. 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

  3. Open Architecture Standard for NASA's Software-Defined Space Telecommunications Radio Systems

    NASA Technical Reports Server (NTRS)

    Reinhart, Richard C.; Johnson, Sandra K.; Kacpura, Thomas J.; Hall, Charles S.; Smith, Carl R.; Liebetreu, John

    2008-01-01

    NASA is developing an architecture standard for software-defined radios used in space- and ground-based platforms to enable commonality among radio developments to enhance capability and services while reducing mission and programmatic risk. Transceivers (or transponders) with functionality primarily defined in software (e.g., firmware) have the ability to change their functional behavior through software alone. This radio architecture standard offers value by employing common waveform software interfaces, method of instantiation, operation, and testing among different compliant hardware and software products. These common interfaces within the architecture abstract application software from the underlying hardware to enable technology insertion independently at either the software or hardware layer. This paper presents the initial Space Telecommunications Radio System (STRS) Architecture for NASA missions to provide the desired software abstraction and flexibility while minimizing the resources necessary to support the architecture.

  4. Pattern Recognition Software and Techniques for Biological Image Analysis

    PubMed Central

    Shamir, Lior; Delaney, John D.; Orlov, Nikita; Eckley, D. Mark; Goldberg, Ilya G.

    2010-01-01

    The increasing prevalence of automated image acquisition systems is enabling new types of microscopy experiments that generate large image datasets. However, there is a perceived lack of robust image analysis systems required to process these diverse datasets. Most automated image analysis systems are tailored for specific types of microscopy, contrast methods, probes, and even cell types. This imposes significant constraints on experimental design, limiting their application to the narrow set of imaging methods for which they were designed. One of the approaches to address these limitations is pattern recognition, which was originally developed for remote sensing, and is increasingly being applied to the biology domain. This approach relies on training a computer to recognize patterns in images rather than developing algorithms or tuning parameters for specific image processing tasks. The generality of this approach promises to enable data mining in extensive image repositories, and provide objective and quantitative imaging assays for routine use. Here, we provide a brief overview of the technologies behind pattern recognition and its use in computer vision for biological and biomedical imaging. We list available software tools that can be used by biologists and suggest practical experimental considerations to make the best use of pattern recognition techniques for imaging assays. PMID:21124870

  5. Pattern recognition software and techniques for biological image analysis.

    PubMed

    Shamir, Lior; Delaney, John D; Orlov, Nikita; Eckley, D Mark; Goldberg, Ilya G

    2010-11-24

    The increasing prevalence of automated image acquisition systems is enabling new types of microscopy experiments that generate large image datasets. However, there is a perceived lack of robust image analysis systems required to process these diverse datasets. Most automated image analysis systems are tailored for specific types of microscopy, contrast methods, probes, and even cell types. This imposes significant constraints on experimental design, limiting their application to the narrow set of imaging methods for which they were designed. One of the approaches to address these limitations is pattern recognition, which was originally developed for remote sensing, and is increasingly being applied to the biology domain. This approach relies on training a computer to recognize patterns in images rather than developing algorithms or tuning parameters for specific image processing tasks. The generality of this approach promises to enable data mining in extensive image repositories, and provide objective and quantitative imaging assays for routine use. Here, we provide a brief overview of the technologies behind pattern recognition and its use in computer vision for biological and biomedical imaging. We list available software tools that can be used by biologists and suggest practical experimental considerations to make the best use of pattern recognition techniques for imaging assays.

  6. Image Fusion Software in the Clearpem-Sonic Project

    NASA Astrophysics Data System (ADS)

    Pizzichemi, M.; di Vara, N.; Cucciati, G.; Ghezzi, A.; Paganoni, M.; Farina, F.; Frisch, B.; Bugalho, R.

    2012-08-01

    ClearPEM-Sonic is a mammography scanner that combines Positron Emission Tomography with 3D ultrasound echographic and elastographic imaging. It has been developed to improve early stage detection of breast cancer by combining metabolic and anatomical information. The PET system has been developed by the Crystal Clear Collaboration, while the 3D ultrasound probe has been provided by SuperSonic Imagine. In this framework, the visualization and fusion software is an essential tool for the radiologists in the diagnostic process. This contribution discusses the design choices, the issues faced during the implementation, and the commissioning of the software tools developed for ClearPEM-Sonic.

  7. Development of standard digital images for pneumoconiosis.

    PubMed

    Lee, Won-Jeong; Choi, Byung-Soon; Kim, Sung Jin; Park, Choong-Ki; Park, Jai-Soung; Tae, Seok; Hering, Kurt Georg

    2011-11-01

    We developed the standard digital images (SDIs) to be used in the classification and recognition of pneumoconiosis. From July 3, 2006 through August 31, 2007, 531 retired male workers exposed to inorganic dust were examined by digital (DR) and analog radiography (AR) on the same day, after being approved by our institutional review board and obtaining informed consent from all participants. All images were twice classified according to the International Labour Office (ILO) 2000 guidelines with reference to ILO standard analog radiographs (SARs) by four chest radiologists. After consensus reading on 349 digital images matched with the first selected analog images, 120 digital images were selected as the SDIs that considered the distribution of pneumoconiosis findings. Images with profusion category 0/1, 1, 2, and 3 were 12, 50, 40, and 15, respectively, and a large opacity were in 43 images (A = 20, B = 22, C = 1). Among pleural abnormality, costophrenic angle obliteration, pleural plaque and thickening were in 11 (9.2%), 31 (25.8%), and 9 (7.5%) images, respectively. Twenty-one of 29 symbols were present except cp, ef, ho, id, me, pa, ra, and rp. A set of 120 SDIs had more various pneumoconiosis findings than ILO SARs that were developed from adequate methods. It can be used as digital reference images for the recognition and classification of pneumoconiosis.

  8. Standardizing PhenoCam Image Processing and Data Products

    NASA Astrophysics Data System (ADS)

    Milliman, T. E.; Richardson, A. D.; Klosterman, S.; Gray, J. M.; Hufkens, K.; Aubrecht, D.; Chen, M.; Friedl, M. A.

    2014-12-01

    The PhenoCam Network (http://phenocam.unh.edu) contains an archive of imagery from digital webcams to be used for scientific studies of phenological processes of vegetation. The image archive continues to grow and currently has over 4.8 million images representing 850 site-years of data. Time series of broadband reflectance (e.g., red, green, blue, infrared bands) and derivative vegetation indices (e.g. green chromatic coordinate or GCC) are calculated for regions of interest (ROI) within each image series. These time series form the basis for subsequent analysis, such as spring and autumn transition date extraction (using curvature analysis techniques) and modeling the climate-phenology relationship. Processing is relatively straightforward but time consuming, with some sites having more than 100,000 images available. While the PhenoCam Network distributes the original image data, it is our goal to provide higher-level vegetation phenology products, generated in a standardized way, to encourage use of the data without the need to download and analyze individual images. We describe here the details of the standard image processing procedures, and also provide a description of the products that will be available for download. Products currently in development include an "all-image" file, which contains a statistical summary of the red, green and blue bands over the pixels in predefined ROI's for each image from a site. This product is used to generate 1-day and 3-day temporal aggregates with 90th percentile values of GCC for the specified time-periodwith standard image selection/filtering criteria applied. Sample software (in python, R, MATLAB) that can be used to read in and plot these products will also be described.

  9. Open source tools for standardized privacy protection of medical images

    NASA Astrophysics Data System (ADS)

    Lien, Chung-Yueh; Onken, Michael; Eichelberg, Marco; Kao, Tsair; Hein, Andreas

    2011-03-01

    In addition to the primary care context, medical images are often useful for research projects and community healthcare networks, so-called "secondary use". Patient privacy becomes an issue in such scenarios since the disclosure of personal health information (PHI) has to be prevented in a sharing environment. In general, most PHIs should be completely removed from the images according to the respective privacy regulations, but some basic and alleviated data is usually required for accurate image interpretation. Our objective is to utilize and enhance these specifications in order to provide reliable software implementations for de- and re-identification of medical images suitable for online and offline delivery. DICOM (Digital Imaging and Communications in Medicine) images are de-identified by replacing PHI-specific information with values still being reasonable for imaging diagnosis and patient indexing. In this paper, this approach is evaluated based on a prototype implementation built on top of the open source framework DCMTK (DICOM Toolkit) utilizing standardized de- and re-identification mechanisms. A set of tools has been developed for DICOM de-identification that meets privacy requirements of an offline and online sharing environment and fully relies on standard-based methods.

  10. Current and future trends in marine image annotation software

    NASA Astrophysics Data System (ADS)

    Gomes-Pereira, Jose Nuno; Auger, Vincent; Beisiegel, Kolja; Benjamin, Robert; Bergmann, Melanie; Bowden, David; Buhl-Mortensen, Pal; De Leo, Fabio C.; Dionísio, Gisela; Durden, Jennifer M.; Edwards, Luke; Friedman, Ariell; Greinert, Jens; Jacobsen-Stout, Nancy; Lerner, Steve; Leslie, Murray; Nattkemper, Tim W.; Sameoto, Jessica A.; Schoening, Timm; Schouten, Ronald; Seager, James; Singh, Hanumant; Soubigou, Olivier; Tojeira, Inês; van den Beld, Inge; Dias, Frederico; Tempera, Fernando; Santos, Ricardo S.

    2016-12-01

    Given the need to describe, analyze and index large quantities of marine imagery data for exploration and monitoring activities, a range of specialized image annotation tools have been developed worldwide. Image annotation - the process of transposing objects or events represented in a video or still image to the semantic level, may involve human interactions and computer-assisted solutions. Marine image annotation software (MIAS) have enabled over 500 publications to date. We review the functioning, application trends and developments, by comparing general and advanced features of 23 different tools utilized in underwater image analysis. MIAS requiring human input are basically a graphical user interface, with a video player or image browser that recognizes a specific time code or image code, allowing to log events in a time-stamped (and/or geo-referenced) manner. MIAS differ from similar software by the capability of integrating data associated to video collection, the most simple being the position coordinates of the video recording platform. MIAS have three main characteristics: annotating events in real time, posteriorly to annotation and interact with a database. These range from simple annotation interfaces, to full onboard data management systems, with a variety of toolboxes. Advanced packages allow to input and display data from multiple sensors or multiple annotators via intranet or internet. Posterior human-mediated annotation often include tools for data display and image analysis, e.g. length, area, image segmentation, point count; and in a few cases the possibility of browsing and editing previous dive logs or to analyze the annotations. The interaction with a database allows the automatic integration of annotations from different surveys, repeated annotation and collaborative annotation of shared datasets, browsing and querying of data. Progress in the field of automated annotation is mostly in post processing, for stable platforms or still images

  11. The application of image processing software: Photoshop in environmental design

    NASA Astrophysics Data System (ADS)

    Dong, Baohua; Zhang, Chunmi; Zhuo, Chen

    2011-02-01

    In the process of environmental design and creation, the design sketch holds a very important position in that it not only illuminates the design's idea and concept but also shows the design's visual effects to the client. In the field of environmental design, computer aided design has made significant improvement. Many types of specialized design software for environmental performance of the drawings and post artistic processing have been implemented. Additionally, with the use of this software, working efficiency has greatly increased and drawings have become more specific and more specialized. By analyzing the application of photoshop image processing software in environmental design and comparing and contrasting traditional hand drawing and drawing with modern technology, this essay will further explore the way for computer technology to play a bigger role in environmental design.

  12. Software Defined Radio Standard Architecture and its Application to NASA Space Missions

    NASA Technical Reports Server (NTRS)

    Andro, Monty; Reinhart, Richard C.

    2006-01-01

    A software defined radio (SDR) architecture used in space-based platforms proposes to standardize certain aspects of radio development such as interface definitions, functional control and execution, and application software and firmware development. NASA has charted a team to develop an open software defined radio hardware and software architecture to support NASA missions and determine the viability of an Agency-wide Standard. A draft concept of the proposed standard has been released and discussed among organizations in the SDR community. Appropriate leveraging of the JTRS SCA, OMG's SWRadio Architecture and other aspects are considered. A standard radio architecture offers potential value by employing common waveform software instantiation, operation, testing and software maintenance. While software defined radios offer greater flexibility, they also poses challenges to the radio development for the space environment in terms of size, mass and power consumption and available technology. An SDR architecture for space must recognize and address the constraints of space flight hardware, and systems along with flight heritage and culture. NASA is actively participating in the development of technology and standards related to software defined radios. As NASA considers a standard radio architecture for space communications, input and coordination from government agencies, the industry, academia, and standards bodies is key to a successful architecture. The unique aspects of space require thorough investigation of relevant terrestrial technologies properly adapted to space. The talk will describe NASA's current effort to investigate SDR applications to space missions and a brief overview of a candidate architecture under consideration for space based platforms.

  13. Content standards for medical image metadata

    NASA Astrophysics Data System (ADS)

    d'Ornellas, Marcos C.; da Rocha, Rafael P.

    2003-12-01

    Medical images are at the heart of the healthcare diagnostic procedures. They have provided not only a noninvasive mean to view anatomical cross-sections of internal organs but also a mean for physicians to evaluate the patient"s diagnosis and monitor the effects of the treatment. For a Medical Center, the emphasis may shift from the generation of image to post processing and data management since the medical staff may generate even more processed images and other data from the original image after various analyses and post processing. A medical image data repository for health care information system is becoming a critical need. This data repository would contain comprehensive patient records, including information such as clinical data and related diagnostic images, and post-processed images. Due to the large volume and complexity of the data as well as the diversified user access requirements, the implementation of the medical image archive system will be a complex and challenging task. This paper discusses content standards for medical image metadata. In addition it also focuses on the image metadata content evaluation and metadata quality management.

  14. SIVIC: Open-Source, Standards-Based Software for DICOM MR Spectroscopy Workflows

    PubMed Central

    Crane, Jason C.; Olson, Marram P.; Nelson, Sarah J.

    2013-01-01

    Quantitative analysis of magnetic resonance spectroscopic imaging (MRSI) data provides maps of metabolic parameters that show promise for improving medical diagnosis and therapeutic monitoring. While anatomical images are routinely reconstructed on the scanner, formatted using the DICOM standard, and interpreted using PACS workstations, this is not the case for MRSI data. The evaluation of MRSI data is made more complex because files are typically encoded with vendor-specific file formats and there is a lack of standardized tools for reconstruction, processing, and visualization. SIVIC is a flexible open-source software framework and application suite that enables a complete scanner-to-PACS workflow for evaluation and interpretation of MRSI data. It supports conversion of vendor-specific formats into the DICOM MR spectroscopy (MRS) standard, provides modular and extensible reconstruction and analysis pipelines, and provides tools to support the unique visualization requirements associated with such data. Workflows are presented which demonstrate the routine use of SIVIC to support the acquisition, analysis, and delivery to PACS of clinical 1H MRSI datasets at UCSF. PMID:23970895

  15. Determining Angle of Humeral Torsion Using Image Software Technique

    PubMed Central

    Sethi, Madhu; Vasudeva, Neelam

    2016-01-01

    Introduction Several researches have been done on the measurement of angles of humeral torsion in different parts of the world. Previously described methods were more complicated, not much accurate, cumbersome or required sophisticated instruments. Aim The present study was conducted with the aim to determine the angles of humeral torsion with a newer simple technique using digital images and image tool software. Materials and Methods A total of 250 dry normal adult human humeri were obtained from the bone bank of Department of Anatomy. The length and mid-shaft circumference of each bone was measured with the help of measuring tape. The angle of humeral torsion was measured directly from the digital images by the image analysis using Image Tool 3.0 software program. The data was analysed statistically with SPSS version 17 using unpaired t-test and Spearman’s rank order correlation coefficient. Results The mean angle of torsion was 64.57°±7.56°. On the right side it was 66.84°±9.69°, whereas, on the left side it was found to be 63.31±9.50°. The mean humeral length was 31.6 cm on right side and 30.33 cm on left side. Mid shaft circumference was 5.79 on right side and 5.63 cm on left side. No statistical differences were seen in angles between right and left humeri (p>0.001). Conclusion From our study, it was concluded that circumference of shaft is inversely proportional to angle of humeral torsion. The length and side of humerus has no relation with the humeral torsion. With advancement of digital technology, it is better to use new image softwares for anatomical studies. PMID:27891326

  16. Software for visualization, analysis, and manipulation of laser scan images

    NASA Astrophysics Data System (ADS)

    Burnsides, Dennis B.

    1997-03-01

    The recent introduction of laser surface scanning to scientific applications presents a challenge to computer scientists and engineers. Full utilization of this two- dimensional (2-D) and three-dimensional (3-D) data requires advances in techniques and methods for data processing and visualization. This paper explores the development of software to support the visualization, analysis and manipulation of laser scan images. Specific examples presented are from on-going efforts at the Air Force Computerized Anthropometric Research and Design (CARD) Laboratory.

  17. Web-based interactive 2D/3D medical image processing and visualization software.

    PubMed

    Mahmoudi, Seyyed Ehsan; Akhondi-Asl, Alireza; Rahmani, Roohollah; Faghih-Roohi, Shahrooz; Taimouri, Vahid; Sabouri, Ahmad; Soltanian-Zadeh, Hamid

    2010-05-01

    There are many medical image processing software tools available for research and diagnosis purposes. However, most of these tools are available only as local applications. This limits the accessibility of the software to a specific machine, and thus the data and processing power of that application are not available to other workstations. Further, there are operating system and processing power limitations which prevent such applications from running on every type of workstation. By developing web-based tools, it is possible for users to access the medical image processing functionalities wherever the internet is available. In this paper, we introduce a pure web-based, interactive, extendable, 2D and 3D medical image processing and visualization application that requires no client installation. Our software uses a four-layered design consisting of an algorithm layer, web-user-interface layer, server communication layer, and wrapper layer. To compete with extendibility of the current local medical image processing software, each layer is highly independent of other layers. A wide range of medical image preprocessing, registration, and segmentation methods are implemented using open source libraries. Desktop-like user interaction is provided by using AJAX technology in the web-user-interface. For the visualization functionality of the software, the VRML standard is used to provide 3D features over the web. Integration of these technologies has allowed implementation of our purely web-based software with high functionality without requiring powerful computational resources in the client side. The user-interface is designed such that the users can select appropriate parameters for practical research and clinical studies.

  18. Software phantom for the synthesis of equilibrium radionuclide ventriculography images.

    PubMed

    Ruiz-de-Jesus, Oscar; Yanez-Suarez, Oscar; Jimenez-Angeles, Luis; Vallejo-Venegas, Enrique

    2006-01-01

    This paper presents the novel design of a software phantom for the evaluation of equilibrium radionuclide ventriculography systems. Through singular value decomposition, the data matrix corresponding to an equilibrium image series is decomposed into both spatial and temporal fundamental components that can be parametrized. This parametric model allows for the application of user-controlled conditions related to a desired dynamic behavior. Being invertible, the decomposition is used to regenerate the radionuclide image series, which is then translated into a DICOM ventriculography file that can be read by commercial equipment.

  19. Sungrabber - Software for Measurements on Solar Synoptic Images

    NASA Astrophysics Data System (ADS)

    Hržina, D.; Roša, D.; Hanslmeier, A.; Ruždjak, V.; Brajša, R.

    Measurement of positions of the tracers on synoptic solar images and conversion to heliographic coordinates is a time-consuming procedure with different sources of errors. To make measurements faster and easier, the application "Sungrabber" was developed. The data of the measured heliographic coordinates are stored in text files which are linked to the related solar images, which allows also a fast and simple comparison of the measurements from different sources. Extension of the software is possible and therefore Sungrabber can be used for different purposes (e.g. determining the solar rotation rate, proper motions of the tracers on the Sun, etc.).

  20. Parallel-Processing Software for Creating Mosaic Images

    NASA Technical Reports Server (NTRS)

    Klimeck, Gerhard; Deen, Robert; McCauley, Michael; DeJong, Eric

    2008-01-01

    A computer program implements parallel processing for nearly real-time creation of panoramic mosaics of images of terrain acquired by video cameras on an exploratory robotic vehicle (e.g., a Mars rover). Because the original images are typically acquired at various camera positions and orientations, it is necessary to warp the images into the reference frame of the mosaic before stitching them together to create the mosaic. [Also see "Parallel-Processing Software for Correlating Stereo Images," Software Supplement to NASA Tech Briefs, Vol. 31, No. 9 (September 2007) page 26.] The warping algorithm in this computer program reflects the considerations that (1) for every pixel in the desired final mosaic, a good corresponding point must be found in one or more of the original images and (2) for this purpose, one needs a good mathematical model of the cameras and a good correlation of individual pixels with respect to their positions in three dimensions. The desired mosaic is divided into slices, each of which is assigned to one of a number of central processing units (CPUs) operating simultaneously. The results from the CPUs are gathered and placed into the final mosaic. The time taken to create the mosaic depends upon the number of CPUs, the speed of each CPU, and whether a local or a remote data-staging mechanism is used.

  1. A standard interface between simulation programs and systems analysis software.

    PubMed

    Reichert, P

    2006-01-01

    A simple interface between simulation programs and systems analytical software is proposed. This interface is designed to facilitate linkage of environmental simulation programs with systems analytical software and thus can contribute to remedying the deficiency in applying systems analytical techniques to environmental modelling studies. The proposed concept, consisting of a text file interface combined with a batch mode simulation program call, is independent of model structure, operating system and programming language. It is open for implementation by academic and commercial simulation and systems analytical software developers and is very simple to implement. Its practicability is demonstrated by implementations for three environmental simulation packages (AQUASIM, SWAT and LEACHM) and two systems analytical program packages (UNCSIM, SUFI). The properties listed above and the demonstration of the ease of implementation of the approach are prerequisites for the stimulation of a widespread implementation of the proposed interface that would be beneficial for the dissemination of systems analytical techniques in the environmental and engineering sciences. Furthermore, such a development could stimulate the transfer of systems analytical techniques between different fields of application.

  2. The quest for standards in medical imaging.

    PubMed

    Gibaud, Bernard

    2011-05-01

    This article focuses on standards supporting interoperability and system integration in the medical imaging domain. We introduce the basic concepts and actors and we review the most salient achievements in this domain, especially with the DICOM standard, and the definition of IHE integration profiles. We analyze and discuss what was successful, and what could still be more widely adopted by industry. We then sketch out a perspective of what should be done next, based on our vision of new requirements for the next decade. In particular, we discuss the challenges of a more explicit sharing of image and image processing semantics, and we discuss the help that semantic web technologies (and especially ontologies) may bring to achieving this goal.

  3. Software tools of the Computis European project to process mass spectrometry images.

    PubMed

    Robbe, Marie-France; Both, Jean-Pierre; Prideaux, Brendan; Klinkert, Ivo; Picaud, Vincent; Schramm, Thorsten; Hester, Atfons; Guevara, Victor; Stoeckli, Markus; Roempp, Andreas; Heeren, Ron M A; Spengler, Bernhard; Gala, Olivier; Haan, Serge

    2014-01-01

    Among the needs usually expressed by teams using mass spectrometry imaging, one that often arises is that for user-friendly software able to manage huge data volumes quickly and to provide efficient assistance for the interpretation of data. To answer this need, the Computis European project developed several complementary software tools to process mass spectrometry imaging data. Data Cube Explorer provides a simple spatial and spectral exploration for matrix-assisted laser desorption/ionisation-time of flight (MALDI-ToF) and time of flight-secondary-ion mass spectrometry (ToF-SIMS) data. SpectViewer offers visualisation functions, assistance to the interpretation of data, classification functionalities, peak list extraction to interrogate biological database and image overlay, and it can process data issued from MALDI-ToF, ToF-SIMS and desorption electrospray ionisation (DESI) equipment. EasyReg2D is able to register two images, in American Standard Code for Information Interchange (ASCII) format, issued from different technologies. The collaboration between the teams was hampered by the multiplicity of equipment and data formats, so the project also developed a common data format (imzML) to facilitate the exchange of experimental data and their interpretation by the different software tools. The BioMap platform for visualisation and exploration of MALDI-ToF and DESI images was adapted to parse imzML files, enabling its access to all project partners and, more globally, to a larger community of users. Considering the huge advantages brought by the imzML standard format, a specific editor (vBrowser) for imzML files and converters from proprietary formats to imzML were developed to enable the use of the imzML format by a broad scientific community. This initiative paves the way toward the development of a large panel of software tools able to process mass spectrometry imaging datasets in the future.

  4. Woods Hole Image Processing System Software implementation; using NetCDF as a software interface for image processing

    USGS Publications Warehouse

    Paskevich, Valerie F.

    1992-01-01

    The Branch of Atlantic Marine Geology has been involved in the collection, processing and digital mosaicking of high, medium and low-resolution side-scan sonar data during the past 6 years. In the past, processing and digital mosaicking has been accomplished with a dedicated, shore-based computer system. With the need to process sidescan data in the field with increased power and reduced cost of major workstations, a need to have an image processing package on a UNIX based computer system which could be utilized in the field as well as be more generally available to Branch personnel was identified. This report describes the initial development of that package referred to as the Woods Hole Image Processing System (WHIPS). The software was developed using the Unidata NetCDF software interface to allow data to be more readily portable between different computer operating systems.

  5. Development of Software to Model AXAF-I Image Quality

    NASA Technical Reports Server (NTRS)

    Ahmad, Anees; Hawkins, Lamar

    1996-01-01

    This draft final report describes the work performed under the delivery order number 145 from May 1995 through August 1996. The scope of work included a number of software development tasks for the performance modeling of AXAF-I. A number of new capabilities and functions have been added to the GT software, which is the command mode version of the GRAZTRACE software, originally developed by MSFC. A structural data interface has been developed for the EAL (old SPAR) finite element analysis FEA program, which is being used by MSFC Structural Analysis group for the analysis of AXAF-I. This interface utility can read the structural deformation file from the EAL and other finite element analysis programs such as NASTRAN and COSMOS/M, and convert the data to a suitable format that can be used for the deformation ray-tracing to predict the image quality for a distorted mirror. There is a provision in this utility to expand the data from finite element models assuming 180 degrees symmetry. This utility has been used to predict image characteristics for the AXAF-I HRMA, when subjected to gravity effects in the horizontal x-ray ground test configuration. The development of the metrology data processing interface software has also been completed. It can read the HDOS FITS format surface map files, manipulate and filter the metrology data, and produce a deformation file, which can be used by GT for ray tracing for the mirror surface figure errors. This utility has been used to determine the optimum alignment (axial spacing and clocking) for the four pairs of AXAF-I mirrors. Based on this optimized alignment, the geometric images and effective focal lengths for the as built mirrors were predicted to cross check the results obtained by Kodak.

  6. Demineralization Depth Using QLF and a Novel Image Processing Software

    PubMed Central

    Wu, Jun; Donly, Zachary R.; Donly, Kevin J.; Hackmyer, Steven

    2010-01-01

    Quantitative Light-Induced fluorescence (QLF) has been widely used to detect tooth demineralization indicated by fluorescence loss with respect to surrounding sound enamel. The correlation between fluorescence loss and demineralization depth is not fully understood. The purpose of this project was to study this correlation to estimate demineralization depth. Extracted teeth were collected. Artificial caries-like lesions were created and imaged with QLF. Novel image processing software was developed to measure the largest percent of fluorescence loss in the region of interest. All teeth were then sectioned and imaged by polarized light microscopy. The largest depth of demineralization was measured by NIH ImageJ software. The statistical linear regression method was applied to analyze these data. The linear regression model was Y = 0.32X + 0.17, where X was the percent loss of fluorescence and Y was the depth of demineralization. The correlation coefficient was 0.9696. The two-tailed t-test for coefficient was 7.93, indicating the P-value = .0014. The F test for the entire model was 62.86, which shows the P-value = .0013. The results indicated statistically significant linear correlation between the percent loss of fluorescence and depth of the enamel demineralization. PMID:20445755

  7. Planning the Unplanned Experiment: Assessing the Efficacy of Standards for Safety Critical Software

    NASA Technical Reports Server (NTRS)

    Graydon, Patrick J.; Holloway, C. Michael

    2015-01-01

    We need well-founded means of determining whether software is t for use in safety-critical applications. While software in industries such as aviation has an excellent safety record, the fact that software aws have contributed to deaths illustrates the need for justi ably high con dence in software. It is often argued that software is t for safety-critical use because it conforms to a standard for software in safety-critical systems. But little is known about whether such standards `work.' Reliance upon a standard without knowing whether it works is an experiment; without collecting data to assess the standard, this experiment is unplanned. This paper reports on a workshop intended to explore how standards could practicably be assessed. Planning the Unplanned Experiment: Assessing the Ecacy of Standards for Safety Critical Software (AESSCS) was held on 13 May 2014 in conjunction with the European Dependable Computing Conference (EDCC). We summarize and elaborate on the workshop's discussion of the topic, including both the presented positions and the dialogue that ensued.

  8. Megapixel ion imaging with standard video

    SciTech Connect

    Li Wen; Chambreau, Steven D.; Lahankar, Sridhar A.; Suits, Arthur G.

    2005-06-15

    We present an ion imaging approach employing a real-time ion counting method with standard video. This method employs a center-of-mass calculation of each ion spot (more than 3x3 pixels spread) prior to integration. The results of this algorithm are subpixel precision position data of the corresponding ion spots. These addresses are then converted to the final image with user selected resolution, which can be up to ten times higher than the standard video camera resolution (640x480). This method removes the limiting factor imposed by the resolution of standard video cameras and does so at very low cost. The technique is used in conjunction with dc slice imaging, replacing the local maximum searching algorithm developed by Houston and co-workers [B. Y. Chang, R. C. Hoetzlein, J. A. Mueller, J. D. Geiser, and P. L. Houston, Rev. Sci. Instrum. 69, 1665 (1998)]. The performance is demonstrated using HBr and DBr photodissociation at 193 nm with 3+1 resonance enhanced multiphoton ionization detection of hydrogen and deuterium atom products. The measured velocity resolution for DBr dissociation is 0.50% ({delta}v/v), mainly limited in this case by the bandwidth of the photolysis laser. Issues affecting slice imaging resolution and performance are also discussed.

  9. Standardized food images: A photographing protocol and image database.

    PubMed

    Charbonnier, Lisette; van Meer, Floor; van der Laan, Laura N; Viergever, Max A; Smeets, Paul A M

    2016-01-01

    The regulation of food intake has gained much research interest because of the current obesity epidemic. For research purposes, food images are a good and convenient alternative for real food because many dietary decisions are made based on the sight of foods. Food pictures are assumed to elicit anticipatory responses similar to real foods because of learned associations between visual food characteristics and post-ingestive consequences. In contemporary food science, a wide variety of images are used which introduces between-study variability and hampers comparison and meta-analysis of results. Therefore, we created an easy-to-use photographing protocol which enables researchers to generate high resolution food images appropriate for their study objective and population. In addition, we provide a high quality standardized picture set which was characterized in seven European countries. With the use of this photographing protocol a large number of food images were created. Of these images, 80 were selected based on their recognizability in Scotland, Greece and The Netherlands. We collected image characteristics such as liking, perceived calories and/or perceived healthiness ratings from 449 adults and 191 children. The majority of the foods were recognized and liked at all sites. The differences in liking ratings, perceived calories and perceived healthiness between sites were minimal. Furthermore, perceived caloric content and healthiness ratings correlated strongly (r ≥ 0.8) with actual caloric content in both adults and children. The photographing protocol as well as the images and the data are freely available for research use on http://nutritionalneuroscience.eu/. By providing the research community with standardized images and the tools to create their own, comparability between studies will be improved and a head-start is made for a world-wide standardized food image database.

  10. Software and Algorithms for Biomedical Image Data Processing and Visualization

    NASA Technical Reports Server (NTRS)

    Talukder, Ashit; Lambert, James; Lam, Raymond

    2004-01-01

    A new software equipped with novel image processing algorithms and graphical-user-interface (GUI) tools has been designed for automated analysis and processing of large amounts of biomedical image data. The software, called PlaqTrak, has been specifically used for analysis of plaque on teeth of patients. New algorithms have been developed and implemented to segment teeth of interest from surrounding gum, and a real-time image-based morphing procedure is used to automatically overlay a grid onto each segmented tooth. Pattern recognition methods are used to classify plaque from surrounding gum and enamel, while ignoring glare effects due to the reflection of camera light and ambient light from enamel regions. The PlaqTrak system integrates these components into a single software suite with an easy-to-use GUI (see Figure 1) that allows users to do an end-to-end run of a patient s record, including tooth segmentation of all teeth, grid morphing of each segmented tooth, and plaque classification of each tooth image. The automated and accurate processing of the captured images to segment each tooth [see Figure 2(a)] and then detect plaque on a tooth-by-tooth basis is a critical component of the PlaqTrak system to do clinical trials and analysis with minimal human intervention. These features offer distinct advantages over other competing systems that analyze groups of teeth or synthetic teeth. PlaqTrak divides each segmented tooth into eight regions using an advanced graphics morphing procedure [see results on a chipped tooth in Figure 2(b)], and a pattern recognition classifier is then used to locate plaque [red regions in Figure 2(d)] and enamel regions. The morphing allows analysis within regions of teeth, thereby facilitating detailed statistical analysis such as the amount of plaque present on the biting surfaces on teeth. This software system is applicable to a host of biomedical applications, such as cell analysis and life detection, or robotic applications, such

  11. Software architecture standard for simulation virtual machine, version 2.0

    NASA Technical Reports Server (NTRS)

    Sturtevant, Robert; Wessale, William

    1994-01-01

    The Simulation Virtual Machine (SBM) is an Ada architecture which eases the effort involved in the real-time software maintenance and sustaining engineering. The Software Architecture Standard defines the infrastructure which all the simulation models are built from. SVM was developed for and used in the Space Station Verification and Training Facility.

  12. Software Standards and Procedures Manual for the JNGG Graphics Program

    DTIC Science & Technology

    1990-12-01

    from compilation depending upon the outcome of some test usiing some combination of appropriate commands (e.g., #if, #else, #ifdef, #ifndef, # elif ...defunct WWMCCS Standard Graphic Terminal; the Aydin 5807 processor WWS ------------ WAM Workstation; previously known as the WIS Workstation 4-7 THIS

  13. Towards establishing compact imaging spectrometer standards

    USGS Publications Warehouse

    Slonecker, E. Terrence; Allen, David W.; Resmini, Ronald G.

    2016-01-01

    Remote sensing science is currently undergoing a tremendous expansion in the area of hyperspectral imaging (HSI) technology. Spurred largely by the explosive growth of Unmanned Aerial Vehicles (UAV), sometimes called Unmanned Aircraft Systems (UAS), or drones, HSI capabilities that once required access to one of only a handful of very specialized and expensive sensor systems are now miniaturized and widely available commercially. Small compact imaging spectrometers (CIS) now on the market offer a number of hyperspectral imaging capabilities in terms of spectral range and sampling. The potential uses of HSI/CIS on UAVs/UASs seem limitless. However, the rapid expansion of unmanned aircraft and small hyperspectral sensor capabilities has created a number of questions related to technological, legal, and operational capabilities. Lightweight sensor systems suitable for UAV platforms are being advertised in the trade literature at an ever-expanding rate with no standardization of system performance specifications or terms of reference. To address this issue, both the U.S. Geological Survey and the National Institute of Standards and Technology are eveloping draft standards to meet these issues. This paper presents the outline of a combined USGS/NIST cooperative strategy to develop and test a characterization methodology to meet the needs of a new and expanding UAV/CIS/HSI user community.

  14. IDL Object Oriented Software for Hinode/XRT Image Analysis

    NASA Astrophysics Data System (ADS)

    Higgins, P. A.; Gallagher, P. T.

    2008-09-01

    We have developed a set of object oriented IDL routines that enable users to search, download and analyse images from the X-Ray Telescope (XRT) on-board Hinode. In this paper, we give specific examples of how the object can be used and how multi-instrument data analysis can be performed. The XRT object is a highly versatile and powerful IDL object, which will prove to be a useful tool for solar researchers. This software utilizes the generic Framework object available within the GEN branch of SolarSoft.

  15. Planning the Unplanned Experiment: Towards Assessing the Efficacy of Standards for Safety-Critical Software

    NASA Technical Reports Server (NTRS)

    Graydon, Patrick J.; Holloway, C. M.

    2015-01-01

    Safe use of software in safety-critical applications requires well-founded means of determining whether software is fit for such use. While software in industries such as aviation has a good safety record, little is known about whether standards for software in safety-critical applications 'work' (or even what that means). It is often (implicitly) argued that software is fit for safety-critical use because it conforms to an appropriate standard. Without knowing whether a standard works, such reliance is an experiment; without carefully collecting assessment data, that experiment is unplanned. To help plan the experiment, we organized a workshop to develop practical ideas for assessing software safety standards. In this paper, we relate and elaborate on the workshop discussion, which revealed subtle but important study design considerations and practical barriers to collecting appropriate historical data and recruiting appropriate experimental subjects. We discuss assessing standards as written and as applied, several candidate definitions for what it means for a standard to 'work,' and key assessment strategies and study techniques and the pros and cons of each. Finally, we conclude with thoughts about the kinds of research that will be required and how academia, industry, and regulators might collaborate to overcome the noted barriers.

  16. OsiriX: an open-source software for navigating in multidimensional DICOM images.

    PubMed

    Rosset, Antoine; Spadola, Luca; Ratib, Osman

    2004-09-01

    A multidimensional image navigation and display software was designed for display and interpretation of large sets of multidimensional and multimodality images such as combined PET-CT studies. The software is developed in Objective-C on a Macintosh platform under the MacOS X operating system using the GNUstep development environment. It also benefits from the extremely fast and optimized 3D graphic capabilities of the OpenGL graphic standard widely used for computer games optimized for taking advantage of any hardware graphic accelerator boards available. In the design of the software special attention was given to adapt the user interface to the specific and complex tasks of navigating through large sets of image data. An interactive jog-wheel device widely used in the video and movie industry was implemented to allow users to navigate in the different dimensions of an image set much faster than with a traditional mouse or on-screen cursors and sliders. The program can easily be adapted for very specific tasks that require a limited number of functions, by adding and removing tools from the program's toolbar and avoiding an overwhelming number of unnecessary tools and functions. The processing and image rendering tools of the software are based on the open-source libraries ITK and VTK. This ensures that all new developments in image processing that could emerge from other academic institutions using these libraries can be directly ported to the OsiriX program. OsiriX is provided free of charge under the GNU open-source licensing agreement at http://homepage.mac.com/rossetantoine/osirix.

  17. Special Software for Planetary Image Processing and Research

    NASA Astrophysics Data System (ADS)

    Zubarev, A. E.; Nadezhdina, I. E.; Kozlova, N. A.; Brusnikin, E. S.; Karachevtseva, I. P.

    2016-06-01

    The special modules of photogrammetric processing of remote sensing data that provide the opportunity to effectively organize and optimize the planetary studies were developed. As basic application the commercial software package PHOTOMOD™ is used. Special modules were created to perform various types of data processing: calculation of preliminary navigation parameters, calculation of shape parameters of celestial body, global view image orthorectification, estimation of Sun illumination and Earth visibilities from planetary surface. For photogrammetric processing the different types of data have been used, including images of the Moon, Mars, Mercury, Phobos, Galilean satellites and Enceladus obtained by frame or push-broom cameras. We used modern planetary data and images that were taken over the years, shooting from orbit flight path with various illumination and resolution as well as obtained by planetary rovers from surface. Planetary data image processing is a complex task, and as usual it can take from few months to years. We present our efficient pipeline procedure that provides the possibilities to obtain different data products and supports a long way from planetary images to celestial body maps. The obtained data - new three-dimensional control point networks, elevation models, orthomosaics - provided accurate maps production: a new Phobos atlas (Karachevtseva et al., 2015) and various thematic maps that derived from studies of planetary surface (Karachevtseva et al., 2016a).

  18. Software architecture for intelligent image processing using Prolog

    NASA Astrophysics Data System (ADS)

    Jones, Andrew C.; Batchelor, Bruce G.

    1994-10-01

    We describe a prototype system for interactive image processing using Prolog, implemented by the first author on an Apple Macintosh computer. This system is inspired by Prolog+, but differs from it in two particularly important respects. The first is that whereas Prolog+ assumes the availability of dedicated image processing hardware, with which the Prolog system communicates, our present system implements image processing functions in software using the C programming language. The second difference is that although our present system supports Prolog+ commands, these are implemented in terms of lower-level Prolog predicates which provide a more flexible approach to image manipulation. We discuss the impact of the Apple Macintosh operating system upon the implementation of the image-processing functions, and the interface between these functions and the Prolog system. We also explain how the Prolog+ commands have been implemented. The system described in this paper is a fairly early prototype, and we outline how we intend to develop the system, a task which is expedited by the extensible architecture we have implemented.

  19. 'Face value': new medical imaging software in commercial view.

    PubMed

    Coopmans, Catelijne

    2011-04-01

    Based on three ethnographic vignettes describing the engagements of a small start-up company with prospective competitors, partners and customers, this paper shows how commercial considerations are folded into the ways visual images become 'seeable'. When company members mount demonstrations of prototype mammography software, they seek to generate interest but also to protect their intellectual property. Pivotal to these efforts to manage revelation and concealment is the visual interface, which is variously performed as obstacle and ally in the development of a profitable product. Using the concept of 'face value', the paper seeks to develop further insight into contemporary dynamics of seeing and showing by tracing the way techno-visual presentations and commercial considerations become entangled in practice. It also draws attention to the salience and significance of enactments of surface and depth in image-based practices.

  20. Development of Automated Image Analysis Software for Suspended Marine Particle Classification

    DTIC Science & Technology

    2003-09-30

    Development of Automated Image Analysis Software for Suspended Marine Particle Classification Scott Samson Center for Ocean Technology...REPORT TYPE 3. DATES COVERED 00-00-2003 to 00-00-2003 4. TITLE AND SUBTITLE Development of Automated Image Analysis Software for Suspended...objective is to develop automated image analysis software to reduce the effort and time required for manual identification of plankton images. Automated

  1. Software development for ACR-approved phantom-based nuclear medicine tomographic image quality control with cross-platform compatibility

    NASA Astrophysics Data System (ADS)

    Oh, Jungsu S.; Choi, Jae Min; Nam, Ki Pyo; Chae, Sun Young; Ryu, Jin-Sook; Moon, Dae Hyuk; Kim, Jae Seung

    2015-07-01

    Quality control and quality assurance (QC/QA) have been two of the most important issues in modern nuclear medicine (NM) imaging for both clinical practices and academic research. Whereas quantitative QC analysis software is common to modern positron emission tomography (PET) scanners, the QC of gamma cameras and/or single-photon-emission computed tomography (SPECT) scanners has not been sufficiently addressed. Although a thorough standard operating process (SOP) for mechanical and software maintenance may help the QC/QA of a gamma camera and SPECT-computed tomography (CT), no previous study has addressed a unified platform or process to decipher or analyze SPECT phantom images acquired from various scanners thus far. In addition, a few approaches have established cross-platform software to enable the technologists and physicists to assess the variety of SPECT scanners from different manufacturers. To resolve these issues, we have developed Interactive Data Language (IDL)-based in-house software for crossplatform (in terms of not only operating systems (OS) but also manufacturers) analyses of the QC data on an ACR SPECT phantom, which is essential for assessing and assuring the tomographical image quality of SPECT. We applied our devised software to our routine quarterly QC of ACR SPECT phantom images acquired from a number of platforms (OS/manufacturers). Based on our experience, we suggest that our devised software can offer a unified platform that allows images acquired from various types of scanners to be analyzed with great precision and accuracy.

  2. Vobi One: a data processing software package for functional optical imaging

    PubMed Central

    Takerkart, Sylvain; Katz, Philippe; Garcia, Flavien; Roux, Sébastien; Reynaud, Alexandre; Chavane, Frédéric

    2014-01-01

    Optical imaging is the only technique that allows to record the activity of a neuronal population at the mesoscopic scale. A large region of the cortex (10–20 mm diameter) is directly imaged with a CCD camera while the animal performs a behavioral task, producing spatio-temporal data with an unprecedented combination of spatial and temporal resolutions (respectively, tens of micrometers and milliseconds). However, researchers who have developed and used this technique have relied on heterogeneous software and methods to analyze their data. In this paper, we introduce Vobi One, a software package entirely dedicated to the processing of functional optical imaging data. It has been designed to facilitate the processing of data and the comparison of different analysis methods. Moreover, it should help bring good analysis practices to the community because it relies on a database and a standard format for data handling and it provides tools that allow producing reproducible research. Vobi One is an extension of the BrainVISA software platform, entirely written with the Python programming language, open source and freely available for download at https://trac.int.univ-amu.fr/vobi_one. PMID:24478623

  3. Development of a Consensus Standard for Verification and Validation of Nuclear System Thermal-Fluids Software

    SciTech Connect

    Edwin A. Harvego; Richard R. Schultz; Ryan L. Crane

    2011-12-01

    With the resurgence of nuclear power and increased interest in advanced nuclear reactors as an option to supply abundant energy without the associated greenhouse gas emissions of the more conventional fossil fuel energy sources, there is a need to establish internationally recognized standards for the verification and validation (V&V) of software used to calculate the thermal-hydraulic behavior of advanced reactor designs for both normal operation and hypothetical accident conditions. To address this need, ASME (American Society of Mechanical Engineers) Standards and Certification has established the V&V 30 Committee, under the jurisdiction of the V&V Standards Committee, to develop a consensus standard for verification and validation of software used for design and analysis of advanced reactor systems. The initial focus of this committee will be on the V&V of system analysis and computational fluid dynamics (CFD) software for nuclear applications. To limit the scope of the effort, the committee will further limit its focus to software to be used in the licensing of High-Temperature Gas-Cooled Reactors. In this framework, the Standard should conform to Nuclear Regulatory Commission (NRC) and other regulatory practices, procedures and methods for licensing of nuclear power plants as embodied in the United States (U.S.) Code of Federal Regulations and other pertinent documents such as Regulatory Guide 1.203, 'Transient and Accident Analysis Methods' and NUREG-0800, 'NRC Standard Review Plan'. In addition, the Standard should be consistent with applicable sections of ASME NQA-1-2008 'Quality Assurance Requirements for Nuclear Facility Applications (QA)'. This paper describes the general requirements for the proposed V&V 30 Standard, which includes; (a) applicable NRC and other regulatory requirements for defining the operational and accident domain of a nuclear system that must be considered if the system is to be licensed, (b) the corresponding calculation domain of

  4. Two-Dimensional Gel Electrophoresis Image Analysis via Dedicated Software Packages.

    PubMed

    Maurer, Martin H

    2016-01-01

    Analyzing two-dimensional gel electrophoretic images is supported by a number of freely and commercially available software. Although the respective program is highly specific, all the programs follow certain standardized algorithms. General steps are: (1) detecting and separating individual spots, (2) subtracting background, (3) creating a reference gel and (4) matching the spots to the reference gel, (5) modifying the reference gel, (6) normalizing the gel measurements for comparison, (7) calibrating for isoelectric point and molecular weight markers, and moreover, (8) constructing a database containing the measurement results and (9) comparing data by statistical and bioinformatic methods.

  5. Predictive images of postoperative levator resection outcome using image processing software

    PubMed Central

    Mawatari, Yuki; Fukushima, Mikiko

    2016-01-01

    Purpose This study aims to evaluate the efficacy of processed images to predict postoperative appearance following levator resection. Methods Analysis involved 109 eyes from 65 patients with blepharoptosis who underwent advancement of levator aponeurosis and Müller’s muscle complex (levator resection). Predictive images were prepared from preoperative photographs using the image processing software (Adobe Photoshop®). Images of selected eyes were digitally enlarged in an appropriate manner and shown to patients prior to surgery. Results Approximately 1 month postoperatively, we surveyed our patients using questionnaires. Fifty-six patients (89.2%) were satisfied with their postoperative appearances, and 55 patients (84.8%) positively responded to the usefulness of processed images to predict postoperative appearance. Conclusion Showing processed images that predict postoperative appearance to patients prior to blepharoptosis surgery can be useful for those patients concerned with their postoperative appearance. This approach may serve as a useful tool to simulate blepharoptosis surgery. PMID:27757008

  6. Understanding the Perception of Very Small Software Companies towards the Adoption of Process Standards

    NASA Astrophysics Data System (ADS)

    Basri, Shuib; O'Connor, Rory V.

    This paper is concerned with understanding the issues that affect the adoption of software process standards by Very Small Entities (VSEs), their needs from process standards and their willingness to engage with the new ISO/IEC 29110 standard in particular. In order to achieve this goal, a series of industry data collection studies were undertaken with a collection of VSEs. A twin track approach of a qualitative data collection (interviews and focus groups) and quantitative data collection (questionnaire) were undertaken. Data analysis was being completed separately and the final results were merged, using the coding mechanisms of grounded theory. This paper serves as a roadmap for both researchers wishing to understand the issues of process standards adoption by very small companies and also for the software process standards community.

  7. A comprehensive software system for image processing and programming. Final report

    SciTech Connect

    Rasure, J.; Hallett, S.; Jordan, R.

    1994-12-31

    XVision is an example of a comprehensive software system dedicated to the processing of multidimensional scientific data. Because it is comprehensive it is necessarily complex. This design complexity is dealt with by considering XVision as nine overlapping software systems, their components and the required standards. The complexity seen by a user of XVision is minimized by the different interfaces providing access to the image processing routines as well as an interface to ease the incorporation of new routines. The XVision project has stressed the importance of having: (1) interfaces to accommodate users with differing preferences and backgrounds and (2) tools to support the programmer and the scientist. The result is a system that provides a framework for building a powerful research, education and development tool.

  8. A Survey of DICOM Viewer Software to Integrate Clinical Research and Medical Imaging.

    PubMed

    Haak, Daniel; Page, Charles-E; Deserno, Thomas M

    2016-04-01

    The digital imaging and communications in medicine (DICOM) protocol is the leading standard for image data management in healthcare. Imaging biomarkers and image-based surrogate endpoints in clinical trials and medical registries require DICOM viewer software with advanced functionality for visualization and interfaces for integration. In this paper, a comprehensive evaluation of 28 DICOM viewers is performed. The evaluation criteria are obtained from application scenarios in clinical research rather than patient care. They include (i) platform, (ii) interface, (iii) support, (iv) two-dimensional (2D), and (v) three-dimensional (3D) viewing. On the average, 4.48 and 1.43 of overall 8 2D and 5 3D image viewing criteria are satisfied, respectively. Suitable DICOM interfaces for central viewing in hospitals are provided by GingkoCADx, MIPAV, and OsiriX Lite. The viewers ImageJ, MicroView, MIPAV, and OsiriX Lite offer all included 3D-rendering features for advanced viewing. Interfaces needed for decentral viewing in web-based systems are offered by Oviyam, Weasis, and Xero. Focusing on open source components, MIPAV is the best candidate for 3D imaging as well as DICOM communication. Weasis is superior for workflow optimization in clinical trials. Our evaluation shows that advanced visualization and suitable interfaces can also be found in the open source field and not only in commercial products.

  9. Collaboration using open standards and open source software (examples of DIAS/CEOS Water Portal)

    NASA Astrophysics Data System (ADS)

    Miura, S.; Sekioka, S.; Kuroiwa, K.; Kudo, Y.

    2015-12-01

    The DIAS/CEOS Water Portal is a part of the DIAS (Data Integration and Analysis System, http://www.editoria.u-tokyo.ac.jp/projects/dias/?locale=en_US) systems for data distribution for users including, but not limited to, scientists, decision makers and officers like river administrators. One of the functions of this portal is to enable one-stop search and access variable water related data archived multiple data centers located all over the world. This portal itself does not store data. Instead, according to requests made by users on the web page, it retrieves data from distributed data centers on-the-fly and lets them download and see rendered images/plots. Our system mainly relies on the open source software GI-cat (http://essi-lab.eu/do/view/GIcat) and open standards such as OGC-CSW, Opensearch and OPeNDAP protocol to enable the above functions. Details on how it works will be introduced during the presentation. Although some data centers have unique meta data format and/or data search protocols, our portal's brokering function enables users to search across various data centers at one time. And this portal is also connected to other data brokering systems, including GEOSS DAB (Discovery and Access Broker). As a result, users can search over thousands of datasets, millions of files at one time. Users can access the DIAS/CEOS Water Portal system at http://waterportal.ceos.org/.

  10. Variability of standard liver volume estimation versus software-assisted total liver volume measurement.

    PubMed

    Pomposelli, James J; Tongyoo, Assanee; Wald, Christoph; Pomfret, Elizabeth A

    2012-09-01

    The estimation of the standard liver volume (SLV) is an important component of the evaluation of potential living liver donors and the surgical planning for resection for tumors. At least 16 different formulas for estimating SLV have been published in the worldwide literature. More recently, several proprietary software-assisted image postprocessing (SAIP) programs have been developed to provide accurate volume measurements based on the actual anatomy of a specific patient. Using SAIP, we measured SLV in 375 healthy potential liver donors and compared the results to SLV values that were estimated with the previously published formulas and each donor's demographic and anthropomorphic data. The percentage errors of the 16 SLV formulas versus SAIP varied by more than 59% (from -21.6% to +37.7%). One formula was not statistically different from SAIP with respect to the percentage error (-1.2%), and another formula was not statistically different with respect to the absolute liver volume (18 mL). More than 75% of the estimated SLV values produced by these 2 formulas had percentage errors within ±15%, and the formulas provided good predictions within acceptable agreement (±15%) on scatter plots. Because of the wide variability, care must be taken when a formula is being chosen for estimating SLV, but the 2 aforementioned formulas provided the most accurate results with our patient demographics.

  11. [Study on the image file conformance to DICOM standard about medical imaging device].

    PubMed

    Qiu, Minghui

    2013-09-01

    The format of medical image file conformance to DICOM standard have important influence on users of the PACS. This paper summarized the results of the writer's study on the image file conformance to DICOM standard about medical imaging device for many years. The questions of medical image file no conformance to DICOM standard are pointed in detail and the questions resulted from the troubled image files are analyzed. Finally, the methods of avoiding image file no conformance to DICOM standard are presented.

  12. Towards an Improvement of Software Development Processes through Standard Business Rules

    NASA Astrophysics Data System (ADS)

    Martínez-Fernández, José L.; Martínez, Paloma; González-Cristóbal, José C.

    The automation of software development processes is a desirable goal of current software companies which would lead to a cost reduction in software production. This automation is the backbone of approaches such as Model Driven Architecture (MDA) or Software Factories. This paper proposes the use of standard Business Rules (using Rules Interchange Format, RIF) to specify application functionality along with a platform to produce automatic implementations for them. The novelty of this proposal is to introduce Business Rules at all levels of MDA architecture in a software development process, providing a supporting tool where production Business Rules are considered at every abstraction level. Production Business Rules are represented through standard languages, rule engine vendor independence is assured via automatic transformation between rule languages, and Business Rules reuse is made possible. The objective is to get the development of production Business Rules closer to non-technical people involved in the software development process through the use of natural language processing approaches, automatic transformations among models and semantic web languages such as Ontology Web Language (OWL).

  13. Efficient 3D rendering for web-based medical imaging software: a proof of concept

    NASA Astrophysics Data System (ADS)

    Cantor-Rivera, Diego; Bartha, Robert; Peters, Terry

    2011-03-01

    Medical Imaging Software (MIS) found in research and in clinical practice, such as in Picture and Archiving Communication Systems (PACS) and Radiology Information Systems (RIS), has not been able to take full advantage of the Internet as a deployment platform. MIS is usually tightly coupled to algorithms that have substantial hardware and software requirements. Consequently, MIS is deployed on thick clients which usually leads project managers to allocate more resources during the deployment phase of the application than the resources that would be allocated if the application were deployed through a web interface.To minimize the costs associated with this scenario, many software providers use or develop plug-ins to provide the delivery platform (internet browser) with the features to load, interact and analyze medical images. Nevertheless there has not been a successful standard means to achieve this goal so far. This paper presents a study of WebGL as an alternative to plug-in development for efficient rendering of 3D medical models and DICOM images. WebGL is a technology that enables the internet browser to have access to the local graphics hardware in a native fashion. Because it is based in OpenGL, a widely accepted graphic industry standard, WebGL is being implemented in most of the major commercial browsers. After a discussion on the details of the technology, a series of experiments are presented to determine the operational boundaries in which WebGL is adequate for MIS. A comparison with current alternatives is also addressed. Finally conclusions and future work are discussed.

  14. Software defined multi-spectral imaging for Arctic sensor networks

    NASA Astrophysics Data System (ADS)

    Siewert, Sam; Angoth, Vivek; Krishnamurthy, Ramnarayan; Mani, Karthikeyan; Mock, Kenrick; Singh, Surjith B.; Srivistava, Saurav; Wagner, Chris; Claus, Ryan; Vis, Matthew Demi

    2016-05-01

    Availability of off-the-shelf infrared sensors combined with high definition visible cameras has made possible the construction of a Software Defined Multi-Spectral Imager (SDMSI) combining long-wave, near-infrared and visible imaging. The SDMSI requires a real-time embedded processor to fuse images and to create real-time depth maps for opportunistic uplink in sensor networks. Researchers at Embry Riddle Aeronautical University working with University of Alaska Anchorage at the Arctic Domain Awareness Center and the University of Colorado Boulder have built several versions of a low-cost drop-in-place SDMSI to test alternatives for power efficient image fusion. The SDMSI is intended for use in field applications including marine security, search and rescue operations and environmental surveys in the Arctic region. Based on Arctic marine sensor network mission goals, the team has designed the SDMSI to include features to rank images based on saliency and to provide on camera fusion and depth mapping. A major challenge has been the design of the camera computing system to operate within a 10 to 20 Watt power budget. This paper presents a power analysis of three options: 1) multi-core, 2) field programmable gate array with multi-core, and 3) graphics processing units with multi-core. For each test, power consumed for common fusion workloads has been measured at a range of frame rates and resolutions. Detailed analyses from our power efficiency comparison for workloads specific to stereo depth mapping and sensor fusion are summarized. Preliminary mission feasibility results from testing with off-the-shelf long-wave infrared and visible cameras in Alaska and Arizona are also summarized to demonstrate the value of the SDMSI for applications such as ice tracking, ocean color, soil moisture, animal and marine vessel detection and tracking. The goal is to select the most power efficient solution for the SDMSI for use on UAVs (Unoccupied Aerial Vehicles) and other drop

  15. The family of standard hydrogen monitoring system computer software design description: Revision 2

    SciTech Connect

    Bender, R.M.

    1994-11-16

    In March 1990, 23 waste tanks at the Hanford Nuclear Reservation were identified as having the potential for the buildup of gas to a flammable or explosive level. As a result of the potential for hydrogen gas buildup, a project was initiated to design a standard hydrogen monitoring system (SHMS) for use at any waste tank to analyze gas samples for hydrogen content. Since it was originally deployed three years ago, two variations of the original system have been developed: the SHMS-B and SHMS-C. All three are currently in operation at the tank farms and will be discussed in this document. To avoid confusion in this document, when a feature is common to all three of the SHMS variants, it will be referred to as ``The family of SHMS.`` When it is specific to only one or two, they will be identified. The purpose of this computer software design document is to provide the following: the computer software requirements specification that documents the essential requirements of the computer software and its external interfaces; the computer software design description; the computer software user documentation for using and maintaining the computer software and any dedicated hardware; and the requirements for computer software design verification and validation.

  16. The Effects of Personalized Practice Software on Learning Math Standards in the Third through Fifth Grades

    ERIC Educational Resources Information Center

    Gomez, Angela Nicole

    2012-01-01

    The purpose of this study was to investigate the effectiveness of "MathFacts in a Flash" software in helping students learn math standards. In each of their classes, the third-, fourth-, and fifth-grade students in a small private Roman Catholic school from the Pacific Northwest were randomly assigned either to a control group that used…

  17. JUPOS : Amateur analysis of Jupiter images with specialized measurement software

    NASA Astrophysics Data System (ADS)

    Jacquesson, M.; Mettig, H.-J.

    2008-09-01

    spectral range (sorted by descending priority): o color o monochrome red o IR broadband o green o not blue except for particular cases o not narrow band (except for methane band at 889nm) 5) Correct alignment of RGB color images from 3 monochrome frames 6) Choose images of better quality if several are available from about the same time An important prerequisite: adjust the outline frame correctly - Problems: o phase (darkening of the terminator) o limb darkening o tilt of the image (belt edges are not always horizontal) o north-south asymmetries (rare) o mirror-inverted images o invisibility of the illuminated limb on IR broad band and methane images - How to adjust the outline frame : o increase the luminosity and gamma to display the "real limb". This solution is not sufficient: many images do not show the real limb because of the image processing o use positions of satellites and shadows if visible o refer to latitudes of permanent or long lived objects, but only from recent images as their latitude can vary o setting the frame first on: the limb; the north and south poles; NOT at the terminator o in a series of images taken about 1 ½ hours apart, the same object must have the same position (+/- 0.5°) Measuring objects : 1) Place the WinJUPOS cursor onto the feature's centre - What to measure, what to omit? o some regions of Jupiter with big activity (SEB at present) show many small features that we omit because - finest details are often indistinguishable from image artefacts and noise - they are often short-living, and appear as "noise" in drift charts o omit measuring features too close to the planet's limb o problem with measuring the center of extended objects (e.g. GRS) : visual estimation can give a systematic error. The solution: rotate the image o diffuse features have no clear boundaries 2) Enter the standard JUPOS code of the object (longitude and latitude are automatically computed) 3) Optional: add a description of particular characteristics of the

  18. WorkstationJ: workstation emulation software for medical image perception and technology evaluation research

    NASA Astrophysics Data System (ADS)

    Schartz, Kevin M.; Berbaum, Kevin S.; Caldwell, Robert T.; Madsen, Mark T.

    2007-03-01

    We developed image presentation software that mimics the functionality available in the clinic, but also records time-stamped, observer-display interactions and is readily deployable on diverse workstations making it possible to collect comparable observer data at multiple sites. Commercial image presentation software for clinical use has limited application for research on image perception, ergonomics, computer-aids and informatics because it does not collect observer responses, or other information on observer-display interactions, in real time. It is also very difficult to collect observer data from multiple institutions unless the same commercial software is available at different sites. Our software not only records observer reports of abnormalities and their locations, but also inspection time until report, inspection time for each computed radiograph and for each slice of tomographic studies, window/level, and magnification settings used by the observer. The software is a modified version of the open source ImageJ software available from the National Institutes of Health. Our software involves changes to the base code and extensive new plugin code. Our free software is currently capable of displaying computed tomography and computed radiography images. The software is packaged as Java class files and can be used on Windows, Linux, or Mac systems. By deploying our software together with experiment-specific script files that administer experimental procedures and image file handling, multi-institutional studies can be conducted that increase reader and/or case sample sizes or add experimental conditions.

  19. Development of Automated Image Analysis Software for Suspended Marine Particle Classification

    DTIC Science & Technology

    2002-09-30

    Development of Automated Image Analysis Software for Suspended Marine Particle Classification Scott Samson Center for Ocean Technology...and global water column. 1 OBJECTIVES The project’s objective is to develop automated image analysis software to reduce the effort and time

  20. Design and validation of Segment - freely available software for cardiovascular image analysis

    PubMed Central

    2010-01-01

    Background Commercially available software for cardiovascular image analysis often has limited functionality and frequently lacks the careful validation that is required for clinical studies. We have already implemented a cardiovascular image analysis software package and released it as freeware for the research community. However, it was distributed as a stand-alone application and other researchers could not extend it by writing their own custom image analysis algorithms. We believe that the work required to make a clinically applicable prototype can be reduced by making the software extensible, so that researchers can develop their own modules or improvements. Such an initiative might then serve as a bridge between image analysis research and cardiovascular research. The aim of this article is therefore to present the design and validation of a cardiovascular image analysis software package (Segment) and to announce its release in a source code format. Results Segment can be used for image analysis in magnetic resonance imaging (MRI), computed tomography (CT), single photon emission computed tomography (SPECT) and positron emission tomography (PET). Some of its main features include loading of DICOM images from all major scanner vendors, simultaneous display of multiple image stacks and plane intersections, automated segmentation of the left ventricle, quantification of MRI flow, tools for manual and general object segmentation, quantitative regional wall motion analysis, myocardial viability analysis and image fusion tools. Here we present an overview of the validation results and validation procedures for the functionality of the software. We describe a technique to ensure continued accuracy and validity of the software by implementing and using a test script that tests the functionality of the software and validates the output. The software has been made freely available for research purposes in a source code format on the project home page http

  1. Software.

    ERIC Educational Resources Information Center

    Journal of Chemical Education, 1989

    1989-01-01

    Presented are reviews of two computer software packages for Apple II computers; "Organic Spectroscopy," and "Videodisc Display Program" for use with "The Periodic Table Videodisc." A sample spectrograph from "Organic Spectroscopy" is included. (CW)

  2. The 3D scanner prototype utilize object profile imaging using line laser and octave software

    NASA Astrophysics Data System (ADS)

    Nurdini, Mugi; Manunggal, Trikarsa Tirtadwipa; Samsi, Agus

    2016-11-01

    Three-dimensional scanner or 3D Scanner is a device to reconstruct the real object into digital form on a computer. 3D Scanner is a technology that is being developed, especially in developed countries, where the current 3D Scanner devices is the advanced version with a very expensive prices. This study is basically a simple prototype of 3D Scanner with a very low investment costs. 3D Scanner prototype device consists of a webcam, a rotating desk system controlled by a stepper motor and Arduino UNO, and a line laser. Objects that limit the research is the object with same radius from its center point (object pivot). Scanning is performed by using object profile imaging by line laser which is then captured by the camera and processed by a computer (image processing) using Octave software. On each image acquisition, the scanned object on a rotating desk rotated by a certain degree, so for one full turn multiple images of a number of existing side are finally obtained. Then, the profile of the entire images is extracted in order to obtain digital object dimension. Digital dimension is calibrated by length standard, called gage block. Overall dimensions are then digitally reconstructed into a three-dimensional object. Validation of the scanned object reconstruction of the original object dimensions expressed as a percentage error. Based on the results of data validation, horizontal dimension error is about 5% to 23% and vertical dimension error is about +/- 3%.

  3. Automated facial coding software outperforms people in recognizing neutral faces as neutral from standardized datasets.

    PubMed

    Lewinski, Peter

    2015-01-01

    Little is known about people's accuracy of recognizing neutral faces as neutral. In this paper, I demonstrate the importance of knowing how well people recognize neutral faces. I contrasted human recognition scores of 100 typical, neutral front-up facial images with scores of an arguably objective judge - automated facial coding (AFC) software. I hypothesized that the software would outperform humans in recognizing neutral faces because of the inherently objective nature of computer algorithms. Results confirmed this hypothesis. I provided the first-ever evidence that computer software (90%) was more accurate in recognizing neutral faces than people were (59%). I posited two theoretical mechanisms, i.e., smile-as-a-baseline and false recognition of emotion, as possible explanations for my findings.

  4. Automated facial coding software outperforms people in recognizing neutral faces as neutral from standardized datasets

    PubMed Central

    Lewinski, Peter

    2015-01-01

    Little is known about people’s accuracy of recognizing neutral faces as neutral. In this paper, I demonstrate the importance of knowing how well people recognize neutral faces. I contrasted human recognition scores of 100 typical, neutral front-up facial images with scores of an arguably objective judge – automated facial coding (AFC) software. I hypothesized that the software would outperform humans in recognizing neutral faces because of the inherently objective nature of computer algorithms. Results confirmed this hypothesis. I provided the first-ever evidence that computer software (90%) was more accurate in recognizing neutral faces than people were (59%). I posited two theoretical mechanisms, i.e., smile-as-a-baseline and false recognition of emotion, as possible explanations for my findings. PMID:26441761

  5. BioBrick assembly standards and techniques and associated software tools.

    PubMed

    Røkke, Gunvor; Korvald, Eirin; Pahr, Jarle; Oyås, Ove; Lale, Rahmi

    2014-01-01

    The BioBrick idea was developed to introduce the engineering principles of abstraction and standardization into synthetic biology. BioBricks are DNA sequences that serve a defined biological function and can be readily assembled with any other BioBrick parts to create new BioBricks with novel properties. In order to achieve this, several assembly standards can be used. Which assembly standards a BioBrick is compatible with, depends on the prefix and suffix sequences surrounding the part. In this chapter, five of the most common assembly standards will be described, as well as some of the most used assembly techniques, cloning procedures, and a presentation of the available software tools that can be used for deciding on the best method for assembling of different BioBricks, and searching for BioBrick parts in the Registry of Standard Biological Parts database.

  6. GRO/EGRET data analysis software: An integrated system of custom and commercial software using standard interfaces

    NASA Technical Reports Server (NTRS)

    Laubenthal, N. A.; Bertsch, D.; Lal, N.; Etienne, A.; Mcdonald, L.; Mattox, J.; Sreekumar, P.; Nolan, P.; Fierro, J.

    1992-01-01

    The Energetic Gamma Ray Telescope Experiment (EGRET) on the Compton Gamma Ray Observatory has been in orbit for more than a year and is being used to map the full sky for gamma rays in a wide energy range from 30 to 20,000 MeV. Already these measurements have resulted in a wide range of exciting new information on quasars, pulsars, galactic sources, and diffuse gamma ray emission. The central part of the analysis is done with sky maps that typically cover an 80 x 80 degree section of the sky for an exposure time of several days. Specific software developed for this program generates the counts, exposure, and intensity maps. The analysis is done on a network of UNIX based workstations and takes full advantage of a custom-built user interface called X-dialog. The maps that are generated are stored in the FITS format for a collection of energies. These, along with similar diffuse emission background maps generated from a model calculation, serve as input to a maximum likelihood program that produces maps of likelihood with optional contours that are used to evaluate regions for sources. Likelihood also evaluates the background corrected intensity at each location for each energy interval from which spectra can be generated. Being in a standard FITS format permits all of the maps to be easily accessed by the full complement of tools available in several commercial astronomical analysis systems. In the EGRET case, IDL is used to produce graphics plots in two and three dimensions and to quickly implement any special evaluation that might be desired. Other custom-built software, such as the spectral and pulsar analyses, take advantage of the XView toolkit for display and Postscript output for the color hard copy. This poster paper outlines the data flow and provides examples of the user interfaces and output products. It stresses the advantages that are derived from the integration of the specific instrument-unique software and powerful commercial tools for graphics and

  7. NEIGHBOUR-IN: Image processing software for spatial analysis of animal grouping

    PubMed Central

    Caubet, Yves; Richard, Freddie-Jeanne

    2015-01-01

    Abstract Animal grouping is a very complex process that occurs in many species, involving many individuals under the influence of different mechanisms. To investigate this process, we have created an image processing software, called NEIGHBOUR-IN, designed to analyse individuals’ coordinates belonging to up to three different groups. The software also includes statistical analysis and indexes to discriminate aggregates based on spatial localisation of individuals and their neighbours. After the description of the software, the indexes computed by the software are illustrated using both artificial patterns and case studies using the spatial distribution of woodlice. The added strengths of this software and methods are also discussed. PMID:26261448

  8. NEIGHBOUR-IN: Image processing software for spatial analysis of animal grouping.

    PubMed

    Caubet, Yves; Richard, Freddie-Jeanne

    2015-01-01

    Animal grouping is a very complex process that occurs in many species, involving many individuals under the influence of different mechanisms. To investigate this process, we have created an image processing software, called NEIGHBOUR-IN, designed to analyse individuals' coordinates belonging to up to three different groups. The software also includes statistical analysis and indexes to discriminate aggregates based on spatial localisation of individuals and their neighbours. After the description of the software, the indexes computed by the software are illustrated using both artificial patterns and case studies using the spatial distribution of woodlice. The added strengths of this software and methods are also discussed.

  9. Platform-independent software for medical image processing on the Internet

    NASA Astrophysics Data System (ADS)

    Mancuso, Michael E.; Pathak, Sayan D.; Kim, Yongmin

    1997-05-01

    We have developed a software tool for image processing over the Internet. The tool is a general purpose, easy to use, flexible, platform independent image processing software package with functions most commonly used in medical image processing.It provides for processing of medical images located wither remotely on the Internet or locally. The software was written in Java - the new programming language developed by Sun Microsystems. It was compiled and tested using Microsoft's Visual Java 1.0 and Microsoft's Just in Time Compiler 1.00.6211. The software is simple and easy to use. In order to use the tool, the user needs to download the software from our site before he/she runs it using any Java interpreter, such as those supplied by Sun, Symantec, Borland or Microsoft. Future versions of the operating systems supplied by Sun, Microsoft, Apple, IBM, and others will include Java interpreters. The software is then able to access and process any image on the iNternet or on the local computer. Using a 512 X 512 X 8-bit image, a 3 X 3 convolution took 0.88 seconds on an Intel Pentium Pro PC running at 200 MHz with 64 Mbytes of memory. A window/level operation took 0.38 seconds while a 3 X 3 median filter took 0.71 seconds. These performance numbers demonstrate the feasibility of using this software interactively on desktop computes. Our software tool supports various image processing techniques commonly used in medical image processing and can run without the need of any specialized hardware. It can become an easily accessible resource over the Internet to promote the learning and of understanding image processing algorithms. Also, it could facilitate sharing of medical image databases and collaboration amongst researchers and clinicians, regardless of location.

  10. Integration of XNAT/PACS, DICOM, and research software for automated multi-modal image analysis

    NASA Astrophysics Data System (ADS)

    Gao, Yurui; Burns, Scott S.; Lauzon, Carolyn B.; Fong, Andrew E.; James, Terry A.; Lubar, Joel F.; Thatcher, Robert W.; Twillie, David A.; Wirt, Michael D.; Zola, Marc A.; Logan, Bret W.; Anderson, Adam W.; Landman, Bennett A.

    2013-03-01

    Traumatic brain injury (TBI) is an increasingly important public health concern. While there are several promising avenues of intervention, clinical assessments are relatively coarse and comparative quantitative analysis is an emerging field. Imaging data provide potentially useful information for evaluating TBI across functional, structural, and microstructural phenotypes. Integration and management of disparate data types are major obstacles. In a multi-institution collaboration, we are collecting electroencephalogy (EEG), structural MRI, diffusion tensor MRI (DTI), and single photon emission computed tomography (SPECT) from a large cohort of US Army service members exposed to mild or moderate TBI who are undergoing experimental treatment. We have constructed a robust informatics backbone for this project centered on the DICOM standard and eXtensible Neuroimaging Archive Toolkit (XNAT) server. Herein, we discuss (1) optimization of data transmission, validation and storage, (2) quality assurance and workflow management, and (3) integration of high performance computing with research software.

  11. Integration of XNAT/PACS, DICOM, and Research Software for Automated Multi-modal Image Analysis

    PubMed Central

    Gao, Yurui; Burns, Scott S.; Lauzon, Carolyn B.; Fong, Andrew E.; James, Terry A.; Lubar, Joel F.; Thatcher, Robert W.; Twillie, David A.; Wirt, Michael D.; Zola, Marc A.; Logan, Bret W.; Anderson, Adam W.; Landman, Bennett A.

    2013-01-01

    Traumatic brain injury (TBI) is an increasingly important public health concern. While there are several promising avenues of intervention, clinical assessments are relatively coarse and comparative quantitative analysis is an emerging field. Imaging data provide potentially useful information for evaluating TBI across functional, structural, and microstructural phenotypes. Integration and management of disparate data types are major obstacles. In a multi-institution collaboration, we are collecting electroencephalogy (EEG), structural MRI, diffusion tensor MRI (DTI), and single photon emission computed tomography (SPECT) from a large cohort of US Army service members exposed to mild or moderate TBI who are undergoing experimental treatment. We have constructed a robust informatics backbone for this project centered on the DICOM standard and eXtensible Neuroimaging Archive Toolkit (XNAT) server. Herein, we discuss (1) optimization of data transmission, validation and storage, (2) quality assurance and workflow management, and (3) integration of high performance computing with research software. PMID:24386548

  12. Comparison of grey scale median (GSM) measurement in ultrasound images of human carotid plaques using two different softwares.

    PubMed

    Östling, Gerd; Persson, Margaretha; Hedblad, Bo; Gonçalves, Isabel

    2013-11-01

    Grey scale median (GSM) measured on ultrasound images of carotid plaques has been used for several years now in research to find the vulnerable plaque. Centres have used different software and also different methods for GSM measurement. This has resulted in a wide range of GSM values and cut-off values for the detection of the vulnerable plaque. The aim of this study was to compare the values obtained with two different softwares, using different standardization methods, for the measurement of GSM on ultrasound images of carotid human plaques. GSM was measured with Adobe Photoshop(®) and with Artery Measurement System (AMS) on duplex ultrasound images of 100 consecutive medium- to large-sized carotid plaques of the Beta-blocker Cholesterol-lowering Asymptomatic Plaque Study (BCAPS). The mean values of GSM were 35·2 ± 19·3 and 55·8 ± 22·5 for Adobe Photoshop(®) and AMS, respectively. Mean difference was 20·45 (95% CI: 19·17-21·73). Although the absolute values of GSM differed, the agreement between the two measurements was good, correlation coefficient 0·95. A chi-square test revealed a kappa value of 0·68 when studying quartiles of GSM. The intra-observer variability was 1·9% for AMS and 2·5% for Adobe Photoshop. The difference between softwares and standardization methods must be taken into consideration when comparing studies. To avoid these problems, researcher should come to a consensus regarding software and standardization method for GSM measurement on ultrasound images of plaque in the arteries.

  13. Metrology Standards for Quantitative Imaging Biomarkers.

    PubMed

    Sullivan, Daniel C; Obuchowski, Nancy A; Kessler, Larry G; Raunig, David L; Gatsonis, Constantine; Huang, Erich P; Kondratovich, Marina; McShane, Lisa M; Reeves, Anthony P; Barboriak, Daniel P; Guimaraes, Alexander R; Wahl, Richard L

    2015-12-01

    Although investigators in the imaging community have been active in developing and evaluating quantitative imaging biomarkers (QIBs), the development and implementation of QIBs have been hampered by the inconsistent or incorrect use of terminology or methods for technical performance and statistical concepts. Technical performance is an assessment of how a test performs in reference objects or subjects under controlled conditions. In this article, some of the relevant statistical concepts are reviewed, methods that can be used for evaluating and comparing QIBs are described, and some of the technical performance issues related to imaging biomarkers are discussed. More consistent and correct use of terminology and study design principles will improve clinical research, advance regulatory science, and foster better care for patients who undergo imaging studies.

  14. A Critical Appraisal of Techniques, Software Packages, and Standards for Quantitative Proteomic Analysis

    PubMed Central

    Lawless, Craig; Hubbard, Simon J.; Fan, Jun; Bessant, Conrad; Hermjakob, Henning; Jones, Andrew R.

    2012-01-01

    Abstract New methods for performing quantitative proteome analyses based on differential labeling protocols or label-free techniques are reported in the literature on an almost monthly basis. In parallel, a correspondingly vast number of software tools for the analysis of quantitative proteomics data has also been described in the literature and produced by private companies. In this article we focus on the review of some of the most popular techniques in the field and present a critical appraisal of several software packages available to process and analyze the data produced. We also describe the importance of community standards to support the wide range of software, which may assist researchers in the analysis of data using different platforms and protocols. It is intended that this review will serve bench scientists both as a useful reference and a guide to the selection and use of different pipelines to perform quantitative proteomics data analysis. We have produced a web-based tool (http://www.proteosuite.org/?q=other_resources) to help researchers find appropriate software for their local instrumentation, available file formats, and quantitative methodology. PMID:22804616

  15. Application of open source image guided therapy software in MR-guided therapies.

    PubMed

    Hata, Nobuhiko; Piper, Steve; Jolesz, Ferenc A; Tempany, Clare M C; Black, Peter McL; Morikawa, Shigehiro; Iseki, Horoshi; Hashizume, Makoto; Kikinis, Ron

    2007-01-01

    We present software engineering methods to provide free open-source software for MR-guided therapy. We report that graphical representation of the surgical tools, interconnectively with the tracking device, patient-to-image registration, and MRI-based thermal mapping are crucial components of MR-guided therapy in sharing such software. Software process includes a network-based distribution mechanism by multi-platform compiling tool CMake, CVS, quality assurance software DART. We developed six procedures in four separate clinical sites using proposed software engineering and process, and found the proposed method is feasible to facilitate multicenter clinical trial of MR-guided therapies. Our future studies include use of the software in non-MR-guided therapies.

  16. Wavelet/scalar quantization compression standard for fingerprint images

    SciTech Connect

    Brislawn, C.M.

    1996-06-12

    US Federal Bureau of Investigation (FBI) has recently formulated a national standard for digitization and compression of gray-scale fingerprint images. Fingerprints are scanned at a spatial resolution of 500 dots per inch, with 8 bits of gray-scale resolution. The compression algorithm for the resulting digital images is based on adaptive uniform scalar quantization of a discrete wavelet transform subband decomposition (wavelet/scalar quantization method). The FBI standard produces archival-quality images at compression ratios of around 15 to 1 and will allow the current database of paper fingerprint cards to be replaced by digital imagery. The compression standard specifies a class of potential encoders and a universal decoder with sufficient generality to reconstruct compressed images produced by any compliant encoder, allowing flexibility for future improvements in encoder technology. A compliance testing program is also being implemented to ensure high standards of image quality and interchangeability of data between different implementations.

  17. 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.

  18. An image-based software tool for screening retinal fundus images using vascular morphology and network transport analysis

    NASA Astrophysics Data System (ADS)

    Clark, Richard D.; Dickrell, Daniel J.; Meadows, David L.

    2014-03-01

    As the number of digital retinal fundus images taken each year grows at an increasing rate, there exists a similarly increasing need for automatic eye disease detection through image-based analysis. A new method has been developed for classifying standard color fundus photographs into both healthy and diseased categories. This classification was based on the calculated network fluid conductance, a function of the geometry and connectivity of the vascular segments. To evaluate the network resistance, the retinal vasculature was first manually separated from the background to ensure an accurate representation of the geometry and connectivity. The arterial and venous networks were then semi-automatically separated into two separate binary images. The connectivity of the arterial network was then determined through a series of morphological image operations. The network comprised of segments of vasculature and points of bifurcation, with each segment having a characteristic geometric and fluid properties. Based on the connectivity and fluid resistance of each vascular segment, an arterial network flow conductance was calculated, which described the ease with which blood can pass through a vascular system. In this work, 27 eyes (13 healthy and 14 diabetic) from patients roughly 65 years in age were evaluated using this methodology. Healthy arterial networks exhibited an average fluid conductance of 419 ± 89 μm3/mPa-s while the average network fluid conductance of the diabetic set was 165 ± 87 μm3/mPa-s (p < 0.001). The results of this new image-based software demonstrated an ability to automatically, quantitatively and efficiently screen diseased eyes from color fundus imagery.

  19. Software Compression for Partially Parallel Imaging with Multi-channels.

    PubMed

    Huang, Feng; Vijayakumar, Sathya; Akao, James

    2005-01-01

    In magnetic resonance imaging, multi-channel phased array coils enjoy a high signal to noise ratio (SNR) and better parallel imaging performance. But with the increase in number of channels, the reconstruction time and requirement for computer memory become inevitable problems. In this work, principle component analysis is applied to reduce the size of data and protect the performance of parallel imaging. Clinical data collected using a 32-channel cardiac coil are used in the experiments. Experimental results show that the proposed method dramatically reduces the processing time without much damage to the reconstructed image.

  20. Fluorescence Image Analyzer - FLIMA: software for quantitative analysis of fluorescence in situ hybridization.

    PubMed

    Silva, H C M; Martins-Júnior, M M C; Ribeiro, L B; Matoso, D A

    2017-03-30

    The Fluorescence Image Analyzer (FLIMA) software was developed for the quantitative analysis of images generated by fluorescence in situ hybridization (FISH). Currently, the images of FISH are examined without a coefficient that enables a comparison between them. Through GD Graphics Library, the FLIMA software calculates the amount of pixels on image and recognizes each present color. The coefficient generated by the algorithm shows the percentage of marks (probes) hybridized on the chromosomes. This software can be used for any type of image generated by a fluorescence microscope and is able to quantify digoxigenin probes exhibiting a red color, biotin probes exhibiting a green color, and double-FISH probes (digoxigenin and biotin used together), where the white color is displayed.

  1. Self-contained off-line media for exchanging medical images using DICOM-compliant standard

    NASA Astrophysics Data System (ADS)

    Ratib, Osman M.; Ligier, Yves; Rosset, Antoine; Staub, Jean-Christophe; Logean, Marianne; Girard, Christian

    2000-05-01

    The goal of this project is to develop and implement off-line DICOM-compliant CD ROMs that contain the necessary software tools for displaying the images and related data on any personal computer. We implemented a hybrid recording technique allowing CD-ROMs for Macintosh and Windows platforms to be fully DICOM compliant. A public domain image viewing program (OSIRIS) is recorded on the CD for display and manipulation of sequences of images. The content of the disk is summarized in a standard HTML file that can be displayed on any web-browser. This allows the images to be easily accessible on any desktop computer, while being also readable on high-end commercial DICOM workstations. The HTML index page contains a set of thumbnails and full-size JPEG images that are directly linked to the original high-resolution DICOM images through an activation of the OSIRIS program. Reports and associated text document are also converted to HTML format to be easily displayable directly within the web browser. This portable solution provides a convenient and low cost alternative to hard copy images for exchange and transmission of images to referring physicians and external care providers without the need for any specialized software or hardware.

  2. The creation of a public database of precision phantoms to facilitate the evaluation and standardization of advanced visualization and quantification software

    NASA Astrophysics Data System (ADS)

    Chen, Joseph J.; Saenz, Naomi J.; Siegel, Eliot L.

    2009-02-01

    In order to validate CT imaging as a biomarker, it is important to ascertain the variability and artifacts associated with various forms of advanced visualization and quantification software. The purpose of the paper is to describe the rationale behind the creation of a free, public resource that contains phantom datasets for CT designed to facilitate testing, development and standardization of advanced visualization and quantification software. For our research, three phantoms were scanned at multiple kVp and mAs settings utilizing a 64-channel MDCT scanner at a collimation of 0.75 mm. Images were reconstructed at a slice thickness of 0.75 mm and archived in DICOM format. The phantoms consisted of precision spheres, balls of different materials and sizes, and slabs of Last-A-Foam(R) at varying densities. The database of scans is stored in an archive utilizing software developed for the National Cancer Imaging Archive and is publically available. The scans were completed successfully and the datasets are available for free and unrestricted download. The CT images can be accessed in DICOM format via http or FTP or utilizing caGRID. A DICOM database of phantom data was successfully created and made available to the public. We anticipate that this database will be useful as a reference for physicists for quality control purposes, for developers of advanced visualization and quantification software, and for others who need to test the performance of their systems against a known "gold" standard. We plan to add more phantom images in the future and expand to other imaging modalities.

  3. ESO C Library for an Image Processing Software Environment (eclipse)

    NASA Astrophysics Data System (ADS)

    Devillard, N.

    Written in ANSI C, eclipse is a library offering numerous services related to astronomical image processing: FITS data access, various image and cube loading methods, binary image handling and filtering (including convolution and morphological filters), 2-D cross-correlation, connected components, cube and image arithmetic, dead pixel detection and correction, object detection, data extraction, flat-fielding with robust fit, image generation, statistics, photometry, image-space resampling, image combination, and cube stacking. It also contains support for mathematical tools like random number generation, FFT, curve fitting, matrices, fast median computation, and point-pattern matching. The main feature of this library is its ability to handle large amounts of input data (up to 2 GB in the current version) regardless of the amount of memory and swap available on the local machine. Another feature is the very high speed allowed by optimized C, making it an ideal base tool for programming efficient number-crunching applications, e.g., on parallel (Beowulf) systems. Running on all Unix-like platforms, eclipse is portable. A high-level interface to Python is foreseen that would allow programmers to prototype their applications much faster than through C programs.

  4. Eclipse: ESO C Library for an Image Processing Software Environment

    NASA Astrophysics Data System (ADS)

    Devillard, Nicolas

    2011-12-01

    Written in ANSI C, eclipse is a library offering numerous services related to astronomical image processing: FITS data access, various image and cube loading methods, binary image handling and filtering (including convolution and morphological filters), 2-D cross-correlation, connected components, cube and image arithmetic, dead pixel detection and correction, object detection, data extraction, flat-fielding with robust fit, image generation, statistics, photometry, image-space resampling, image combination, and cube stacking. It also contains support for mathematical tools like random number generation, FFT, curve fitting, matrices, fast median computation, and point-pattern matching. The main feature of this library is its ability to handle large amounts of input data (up to 2GB in the current version) regardless of the amount of memory and swap available on the local machine. Another feature is the very high speed allowed by optimized C, making it an ideal base tool for programming efficient number-crunching applications, e.g., on parallel (Beowulf) systems.

  5. Polarization information processing and software system design for simultaneously imaging polarimetry

    NASA Astrophysics Data System (ADS)

    Wang, Yahui; Liu, Jing; Jin, Weiqi; Wen, Renjie

    2015-08-01

    Simultaneous imaging polarimetry can realize real-time polarization imaging of the dynamic scene, which has wide application prospect. This paper first briefly illustrates the design of the double separate Wollaston Prism simultaneous imaging polarimetry, and then emphases are put on the polarization information processing methods and software system design for the designed polarimetry. Polarization information processing methods consist of adaptive image segmentation, high-accuracy image registration, instrument matrix calibration. Morphological image processing was used for image segmentation by taking dilation of an image; The accuracy of image registration can reach 0.1 pixel based on the spatial and frequency domain cross-correlation; Instrument matrix calibration adopted four-point calibration method. The software system was implemented under Windows environment based on C++ programming language, which realized synchronous polarization images acquisition and preservation, image processing and polarization information extraction and display. Polarization data obtained with the designed polarimetry shows that: the polarization information processing methods and its software system effectively performs live realize polarization measurement of the four Stokes parameters of a scene. The polarization information processing methods effectively improved the polarization detection accuracy.

  6. BIRP: Software for interactive search and retrieval of image engineering data

    NASA Technical Reports Server (NTRS)

    Arvidson, R. E.; Bolef, L. K.; Guinness, E. A.; Norberg, P.

    1980-01-01

    Better Image Retrieval Programs (BIRP), a set of programs to interactively sort through and to display a database, such as engineering data for images acquired by spacecraft is described. An overview of the philosophy of BIRP design, the structure of BIRP data files, and examples that illustrate the capabilities of the software are provided.

  7. A Review of Diffusion Tensor Magnetic Resonance Imaging Computational Methods and Software Tools

    PubMed Central

    Hasan, Khader M.; Walimuni, Indika S.; Abid, Humaira; Hahn, Klaus R.

    2010-01-01

    In this work we provide an up-to-date short review of computational magnetic resonance imaging (MRI) and software tools that are widely used to process and analyze diffusion-weighted MRI data. A review of different methods used to acquire, model and analyze diffusion-weighted imaging data (DWI) is first provided with focus on diffusion tensor imaging (DTI). The major preprocessing, processing and post-processing procedures applied to DTI data are discussed. A list of freely available software packages to analyze diffusion MRI data is also provided. PMID:21087766

  8. Spatial data software integration - Merging CAD/CAM/mapping with GIS and image processing

    NASA Technical Reports Server (NTRS)

    Logan, Thomas L.; Bryant, Nevin A.

    1987-01-01

    The integration of CAD/CAM/mapping with image processing using geographic information systems (GISs) as the interface is examined. Particular emphasis is given to the development of software interfaces between JPL's Video Image Communication and Retrieval (VICAR)/Imaged Based Information System (IBIS) raster-based GIS and the CAD/CAM/mapping system. The design and functions of the VICAR and IBIS are described. Vector data capture and editing are studied. Various software programs for interfacing between the VICAR/IBIS and CAD/CAM/mapping are presented and analyzed.

  9. Illinois Occupational Skill Standards: Imaging/Pre-Press Cluster.

    ERIC Educational Resources Information Center

    Illinois Occupational Skill Standards and Credentialing Council, Carbondale.

    This document, which is intended as a guide for work force preparation program providers, details the Illinois occupational skill standards for programs preparing students for employment in occupations in the imaging/pre-press cluster. The document begins with a brief overview of the Illinois perspective on occupational skill standards and…

  10. Role of JTAG2 in coordinating standards for imaging technology

    NASA Astrophysics Data System (ADS)

    McDowell, David Q.

    1998-12-01

    In the modern world of image technology, standards are developed by many different groups, each with specific applications in mind. While some of these groups are part of the accredited standards community - ISO, IEC, CIE, ITU, etc. others are industrial organizations, or consortia.

  11. Pocket-sized versus standard ultrasound machines in abdominal imaging.

    PubMed

    Tse, K H; Luk, W H; Lam, M C

    2014-06-01

    The pocket-sized ultrasound machine has emerged as an invaluable tool for quick assessment in emergency and general practice settings. It is suitable for instant and quick assessment in cardiac imaging. However, its applicability in the imaging of other body parts has yet to be established. In this pictorial review, we compared the performance of the pocketsized ultrasound machine against the standard ultrasound machine for its image quality in common abdominal pathology.

  12. 75 FR 28058 - In the Matter of Certain Digital Imaging Devices and Related Software; Notice of Investigation

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-19

    ... COMMISSION In the Matter of Certain Digital Imaging Devices and Related Software; Notice of Investigation... software by reason of infringement of certain claims of U.S. Patent Nos. 6,031,964 and RE38,911. The... importation of certain digital imaging devices and related software that infringe one or more of claim 1-3...

  13. Software optimization for electrical conductivity imaging in polycrystalline diamond cutters

    SciTech Connect

    Bogdanov, G.; Ludwig, R.; Wiggins, J.; Bertagnolli, K.

    2014-02-18

    We previously reported on an electrical conductivity imaging instrument developed for measurements on polycrystalline diamond cutters. These cylindrical cutters for oil and gas drilling feature a thick polycrystalline diamond layer on a tungsten carbide substrate. The instrument uses electrical impedance tomography to profile the conductivity in the diamond table. Conductivity images must be acquired quickly, on the order of 5 sec per cutter, to be useful in the manufacturing process. This paper reports on successful efforts to optimize the conductivity reconstruction routine, porting major portions of it to NVIDIA GPUs, including a custom CUDA kernel for Jacobian computation.

  14. IDP: Image and data processing (software) in C++

    SciTech Connect

    Lehman, S.

    1994-11-15

    IDP++(Image and Data Processing in C++) is a complied, multidimensional, multi-data type, signal processing environment written in C++. It is being developed within the Radar Ocean Imaging group and is intended as a partial replacement for View. IDP++ takes advantage of the latest object-oriented compiler technology to provide `information hiding.` Users need only know C, not C++. Signals are treated like any other variable with a defined set of operators and functions in an intuitive manner. IDP++ is being designed for real-time environment where interpreted signal processing packages are less efficient.

  15. Image compression software for the SOHO LASCO and EIT experiments

    NASA Technical Reports Server (NTRS)

    Grunes, Mitchell R.; Howard, Russell A.; Hoppel, Karl; Mango, Stephen A.; Wang, Dennis

    1994-01-01

    This paper describes the lossless and lossy image compression algorithms to be used on board the Solar Heliospheric Observatory (SOHO) in conjunction with the Large Angle Spectrometric Coronograph and Extreme Ultraviolet Imaging Telescope experiments. It also shows preliminary results obtained using similar prior imagery and discusses the lossy compression artifacts which will result. This paper is in part intended for the use of SOHO investigators who need to understand the results of SOHO compression in order to better allocate the transmission bits which they have been allocated.

  16. Reliability evaluation of I-123 ADAM SPECT imaging using SPM software and AAL ROI methods

    NASA Astrophysics Data System (ADS)

    Yang, Bang-Hung; Tsai, Sung-Yi; Wang, Shyh-Jen; Su, Tung-Ping; Chou, Yuan-Hwa; Chen, Chia-Chieh; Chen, Jyh-Cheng

    2011-08-01

    The level of serotonin was regulated by serotonin transporter (SERT), which is a decisive protein in regulation of serotonin neurotransmission system. Many psychiatric disorders and therapies were also related to concentration of cerebral serotonin. I-123 ADAM was the novel radiopharmaceutical to image SERT in brain. The aim of this study was to measure reliability of SERT densities of healthy volunteers by automated anatomical labeling (AAL) method. Furthermore, we also used statistic parametric mapping (SPM) on a voxel by voxel analysis to find difference of cortex between test and retest of I-123 ADAM single photon emission computed tomography (SPECT) images.Twenty-one healthy volunteers were scanned twice with SPECT at 4 h after intravenous administration of 185 MBq of 123I-ADAM. The image matrix size was 128×128 and pixel size was 3.9 mm. All images were obtained through filtered back-projection (FBP) reconstruction algorithm. Region of interest (ROI) definition was performed based on the AAL brain template in PMOD version 2.95 software package. ROI demarcations were placed on midbrain, pons, striatum, and cerebellum. All images were spatially normalized to the SPECT MNI (Montreal Neurological Institute) templates supplied with SPM2. And each image was transformed into standard stereotactic space, which was matched to the Talairach and Tournoux atlas. Then differences across scans were statistically estimated on a voxel by voxel analysis using paired t-test (population main effect: 2 cond's, 1 scan/cond.), which was applied to compare concentration of SERT between the test and retest cerebral scans.The average of specific uptake ratio (SUR: target/cerebellum-1) of 123I-ADAM binding to SERT in midbrain was 1.78±0.27, pons was 1.21±0.53, and striatum was 0.79±0.13. The cronbach's α of intra-class correlation coefficient (ICC) was 0.92. Besides, there was also no significant statistical finding in cerebral area using SPM2 analysis. This finding might help us

  17. Do we really need standards in digital image management?

    PubMed Central

    Ho, ELM

    2008-01-01

    Convention dictates that standards are a necessity rather than a luxury. Standards are supposed to improve the exchange of health and image data information resulting in improved quality and efficiency of patient care. True standardisation is some time away yet, as barriers exist with evolving equipment, storage formats and even the standards themselves. The explosive growth in the size and complexity of images such as those generated by multislice computed tomography have driven the need for digital image management, created problems of storage space and costs, and created a challenge for increasing or getting an adequate speed for transmitting, accessing and retrieving the image data. The search for a suitable and practical format for storing the data without loss of information and medico-legal implications has become a necessity and a matter of ‘urgency’. Existing standards are either open or proprietary and must comply with local, regional or national laws. Currently there are the Picture Archiving and Communications System (PACS); Digital Imaging and Communications in Medicine (DICOM); Health Level 7 (HL7) and Integrating the Healthcare Enterprise (IHE). Issues in digital image management can be categorised as operational, procedural, technical and administrative. Standards must stay focussed on the ultimate goal – that is, improved patient care worldwide. PMID:21611012

  18. The FBI compression standard for digitized fingerprint images

    SciTech Connect

    Brislawn, C.M.; Bradley, J.N.; Onyshczak, R.J.; Hopper, T.

    1996-10-01

    The FBI has formulated national standards for digitization and compression of gray-scale fingerprint images. The compression algorithm for the digitized images is based on adaptive uniform scalar quantization of a discrete wavelet transform subband decomposition, a technique referred to as the wavelet/scalar quantization method. The algorithm produces archival-quality images at compression ratios of around 15 to 1 and will allow the current database of paper fingerprint cards to be replaced by digital imagery. A compliance testing program is also being implemented to ensure high standards of image quality and interchangeability of data between different implementations. We will review the current status of the FBI standard, including the compliance testing process and the details of the first-generation encoder.

  19. Development of Software to Model AXAF-I Image Quality

    NASA Technical Reports Server (NTRS)

    Geary, Joseph; Hawkins, Lamar; Ahmad, Anees; Gong, Qian

    1997-01-01

    This report describes work conducted on Delivery Order 181 between October 1996 through June 1997. During this period software was written to: compute axial PSD's from RDOS AXAF-I mirror surface maps; plot axial surface errors and compute PSD's from HDOS "Big 8" axial scans; plot PSD's from FITS format PSD files; plot band-limited RMS vs axial and azimuthal position for multiple PSD files; combine and organize PSD's from multiple mirror surface measurements formatted as input to GRAZTRACE; modify GRAZTRACE to read FITS formatted PSD files; evaluate AXAF-I test results; improve and expand the capabilities of the GT x-ray mirror analysis package. During this period work began on a more user-friendly manual for the GT program, and improvements were made to the on-line help manual.

  20. Image analysis software for following progression of peripheral neuropathy

    NASA Astrophysics Data System (ADS)

    Epplin-Zapf, Thomas; Miller, Clayton; Larkin, Sean; Hermesmeyer, Eduardo; Macy, Jenny; Pellegrini, Marco; Luccarelli, Saverio; Staurenghi, Giovanni; Holmes, Timothy

    2009-02-01

    A relationship has been reported by several research groups [1 - 4] between the density and shapes of nerve fibers in the cornea and the existence and severity of peripheral neuropathy. Peripheral neuropathy is a complication of several prevalent diseases or conditions, which include diabetes, HIV, prolonged alcohol overconsumption and aging. A common clinical technique for confirming the condition is intramuscular electromyography (EMG), which is invasive, so a noninvasive technique like the one proposed here carries important potential advantages for the physician and patient. A software program that automatically detects the nerve fibers, counts them and measures their shapes is being developed and tested. Tests were carried out with a database of subjects with levels of severity of diabetic neuropathy as determined by EMG testing. Results from this testing, that include a linear regression analysis are shown.

  1. Time Efficiency and Diagnostic Accuracy of New Automated Myocardial Perfusion Analysis Software in 320-Row CT Cardiac Imaging

    PubMed Central

    Rief, Matthias; Stenzel, Fabian; Kranz, Anisha; Schlattmann, Peter

    2013-01-01

    Objective We aimed to evaluate the time efficiency and diagnostic accuracy of automated myocardial computed tomography perfusion (CTP) image analysis software. Materials and Methods 320-row CTP was performed in 30 patients, and analyses were conducted independently by three different blinded readers by the use of two recent software releases (version 4.6 and novel version 4.71GR001, Toshiba, Tokyo, Japan). Analysis times were compared, and automated epi- and endocardial contour detection was subjectively rated in five categories (excellent, good, fair, poor and very poor). As semi-quantitative perfusion parameters, myocardial attenuation and transmural perfusion ratio (TPR) were calculated for each myocardial segment and agreement was tested by using the intraclass correlation coefficient (ICC). Conventional coronary angiography served as reference standard. Results The analysis time was significantly reduced with the novel automated software version as compared with the former release (Reader 1: 43:08 ± 11:39 min vs. 09:47 ± 04:51 min, Reader 2: 42:07 ± 06:44 min vs. 09:42 ± 02:50 min and Reader 3: 21:38 ± 3:44 min vs. 07:34 ± 02:12 min; p < 0.001 for all). Epi- and endocardial contour detection for the novel software was rated to be significantly better (p < 0.001) than with the former software. ICCs demonstrated strong agreement (≥ 0.75) for myocardial attenuation in 93% and for TPR in 82%. Diagnostic accuracy for the two software versions was not significantly different (p = 0.169) as compared with conventional coronary angiography. Conclusion The novel automated CTP analysis software offers enhanced time efficiency with an improvement by a factor of about four, while maintaining diagnostic accuracy. PMID:23323027

  2. Validated novel software to measure the conspicuity index of lesions in DICOM images

    NASA Astrophysics Data System (ADS)

    Szczepura, K. R.; Manning, D. J.

    2016-03-01

    A novel software programme and associated Excel spreadsheet has been developed to provide an objective measure of the expected visual detectability of focal abnormalities within DICOM images. ROIs are drawn around the abnormality, the software then fits the lesion using a least squares method to recognize the edges of the lesion based on the full width half maximum. 180 line profiles are then plotted around the lesion, giving 360 edge profiles.

  3. LISIRD 2: Applying Standards and Open Source Software in Exploring and Serving Scientific Data

    NASA Astrophysics Data System (ADS)

    Wilson, A.; Lindholm, D. M.; Ware Dewolfe, A.; Lindholm, C.; Pankratz, C. K.; Snow, M.; Woods, T. N.

    2009-12-01

    The LASP Interactive Solar IRradiance Datacenter (LISIRD), http://lasp.colorado.edu/lisird, seeks to provide exploration of and access to solar irradiance data, models and other related data. These irradiance datasets, from the SME, UARS, TIMED, and SORCE missions, are primarily a function of time and often also wavelength. Their measurements are typically made on a scale of seconds and derived products are provided at daily cadence. The first version of the LISIRD site was built using non standard, proprietary software. The non standard application structure and tight coupling to a variety of dataset representations made changes arduous and maintenance difficult. Eventually the software vender decided to no longer support a critical software component, further decreasing the viability of the site. In LISIRD 2, through the application of the Java EE standard coupled with open source software to fetch and plot the data, the functionality of the original site is being improved while the code structure is being streamlined and simplified. With a relatively minimal effort, the new site can access and serve a greater variety of datasets in an easier fashion, and produce responsive, interactive plots of datasets overlaid and/or linked in time. And it does so using a significantly smaller code base that is, at the same time, much more flexible and extensible. In particular, LISIRD 2 heavily leverages powerful, flexible functionality provided by the Time Series Data Server (TSDS). The OPeNDAP compliant TSDS supports requests for any data that are function of time. It can support scalar, vector, and spectra data types. Through the use of the Unidata NetCDF-Java library and NcML, the TSDS supports multiple input and output formats and is easily extended to support more. It also supports a variety of filters that can be chained and applied to the data on the server before being delivered. TSDS thinning capabilities make it easy for the clients to request appropriate data

  4. Parallel-Processing Software for Correlating Stereo Images

    NASA Technical Reports Server (NTRS)

    Klimeck, Gerhard; Deen, Robert; Mcauley, Michael; DeJong, Eric

    2007-01-01

    A computer program implements parallel- processing algorithms for cor relating images of terrain acquired by stereoscopic pairs of digital stereo cameras on an exploratory robotic vehicle (e.g., a Mars rove r). Such correlations are used to create three-dimensional computatio nal models of the terrain for navigation. In this program, the scene viewed by the cameras is segmented into subimages. Each subimage is assigned to one of a number of central processing units (CPUs) opera ting simultaneously.

  5. JHelioviewer: Open-Source Software for Discovery and Image Access in the Petabyte Age

    NASA Astrophysics Data System (ADS)

    Mueller, D.; Dimitoglou, G.; Garcia Ortiz, J.; Langenberg, M.; Nuhn, M.; Dau, A.; Pagel, S.; Schmidt, L.; Hughitt, V. K.; Ireland, J.; Fleck, B.

    2011-12-01

    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 accessible only from a few repositories and users 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 ESA/NASA 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. In addition, the easy-to-use graphical user interface enables the general public and educators to access, enjoy and reuse data from space missions without barriers.

  6. Starworld: Preparing Accountants for the Future: A Case-Based Approach to Teach International Financial Reporting Standards Using ERP Software

    ERIC Educational Resources Information Center

    Ragan, Joseph M.; Savino, Christopher J.; Parashac, Paul; Hosler, Jonathan C.

    2010-01-01

    International Financial Reporting Standards now constitute an important part of educating young professional accountants. This paper looks at a case based process to teach International Financial Reporting Standards using integrated Enterprise Resource Planning software. The case contained within the paper can be used within a variety of courses…

  7. New StatPhantom software for assessment of digital image quality

    NASA Astrophysics Data System (ADS)

    Gurvich, Victor A.; Davydenko, George I.

    2002-04-01

    The rapid development of digital imaging and computers networks, using Picture Archiving and Communication Systems (PACS) and DICOM compatible devices increase requirements to the quality control process in medical imaging departments, but provide new opportunities for evaluation of image quality. New StatPhantom software simplifies statistical techniques based on modern detection theory and ROC analysis improving the accuracy and reliability of known methods and allowing to implement statistical analysis with phantoms of any design. In contrast to manual statistical methods, all calculation, analysis of results, and test elements positions changes in the image of phantom are implemented by computer. This paper describes the user interface and functionality of StatPhantom software, its opportunities and advantages in the assessment of various imaging modalities, and the diagnostic preference of an observer. The results obtained by the conventional ROC analysis, manual, and computerized statistical methods are analyzed. Different designs of phantoms are considered.

  8. Novel mass spectrometry imaging software assisting labeled normalization and quantitation of drugs and neuropeptides directly in tissue sections.

    PubMed

    Källback, Patrik; Shariatgorji, Mohammadreza; Nilsson, Anna; Andrén, Per E

    2012-08-30

    MALDI MS imaging has been extensively used to produce qualitative distribution maps of proteins, peptides, lipids, small molecule pharmaceuticals and their metabolites directly in biological tissue sections. There is growing demand to quantify the amount of target compounds in the tissue sections of different organs. We present a novel MS imaging software including protocol for the quantitation of drugs, and for the first time, an endogenous neuropeptide directly in tissue sections. After selecting regions of interest on the tissue section, data is read and processed by the software using several available methods for baseline corrections, subtractions, denoising, smoothing, recalibration and normalization. The concentrations of in vivo administered drugs or endogenous compounds are then determined semi-automatically using either external standard curves, or by using labeled compounds, i.e., isotope labeled analogs as standards. As model systems, we have quantified the distribution of imipramine and tiotropium in the brain and lung of dosed rats. Substance P was quantified in different mouse brain structures, which correlated well with previously reported peptide levels. Our approach facilitates quantitative data processing and labeled standards provide better reproducibility and may be considered as an efficient tool to quantify drugs and endogenous compounds in tissue regions of interest.

  9. Web-based spatial analysis with the ILWIS open source GIS software and satellite images from GEONETCast

    NASA Astrophysics Data System (ADS)

    Lemmens, R.; Maathuis, B.; Mannaerts, C.; Foerster, T.; Schaeffer, B.; Wytzisk, A.

    2009-12-01

    fingertips of users around the globe. This user-friendly and low-cost information dissemination provides global information as a basis for decision-making in a number of critical areas, including public health, energy, agriculture, weather, water, climate, natural disasters and ecosystems. GEONETCast makes available satellite images via Digital Video Broadcast (DVB) technology. An OGC WMS interface and plug-ins which convert GEONETCast data streams allow an ILWIS user to integrate various distributed data sources with data locally stored on his machine. Our paper describes a use case in which ILWIS is used with GEONETCast satellite imagery for decision making processes in Ghana. We also explain how the ILWIS software can be extended with additional functionality by means of building plug-ins and unfold our plans to implement other OGC standards, such as WCS and WPS in the same context. Especially, the latter one can be seen as a major step forward in terms of moving well-proven desktop based processing functionality to the web. This enables the embedding of ILWIS functionality in Spatial Data Infrastructures or even the execution in scalable and on-demand cloud computing environments.

  10. Oxygen octahedra picker: A software tool to extract quantitative information from STEM images.

    PubMed

    Wang, Yi; Salzberger, Ute; Sigle, Wilfried; Eren Suyolcu, Y; van Aken, Peter A

    2016-09-01

    In perovskite oxide based materials and hetero-structures there are often strong correlations between oxygen octahedral distortions and functionality. Thus, atomistic understanding of the octahedral distortion, which requires accurate measurements of atomic column positions, will greatly help to engineer their properties. Here, we report the development of a software tool to extract quantitative information of the lattice and of BO6 octahedral distortions from STEM images. Center-of-mass and 2D Gaussian fitting methods are implemented to locate positions of individual atom columns. The precision of atomic column distance measurements is evaluated on both simulated and experimental images. The application of the software tool is demonstrated using practical examples.

  11. Development of a Standard for Verification and Validation of Software Used to Calculate Nuclear System Thermal Fluids Behavior

    SciTech Connect

    Richard R. Schultz; Edwin A. Harvego; Ryan L. Crane

    2010-05-01

    With the resurgence of nuclear power and increased interest in advanced nuclear reactors as an option to supply abundant energy without the associated greenhouse gas emissions of the more conventional fossil fuel energy sources, there is a need to establish internationally recognized standards for the verification and validation (V&V) of software used to calculate the thermal-hydraulic behavior of advanced reactor designs for both normal operation and hypothetical accident conditions. To address this need, ASME (American Society of Mechanical Engineers) Standards and Certification has established the V&V 30 Committee, under the responsibility of the V&V Standards Committee, to develop a consensus Standard for verification and validation of software used for design and analysis of advanced reactor systems. The initial focus of this committee will be on the V&V of system analysis and computational fluid dynamics (CFD) software for nuclear applications. To limit the scope of the effort, the committee will further limit its focus to software to be used in the licensing of High-Temperature Gas-Cooled Reactors. In this framework, the standard should conform to Nuclear Regulatory Commission (NRC) practices, procedures and methods for licensing of nuclear power plants as embodied in the United States (U.S.) Code of Federal Regulations and other pertinent documents such as Regulatory Guide 1.203, “Transient and Accident Analysis Methods” and NUREG-0800, “NRC Standard Review Plan”. In addition, the standard should be consistent with applicable sections of ASME Standard NQA-1 (“Quality Assurance Requirements for Nuclear Facility Applications (QA)”). This paper describes the general requirements for the V&V Standard, which includes; (a) the definition of the operational and accident domain of a nuclear system that must be considered if the system is to licensed, (b) the corresponding calculational domain of the software that should encompass the nuclear operational

  12. 76 FR 51993 - Draft Guidance for Industry on Standards for Clinical Trial Imaging Endpoints; Availability

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-19

    ... standardization of imaging procedures when an important imaging endpoint is used in a clinical trial of a... outlines the major considerations for standardization of image acquisition, image interpretation methods... of image acquisition and interpretation standardization, a medical practice standard and a...

  13. Standard portrait image and image quality assessment: II. Triplet comparison

    NASA Astrophysics Data System (ADS)

    Miyazaki, Keiichi; Kanafusa, Kunihiko; Umemoto, Hiroshi; Takemura, Kazuhiko; Urabe, Hitoshi; Hirai, Keisuke; Ishikawa, Kazuo; Hatada, Toyohiko

    2000-12-01

    We have already proposed a standard portrait for the assessment of preferable skin tone. The present report describes a psycho physical experimental method, i.e., simultaneous triplet comparison that has been developed for the assessment of skin tone by using the portrait and that is characterized not only by a scalability, stability and reproducibility of the resulting scale values, but also by a reduce stress on observers. We have confirmed that the present simultaneous triplet comparison has a degree of scalability and stability almost equivalent to that of paired comparison that is most widely used for similar purposes, and that the stress on observers is about half as much as that of paired comparison.

  14. Standard Health Level Seven for Odontological Digital Imaging

    PubMed Central

    Abril-Gonzalez, Mauricio; Portilla, Fernando A.

    2017-01-01

    Abstract Background: A guide for the implementation of dental digital imaging reports was developed and validated through the International Standard of Health Informatics–Health Level Seven (HL7), achieving interoperability with an electronic system that keeps dental records. Introduction: Digital imaging benefits patients, who can view previous close-ups of dental examinations; providers, because of greater efficiency in managing information; and insurers, because of improved accessibility, patient monitoring, and more efficient cost management. Finally, imaging is beneficial for the dentist who can be more agile in the diagnosis and treatment of patients using this tool. Materials and Methods: The guide was developed under the parameters of an HL7 standard. It was necessary to create a group of dentists and three experts in information and communication technologies from different institutions. Discussion: Diagnostic images scanned with conventional radiology or from a radiovisiograph can be converted to Digital Imaging and Communications in Medicine (DICOM) format, while also retaining patient information. The guide shows how the information of the health record of the patient and the information of the dental image could be standardized in a Clinical Dental Record document using international informatics standard like HL7-V3-CDA document (dental document Level 2). Since it is an informatics standardized document, it could be sent, stored, or displayed using different devices—personal computers or mobile devices—independent of the platform used. Conclusions: Interoperability using dental images and dental record systems reduces adverse events, increases security for the patient, and makes more efficient use of resources. This article makes a contribution to the field of telemedicine in dental informatics. In addition to that, the results could be a reference for projects of electronic medical records when the dental documents are part of them. PMID

  15. A software framework for diagnostic medical image perception with feedback, and a novel perception visualization technique

    NASA Astrophysics Data System (ADS)

    Phillips, Peter W.; Manning, David J.; Donovan, Tim; Crawford, Trevor; Higham, Stephen

    2005-04-01

    This paper describes a software framework and analysis tool to support the collection and analysis of eye movement and perceptual feedback data for a variety of diagnostic imaging modalities. The framework allows the rapid creation of experiment software that can display a collection of medical images of a particular modality, capture eye trace data, and record marks added to an image by the observer, together with their final decision. There are also a number of visualisation techniques for the display of eye trace information. The analysis tool supports the comparison of individual eye traces for a particular observer or traces from multiple observers for a particular image. Saccade and fixation data can be visualised, with user control of fixation identification functions and properties. Observer markings are displayed, and predefined regions of interest are supported. The software also supports some interactive and multi-image modalities. The analysis tool includes a novel visualisation of scan paths across multi-image modalities. Using an exploded 3D view of a stack of MRI scan sections, an observer's scan path can be shown traversing between images, in addition to inspecting them.

  16. Plume Ascent Tracker: Interactive Matlab software for analysis of ascending plumes in image data

    NASA Astrophysics Data System (ADS)

    Valade, S. A.; Harris, A. J. L.; Cerminara, M.

    2014-05-01

    This paper presents Matlab-based software designed to track and analyze an ascending plume as it rises above its source, in image data. It reads data recorded in various formats (video files, image files, or web-camera image streams), and at various wavelengths (infrared, visible, or ultra-violet). Using a set of filters which can be set interactively, the plume is first isolated from its background. A user-friendly interface then allows tracking of plume ascent and various parameters that characterize plume evolution during emission and ascent. These include records of plume height, velocity, acceleration, shape, volume, ash (fine-particle) loading, spreading rate, entrainment coefficient and inclination angle, as well as axial and radial profiles for radius and temperature (if data are radiometric). Image transformations (dilatation, rotation, resampling) can be performed to create new images with a vent-centered metric coordinate system. Applications may interest both plume observers (monitoring agencies) and modelers. For the first group, the software is capable of providing quantitative assessments of plume characteristics from image data, for post-event analysis or in near real-time analysis. For the second group, extracted data can serve as benchmarks for plume ascent models, and as inputs for cloud dispersal models. We here describe the software's tracking methodology and main graphical interfaces, using thermal infrared image data of an ascending volcanic ash plume at Santiaguito volcano.

  17. Towards a multi-site international public dataset for the validation of retinal image analysis software.

    PubMed

    Trucco, Emanuele; Ruggeri, Alfredo

    2013-01-01

    This paper discusses concisely the main issues and challenges posed by the validation of retinal image analysis algorithms. It is designed to set the discussion for the IEEE EBMC 2013 invited session "From laboratory to clinic: the validation of retinal image processing tools ". The session carries forward an international initiative started at EMBC 2011, Boston, which resulted in the first large-consensus paper (14 international sites) on the validation of retinal image processing software, appearing in IOVS. This paper is meant as a focus for the session discussion, but the ubiquity and importance of validation makes its contents, arguably, of interest for the wider medical image processing community.

  18. Despeckle filtering software toolbox for ultrasound imaging of the common carotid artery.

    PubMed

    Loizou, Christos P; Theofanous, Charoula; Pantziaris, Marios; Kasparis, Takis

    2014-04-01

    Ultrasound imaging of the common carotid artery (CCA) is a non-invasive tool used in medicine to assess the severity of atherosclerosis and monitor its progression through time. It is also used in border detection and texture characterization of the atherosclerotic carotid plaque in the CCA, the identification and measurement of the intima-media thickness (IMT) and the lumen diameter that all are very important in the assessment of cardiovascular disease (CVD). Visual perception, however, is hindered by speckle, a multiplicative noise, that degrades the quality of ultrasound B-mode imaging. Noise reduction is therefore essential for improving the visual observation quality or as a pre-processing step for further automated analysis, such as image segmentation of the IMT and the atherosclerotic carotid plaque in ultrasound images. In order to facilitate this preprocessing step, we have developed in MATLAB(®) a unified toolbox that integrates image despeckle filtering (IDF), texture analysis and image quality evaluation techniques to automate the pre-processing and complement the disease evaluation in ultrasound CCA images. The proposed software, is based on a graphical user interface (GUI) and incorporates image normalization, 10 different despeckle filtering techniques (DsFlsmv, DsFwiener, DsFlsminsc, DsFkuwahara, DsFgf, DsFmedian, DsFhmedian, DsFad, DsFnldif, DsFsrad), image intensity normalization, 65 texture features, 15 quantitative image quality metrics and objective image quality evaluation. The software is publicly available in an executable form, which can be downloaded from http://www.cs.ucy.ac.cy/medinfo/. It was validated on 100 ultrasound images of the CCA, by comparing its results with quantitative visual analysis performed by a medical expert. It was observed that the despeckle filters DsFlsmv, and DsFhmedian improved image quality perception (based on the expert's assessment and the image texture and quality metrics). It is anticipated that the

  19. New image processing software for analyzing object size-frequency distributions, geometry, orientation, and spatial distribution

    NASA Astrophysics Data System (ADS)

    Beggan, Ciarán; Hamilton, Christopher W.

    2010-04-01

    Geological Image Analysis Software (GIAS) combines basic tools for calculating object area, abundance, radius, perimeter, eccentricity, orientation, and centroid location, with the first automated method for characterizing the aerial distribution of objects using sample-size-dependent nearest neighbor (NN) statistics. The NN analyses include tests for (1) Poisson, (2) Normalized Poisson, (3) Scavenged k=1, and (4) Scavenged k=2 NN distributions. GIAS is implemented in MATLAB with a Graphical User Interface (GUI) that is available as pre-parsed pseudocode for use with MATLAB, or as a stand-alone application that runs on Windows and Unix systems. GIAS can process raster data (e.g., satellite imagery, photomicrographs, etc.) and tables of object coordinates to characterize the size, geometry, orientation, and spatial organization of a wide range of geological features. This information expedites quantitative measurements of 2D object properties, provides criteria for validating the use of stereology to transform 2D object sections into 3D models, and establishes a standardized NN methodology that can be used to compare the results of different geospatial studies and identify objects using non-morphological parameters.

  20. Development of HydroImage, A User Friendly Hydrogeophysical Characterization Software

    SciTech Connect

    Mok, Chin Man; Hubbard, Susan; Chen, Jinsong; Suribhatla, Raghu; Kaback, Dawn Samara

    2014-01-29

    HydroImage, user friendly software that utilizes high-resolution geophysical data for estimating hydrogeological parameters in subsurface strate, was developed under this grant. HydroImage runs on a personal computer platform to promote broad use by hydrogeologists to further understanding of subsurface processes that govern contaminant fate, transport, and remediation. The unique software provides estimates of hydrogeological properties over continuous volumes of the subsurface, whereas previous approaches only allow estimation of point locations. thus, this unique tool can be used to significantly enhance site conceptual models and improve design and operation of remediation systems. The HydroImage technical approach uses statistical models to integrate geophysical data with borehole geological data and hydrological measurements to produce hydrogeological parameter estimates as 2-D or 3-D images.

  1. Digital processing of side-scan sonar data with the Woods Hole image processing system software

    USGS Publications Warehouse

    Paskevich, Valerie F.

    1992-01-01

    Since 1985, the Branch of Atlantic Marine Geology has been involved in collecting, processing and digitally mosaicking high and low-resolution side-scan sonar data. Recent development of a UNIX-based image-processing software system includes a series of task specific programs for processing side-scan sonar data. This report describes the steps required to process the collected data and to produce an image that has equal along- and across-track resol

  2. Digital image measurement of specimen deformation based on CCD cameras and Image J software: an application to human pelvic biomechanics

    NASA Astrophysics Data System (ADS)

    Jia, Yongwei; Cheng, Liming; Yu, Guangrong; Lou, Yongjian; Yu, Yan; Chen, Bo; Ding, Zuquan

    2008-03-01

    A method of digital image measurement of specimen deformation based on CCD cameras and Image J software was developed. This method was used to measure the biomechanics behavior of human pelvis. Six cadaveric specimens from the third lumbar vertebra to the proximal 1/3 part of femur were tested. The specimens without any structural abnormalities were dissected of all soft tissue, sparing the hip joint capsules and the ligaments of the pelvic ring and floor. Markers with black dot on white background were affixed to the key regions of the pelvis. Axial loading from the proximal lumbar was applied by MTS in the gradient of 0N to 500N, which simulated the double feet standing stance. The anterior and lateral images of the specimen were obtained through two CCD cameras. Based on Image J software, digital image processing software, which can be freely downloaded from the National Institutes of Health, digital 8-bit images were processed. The procedure includes the recognition of digital marker, image invert, sub-pixel reconstruction, image segmentation, center of mass algorithm based on weighted average of pixel gray values. Vertical displacements of S1 (the first sacral vertebrae) in front view and micro-angular rotation of sacroiliac joint in lateral view were calculated according to the marker movement. The results of digital image measurement showed as following: marker image correlation before and after deformation was excellent. The average correlation coefficient was about 0.983. According to the 768 × 576 pixels image (pixel size 0.68mm × 0.68mm), the precision of the displacement detected in our experiment was about 0.018 pixels and the comparatively error could achieve 1.11\\perthou. The average vertical displacement of S1 of the pelvis was 0.8356+/-0.2830mm under vertical load of 500 Newtons and the average micro-angular rotation of sacroiliac joint in lateral view was 0.584+/-0.221°. The load-displacement curves obtained from our optical measure system

  3. Enhancing Image Characteristics of Retinal Images of Aggressive Posterior Retinopathy of Prematurity Using a Novel Software, (RetiView)

    PubMed Central

    Jayadev, Chaitra; Vinekar, Anand; Mohanachandra, Poornima; Desai, Samit; Suveer, Amit; Mangalesh, Shwetha; Bauer, Noel; Shetty, Bhujang

    2015-01-01

    Purpose. To report pilot data from a novel image analysis software “RetiView,” to highlight clinically relevant information in RetCam images of infants with aggressive posterior retinopathy of prematurity (APROP). Methods. Twenty-three imaging sessions of consecutive infants of Asian Indian origin with clinically diagnosed APROP underwent three protocols (Grey Enhanced (GE), Color Enhanced (CE), and “Vesselness Measure” (VNM)) of the software. The postprocessed images were compared to baseline data from the archived unprocessed images and clinical exam by the retinopathy of prematurity (ROP) specialist for anterior extent of the vessels, capillary nonperfusion zones (CNP), loops, hemorrhages, and flat neovascularization. Results. There was better visualization of tortuous loops in the GE protocol (56.5%); “bald” zones within the CNP zones (26.1%), hemorrhages (13%), and edge of the disease (34.8%) in the CE images; neovascularization on both GE and CE protocols (13% each); clinically relevant information in cases with poor pupillary dilatation (8.7%); anterior extent of vessels on the VNM protocol (13%) effecting a “reclassification” from zone 1 to zone 2 posterior. Conclusions. RetiView is a noninvasive and inexpensive method of customized image enhancement to detect clinically difficult characteristics in a subset of APROP images with a potential to influence treatment planning. PMID:26240830

  4. Enhancing Image Characteristics of Retinal Images of Aggressive Posterior Retinopathy of Prematurity Using a Novel Software, (RetiView).

    PubMed

    Jayadev, Chaitra; Vinekar, Anand; Mohanachandra, Poornima; Desai, Samit; Suveer, Amit; Mangalesh, Shwetha; Bauer, Noel; Shetty, Bhujang

    2015-01-01

    Purpose. To report pilot data from a novel image analysis software "RetiView," to highlight clinically relevant information in RetCam images of infants with aggressive posterior retinopathy of prematurity (APROP). Methods. Twenty-three imaging sessions of consecutive infants of Asian Indian origin with clinically diagnosed APROP underwent three protocols (Grey Enhanced (GE), Color Enhanced (CE), and "Vesselness Measure" (VNM)) of the software. The postprocessed images were compared to baseline data from the archived unprocessed images and clinical exam by the retinopathy of prematurity (ROP) specialist for anterior extent of the vessels, capillary nonperfusion zones (CNP), loops, hemorrhages, and flat neovascularization. Results. There was better visualization of tortuous loops in the GE protocol (56.5%); "bald" zones within the CNP zones (26.1%), hemorrhages (13%), and edge of the disease (34.8%) in the CE images; neovascularization on both GE and CE protocols (13% each); clinically relevant information in cases with poor pupillary dilatation (8.7%); anterior extent of vessels on the VNM protocol (13%) effecting a "reclassification" from zone 1 to zone 2 posterior. Conclusions. RetiView is a noninvasive and inexpensive method of customized image enhancement to detect clinically difficult characteristics in a subset of APROP images with a potential to influence treatment planning.

  5. Creation of three-dimensional craniofacial standards from CBCT images

    NASA Astrophysics Data System (ADS)

    Subramanyan, Krishna; Palomo, Martin; Hans, Mark

    2006-03-01

    Low-dose three-dimensional Cone Beam Computed Tomography (CBCT) is becoming increasingly popular in the clinical practice of dental medicine. Two-dimensional Bolton Standards of dentofacial development are routinely used to identify deviations from normal craniofacial anatomy. With the advent of CBCT three dimensional imaging, we propose a set of methods to extend these 2D Bolton Standards to anatomically correct surface based 3D standards to allow analysis of morphometric changes seen in craniofacial complex. To create 3D surface standards, we have implemented series of steps. 1) Converting bi-plane 2D tracings into set of splines 2) Converting the 2D splines curves from bi-plane projection into 3D space curves 3) Creating labeled template of facial and skeletal shapes and 4) Creating 3D average surface Bolton standards. We have used datasets from patients scanned with Hitachi MercuRay CBCT scanner providing high resolution and isotropic CT volume images, digitized Bolton Standards from age 3 to 18 years of lateral and frontal male, female and average tracings and converted them into facial and skeletal 3D space curves. This new 3D standard will help in assessing shape variations due to aging in young population and provide reference to correct facial anomalies in dental medicine.

  6. 3D thermography imaging standardization technique for inflammation diagnosis

    NASA Astrophysics Data System (ADS)

    Ju, Xiangyang; Nebel, Jean-Christophe; Siebert, J. Paul

    2005-01-01

    We develop a 3D thermography imaging standardization technique to allow quantitative data analysis. Medical Digital Infrared Thermal Imaging is very sensitive and reliable mean of graphically mapping and display skin surface temperature. It allows doctors to visualise in colour and quantify temperature changes in skin surface. The spectrum of colours indicates both hot and cold responses which may co-exist if the pain associate with an inflammatory focus excites an increase in sympathetic activity. However, due to thermograph provides only qualitative diagnosis information, it has not gained acceptance in the medical and veterinary communities as a necessary or effective tool in inflammation and tumor detection. Here, our technique is based on the combination of visual 3D imaging technique and thermal imaging technique, which maps the 2D thermography images on to 3D anatomical model. Then we rectify the 3D thermogram into a view independent thermogram and conform it a standard shape template. The combination of these imaging facilities allows the generation of combined 3D and thermal data from which thermal signatures can be quantified.

  7. Capturing a failure of an ASIC in-situ, using infrared radiometry and image processing software

    NASA Technical Reports Server (NTRS)

    Ruiz, Ronald P.

    2003-01-01

    Failures in electronic devices can sometimes be tricky to locate-especially if they are buried inside radiation-shielded containers designed to work in outer space. Such was the case with a malfunctioning ASIC (Application Specific Integrated Circuit) that was drawing excessive power at a specific temperature during temperature cycle testing. To analyze the failure, infrared radiometry (thermography) was used in combination with image processing software to locate precisely where the power was being dissipated at the moment the failure took place. The IR imaging software was used to make the image of the target and background, appear as unity. As testing proceeded and the failure mode was reached, temperature changes revealed the precise location of the fault. The results gave the design engineers the information they needed to fix the problem. This paper describes the techniques and equipment used to accomplish this failure analysis.

  8. IHE cross-enterprise document sharing for imaging: interoperability testing software

    PubMed Central

    2010-01-01

    Background With the deployments of Electronic Health Records (EHR), interoperability testing in healthcare is becoming crucial. EHR enables access to prior diagnostic information in order to assist in health decisions. It is a virtual system that results from the cooperation of several heterogeneous distributed systems. Interoperability between peers is therefore essential. Achieving interoperability requires various types of testing. Implementations need to be tested using software that simulates communication partners, and that provides test data and test plans. Results In this paper we describe a software that is used to test systems that are involved in sharing medical images within the EHR. Our software is used as part of the Integrating the Healthcare Enterprise (IHE) testing process to test the Cross Enterprise Document Sharing for imaging (XDS-I) integration profile. We describe its architecture and functionalities; we also expose the challenges encountered and discuss the elected design solutions. Conclusions EHR is being deployed in several countries. The EHR infrastructure will be continuously evolving to embrace advances in the information technology domain. Our software is built on a web framework to allow for an easy evolution with web technology. The testing software is publicly available; it can be used by system implementers to test their implementations. It can also be used by site integrators to verify and test the interoperability of systems, or by developers to understand specifications ambiguities, or to resolve implementations difficulties. PMID:20858241

  9. Software for MR image overlay guided needle insertions: the clinical translation process

    NASA Astrophysics Data System (ADS)

    Ungi, Tamas; U-Thainual, Paweena; Fritz, Jan; Iordachita, Iulian I.; Flammang, Aaron J.; Carrino, John A.; Fichtinger, Gabor

    2013-03-01

    PURPOSE: Needle guidance software using augmented reality image overlay was translated from the experimental phase to support preclinical and clinical studies. Major functional and structural changes were needed to meet clinical requirements. We present the process applied to fulfill these requirements, and selected features that may be applied in the translational phase of other image-guided surgical navigation systems. METHODS: We used an agile software development process for rapid adaptation to unforeseen clinical requests. The process is based on iterations of operating room test sessions, feedback discussions, and software development sprints. The open-source application framework of 3D Slicer and the NA-MIC kit provided sufficient flexibility and stable software foundations for this work. RESULTS: All requirements were addressed in a process with 19 operating room test iterations. Most features developed in this phase were related to workflow simplification and operator feedback. CONCLUSION: Efficient and affordable modifications were facilitated by an open source application framework and frequent clinical feedback sessions. Results of cadaver experiments show that software requirements were successfully solved after a limited number of operating room tests.

  10. A software to digital image processing to be used in the voxel phantom development.

    PubMed

    Vieira, J W; Lima, F R A

    2009-11-15

    Anthropomorphic models used in computational dosimetry, also denominated phantoms, are based on digital images recorded from scanning of real people by Computed Tomography (CT) or Magnetic Resonance Imaging (MRI). The voxel phantom construction requests computational processing for transformations of image formats, to compact two-dimensional (2-D) images forming of three-dimensional (3-D) matrices, image sampling and quantization, image enhancement, restoration and segmentation, among others. Hardly the researcher of computational dosimetry will find all these available abilities in single software, and almost always this difficulty presents as a result the decrease of the rhythm of his researches or the use, sometimes inadequate, of alternative tools. The need to integrate the several tasks mentioned above to obtain an image that can be used in an exposure computational model motivated the development of the Digital Image Processing (DIP) software, mainly to solve particular problems in Dissertations and Thesis developed by members of the Grupo de Pesquisa em Dosimetria Numérica (GDN/CNPq). Because of this particular objective, the software uses the Portuguese idiom in their implementations and interfaces. This paper presents the second version of the DIP, whose main changes are the more formal organization on menus and menu items, and menu for digital image segmentation. Currently, the DIP contains the menus Fundamentos, Visualizações, Domínio Espacial, Domínio de Frequências, Segmentações and Estudos. Each menu contains items and sub-items with functionalities that, usually, request an image as input and produce an image or an attribute in the output. The DIP reads edits and writes binary files containing the 3-D matrix corresponding to a stack of axial images from a given geometry that can be a human body or other volume of interest. It also can read any type of computational image and to make conversions. When the task involves only an output image

  11. Image contrast enhancement based on a local standard deviation model

    SciTech Connect

    Chang, Dah-Chung; Wu, Wen-Rong

    1996-12-31

    The adaptive contrast enhancement (ACE) algorithm is a widely used image enhancement method, which needs a contrast gain to adjust high frequency components of an image. In the literature, the gain is usually inversely proportional to the local standard deviation (LSD) or is a constant. But these cause two problems in practical applications, i.e., noise overenhancement and ringing artifact. In this paper a new gain is developed based on Hunt`s Gaussian image model to prevent the two defects. The new gain is a nonlinear function of LSD and has the desired characteristic emphasizing the LSD regions in which details are concentrated. We have applied the new ACE algorithm to chest x-ray images and the simulations show the effectiveness of the proposed algorithm.

  12. A New Effort for Atmospherical Forecast: Meteorological Image Processing Software (MIPS) for Astronomical Observations

    NASA Astrophysics Data System (ADS)

    Shameoni Niaei, M.; Kilic, Y.; Yildiran, B. E.; Yüzlükoglu, F.; Yesilyaprak, C.

    2016-12-01

    We have described a new software (MIPS) about the analysis and image processing of the meteorological satellite (Meteosat) data for an astronomical observatory. This software will be able to help to make some atmospherical forecast (cloud, humidity, rain) using meteosat data for robotic telescopes. MIPS uses a python library for Eumetsat data that aims to be completely open-source and licenced under GNU/General Public Licence (GPL). MIPS is a platform independent and uses h5py, numpy, and PIL with the general-purpose and high-level programming language Python and the QT framework.

  13. Stain Specific Standardization of Whole-Slide Histopathological Images.

    PubMed

    Bejnordi, Babak Ehteshami; Litjens, Geert; Timofeeva, Nadya; Otte-Höller, Irene; Homeyer, André; Karssemeijer, Nico; van der Laak, Jeroen A W M

    2016-02-01

    Variations in the color and intensity of hematoxylin and eosin (H&E) stained histological slides can potentially hamper the effectiveness of quantitative image analysis. This paper presents a fully automated algorithm for standardization of whole-slide histopathological images to reduce the effect of these variations. The proposed algorithm, called whole-slide image color standardizer (WSICS), utilizes color and spatial information to classify the image pixels into different stain components. The chromatic and density distributions for each of the stain components in the hue-saturation-density color model are aligned to match the corresponding distributions from a template whole-slide image (WSI). The performance of the WSICS algorithm was evaluated on two datasets. The first originated from 125 H&E stained WSIs of lymph nodes, sampled from 3 patients, and stained in 5 different laboratories on different days of the week. The second comprised 30 H&E stained WSIs of rat liver sections. The result of qualitative and quantitative evaluations using the first dataset demonstrate that the WSICS algorithm outperforms competing methods in terms of achieving color constancy. The WSICS algorithm consistently yields the smallest standard deviation and coefficient of variation of the normalized median intensity measure. Using the second dataset, we evaluated the impact of our algorithm on the performance of an already published necrosis quantification system. The performance of this system was significantly improved by utilizing the WSICS algorithm. The results of the empirical evaluations collectively demonstrate the potential contribution of the proposed standardization algorithm to improved diagnostic accuracy and consistency in computer-aided diagnosis for histopathology data.

  14. Grid-less imaging with antiscatter correction software in 2D mammography: the effects on image quality and MGD under a partial virtual clinical validation study

    NASA Astrophysics Data System (ADS)

    Van Peteghem, Nelis; Bemelmans, Frédéric; Bramaje Adversalo, Xenia; Salvagnini, Elena; Marshall, Nicholas; Bosmans, Hilde; Van Ongeval, Chantal

    2016-03-01

    This work investigated the effect of the grid-less acquisition mode with scatter correction software developed by Siemens Healthcare (PRIME mode) on image quality and mean glandular dose (MGD) in a comparative study against a standard mammography system with grid. Image quality was technically quantified with contrast-detail (c-d) analysis and by calculating detectability indices (d') using a non-prewhitening with eye filter model observer (NPWE). MGD was estimated technically using slabs of PMMA and clinically on a set of 11439 patient images. The c-d analysis gave similar results for all mammographic systems examined, although the d' values were slightly lower for the system with PRIME mode when compared to the same system in standard mode (-2.8% to -5.7%, depending on the PMMA thickness). The MGD values corresponding to the PMMA measurements with automatic exposure control indicated a dose reduction from 11.0% to 20.8% for the system with PRIME mode compared to the same system without PRIME mode. The largest dose reductions corresponded to the thinnest PMMA thicknesses. The results from the clinical dosimetry study showed an overall population-averaged dose reduction of 11.6% (up to 27.7% for thinner breasts) for PRIME mode compared to standard mode for breast thicknesses from 20 to 69 mm. These technical image quality measures were then supported using a clinically oriented study whereby simulated clusters of microcalcifications and masses were inserted into patient images and read by radiologists in an AFROC study to quantify their detectability. In line with the technical investigation, no significant difference was found between the two imaging modes (p-value 0.95).

  15. 25 CFR 547.8 - What are the minimum technical software standards applicable to Class II gaming systems?

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... OF CLASS II GAMES § 547.8 What are the minimum technical software standards applicable to Class II... of Class II games. (a) Player interface displays. (1) If not otherwise provided to the player, the player interface shall display the following: (i) The purchase or wager amount; (ii) Game results;...

  16. 25 CFR 547.8 - What are the minimum technical software standards applicable to Class II gaming systems?

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... OF CLASS II GAMES § 547.8 What are the minimum technical software standards applicable to Class II... of Class II games. (a) Player interface displays. (1) If not otherwise provided to the player, the player interface shall display the following: (i) The purchase or wager amount; (ii) Game results;...

  17. 25 CFR 547.8 - What are the minimum technical software standards applicable to Class II gaming systems?

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... OF CLASS II GAMES § 547.8 What are the minimum technical software standards applicable to Class II... of Class II games. (a) Player interface displays. (1) If not otherwise provided to the player, the player interface shall display the following: (i) The purchase or wager amount; (ii) Game results;...

  18. Comparison of human observers and CDCOM software reading for CDMAM images

    NASA Astrophysics Data System (ADS)

    Lanconelli, Nico; Rivetti, Stefano; Golinelli, Paola; Serafini, Marco; Bertolini, Marco; Borasi, Giovanni

    2007-03-01

    Contrast-detail analysis is one the most common way for the assessment of the performance of an imaging system. Usually, the reading of phantoms, such as CDMAM, is obtained by human observers. The main drawbacks of this practice is the presence of inter-observer variability and the great amount of time needed. However, software programs are available, for reading CDMAM images in an automatic way. In this paper we present a comparison of human and software reading of CDMAM images coming from three different FFDM clinical units. Images were acquired at different exposures in the same conditions for the three systems. Once software has completed the reading, the interpretation of the results is achieved on the same way used for the human case. CDCOM results are consistent with human analysis, if we consider figures such as COR and IQF. On the other hand, we find out some discrepancies along the CD curves obtained by human observers, with respect to those estimated by automated CDCOM analysis.

  19. MedXViewer: an extensible web-enabled software package for medical imaging

    NASA Astrophysics Data System (ADS)

    Looney, P. T.; Young, K. C.; Mackenzie, Alistair; Halling-Brown, Mark D.

    2014-03-01

    MedXViewer (Medical eXtensible Viewer) is an application designed to allow workstation-independent, PACS-less viewing and interaction with anonymised medical images (e.g. observer studies). The application was initially implemented for use in digital mammography and tomosynthesis but the flexible software design allows it to be easily extended to other imaging modalities. Regions of interest can be identified by a user and any associated information about a mark, an image or a study can be added. The questions and settings can be easily configured depending on the need of the research allowing both ROC and FROC studies to be performed. The extensible nature of the design allows for other functionality and hanging protocols to be available for each study. Panning, windowing, zooming and moving through slices are all available while modality-specific features can be easily enabled e.g. quadrant zooming in mammographic studies. MedXViewer can integrate with a web-based image database allowing results and images to be stored centrally. The software and images can be downloaded remotely from this centralised data-store. Alternatively, the software can run without a network connection where the images and results can be encrypted and stored locally on a machine or external drive. Due to the advanced workstation-style functionality, the simple deployment on heterogeneous systems over the internet without a requirement for administrative access and the ability to utilise a centralised database, MedXViewer has been used for running remote paper-less observer studies and is capable of providing a training infrastructure and co-ordinating remote collaborative viewing sessions (e.g. cancer reviews, interesting cases).

  20. Technical Note: DIRART- A software suite for deformable image registration and adaptive radiotherapy research

    SciTech Connect

    Yang Deshan; Brame, Scott; El Naqa, Issam; Aditya, Apte; Wu Yu; Murty Goddu, S.; Mutic, Sasa; Deasy, Joseph O.; Low, Daniel A.

    2011-01-15

    Purpose: Recent years have witnessed tremendous progress in image guide radiotherapy technology and a growing interest in the possibilities for adapting treatment planning and delivery over the course of treatment. One obstacle faced by the research community has been the lack of a comprehensive open-source software toolkit dedicated for adaptive radiotherapy (ART). To address this need, the authors have developed a software suite called the Deformable Image Registration and Adaptive Radiotherapy Toolkit (DIRART). Methods: DIRART is an open-source toolkit developed in MATLAB. It is designed in an object-oriented style with focus on user-friendliness, features, and flexibility. It contains four classes of DIR algorithms, including the newer inverse consistency algorithms to provide consistent displacement vector field in both directions. It also contains common ART functions, an integrated graphical user interface, a variety of visualization and image-processing features, dose metric analysis functions, and interface routines. These interface routines make DIRART a powerful complement to the Computational Environment for Radiotherapy Research (CERR) and popular image-processing toolkits such as ITK. Results: DIRART provides a set of image processing/registration algorithms and postprocessing functions to facilitate the development and testing of DIR algorithms. It also offers a good amount of options for DIR results visualization, evaluation, and validation. Conclusions: By exchanging data with treatment planning systems via DICOM-RT files and CERR, and by bringing image registration algorithms closer to radiotherapy applications, DIRART is potentially a convenient and flexible platform that may facilitate ART and DIR research.

  1. Apero, AN Open Source Bundle Adjusment Software for Automatic Calibration and Orientation of Set of Images

    NASA Astrophysics Data System (ADS)

    Pierrot Deseilligny, M.; Clery, I.

    2011-09-01

    IGN has developed a set of photogrammetric tools, APERO and MICMAC, for computing 3D models from set of images. This software, developed initially for its internal needs are now delivered as open source code. This paper focuses on the presentation of APERO the orientation software. Compared to some other free software initiatives, it is probably more complex but also more complete, its targeted user is rather professionals (architects, archaeologist, geomophologist) than people. APERO uses both computer vision approach for estimation of initial solution and photogrammetry for a rigorous compensation of the total error; it has a large library of parametric model of distortion allowing a precise modelization of all the kind of pinhole camera we know, including several model of fish-eye; there is also several tools for geo-referencing the result. The results are illustrated on various application, including the data-set of 3D-Arch workshop.

  2. The Personal Computer as an Analytical Workstation: Interfacing Standard Software Products.

    ERIC Educational Resources Information Center

    Cawley, Jeffery L.

    1984-01-01

    Reviews the functions that should be included in an analytical workstation. Also discusses the common data file structures and the techniques of data interchange between software modules and presents a brief overview of commercial products and their interfacing characteristics. These software include word processors, spreadsheets, database…

  3. The Performance Evaluation of Multi-Image 3d Reconstruction Software with Different Sensors

    NASA Astrophysics Data System (ADS)

    Mousavi, V.; Khosravi, M.; Ahmadi, M.; Noori, N.; Naveh, A. Hosseini; Varshosaz, M.

    2015-12-01

    Today, multi-image 3D reconstruction is an active research field and generating three dimensional model of the objects is one the most discussed issues in Photogrammetry and Computer Vision that can be accomplished using range-based or image-based methods. Very accurate and dense point clouds generated by range-based methods such as structured light systems and laser scanners has introduced them as reliable tools in the industry. Image-based 3D digitization methodologies offer the option of reconstructing an object by a set of unordered images that depict it from different viewpoints. As their hardware requirements are narrowed down to a digital camera and a computer system, they compose an attractive 3D digitization approach, consequently, although range-based methods are generally very accurate, image-based methods are low-cost and can be easily used by non-professional users. One of the factors affecting the accuracy of the obtained model in image-based methods is the software and algorithm used to generate three dimensional model. These algorithms are provided in the form of commercial software, open source and web-based services. Another important factor in the accuracy of the obtained model is the type of sensor used. Due to availability of mobile sensors to the public, popularity of professional sensors and the advent of stereo sensors, a comparison of these three sensors plays an effective role in evaluating and finding the optimized method to generate three-dimensional models. Lots of research has been accomplished to identify a suitable software and algorithm to achieve an accurate and complete model, however little attention is paid to the type of sensors used and its effects on the quality of the final model. The purpose of this paper is deliberation and the introduction of an appropriate combination of a sensor and software to provide a complete model with the highest accuracy. To do this, different software, used in previous studies, were compared and

  4. The Spectral Image Processing System (SIPS): Software for integrated analysis of AVIRIS data

    NASA Technical Reports Server (NTRS)

    Kruse, F. A.; Lefkoff, A. B.; Boardman, J. W.; Heidebrecht, K. B.; Shapiro, A. T.; Barloon, P. J.; Goetz, A. F. H.

    1992-01-01

    The Spectral Image Processing System (SIPS) is a software package developed by the Center for the Study of Earth from Space (CSES) at the University of Colorado, Boulder, in response to a perceived need to provide integrated tools for analysis of imaging spectrometer data both spectrally and spatially. SIPS was specifically designed to deal with data from the Airborne Visible/Infrared Imaging Spectrometer (AVIRIS) and the High Resolution Imaging Spectrometer (HIRIS), but was tested with other datasets including the Geophysical and Environmental Research Imaging Spectrometer (GERIS), GEOSCAN images, and Landsat TM. SIPS was developed using the 'Interactive Data Language' (IDL). It takes advantage of high speed disk access and fast processors running under the UNIX operating system to provide rapid analysis of entire imaging spectrometer datasets. SIPS allows analysis of single or multiple imaging spectrometer data segments at full spatial and spectral resolution. It also allows visualization and interactive analysis of image cubes derived from quantitative analysis procedures such as absorption band characterization and spectral unmixing. SIPS consists of three modules: SIPS Utilities, SIPS_View, and SIPS Analysis. SIPS version 1.1 is described below.

  5. Simulation of tomosynthesis images based on an anthropomorphic software breast tissue phantom

    NASA Astrophysics Data System (ADS)

    Ruiter, Nicole V.; Zhang, Cuiping; Bakic, Predrag R.; Carton, Ann-Katherine; Kuo, Johnny; Maidment, Andrew D. A.

    2008-03-01

    The aim of this work is to provide a simulation framework for generation of synthetic tomosynthesis images to be used for evaluation of future developments in the field of tomosynthesis. An anthropomorphic software tissue phantom was previously used in a number of applications for evaluation of acquisition modalities and image post-processing algorithms for mammograms. This software phantom has been extended for similar use with tomosynthesis. The new features of the simulation framework include a finite element deformation model to obtain realistic mammographic deformation and projection simulation for a variety of tomosynthesis geometries. The resulting projections are provided in DICOM format to be applicable for clinically applied reconstruction algorithms. Examples of simulations using parameters of a currently applied clinical setup are presented. The overall simulation model is generic, allowing multiple degrees of freedom to cover anatomical variety in the amount of glandular tissue, degrees of compression, material models for breast tissues, and tomosynthesis geometries.

  6. Geoscience data standards, software implementations, and the Internet. Where we came from and where we might be going.

    NASA Astrophysics Data System (ADS)

    Blodgett, D. L.

    2014-12-01

    Geographic information science and the coupled database and software systems that have grown from it have been evolving since the early 1990s. The multi-file shapefile package, invented early in this evolution, is an example of a highly generalized file format that can be used as an archival, interchange, and format for program execution. There are other formats, such as GeoTIFF and NetCDF that have similar characteristics. These de-facto standard (in contrast to the formally defined and published standards) formats, while not initially designed for machine-readable web-services, are used in them extensively. Relying on these formats allows legacy software to be adapted to web-services, but may require complicate software development to handle dynamic introspection of these legacy file formats' metadata. A generalized system of web-service types that offer archive, interchange, and run-time capabilities based on commonly implemented file formats and established web-service specifications has emerged from exemplar implementations. For example, an Open Geospatial Consortium (OGC) Web Feature Service is used to serve sites or model polygons and an OGC Sensor Observation Service provides time series data for the sites. The broad system of data formats, web-service types, and freely available software that implements the system will be described. The presentation will include a perspective on the future of this basic system and how it relates to scientific domain specific information models such as the Open Geospatial Consortium standards for geographic, hydrologic, and hydrogeologic data.

  7. 2D-CELL: image processing software for extraction and analysis of 2-dimensional cellular structures

    NASA Astrophysics Data System (ADS)

    Righetti, F.; Telley, H.; Leibling, Th. M.; Mocellin, A.

    1992-01-01

    2D-CELL is a software package for the processing and analyzing of photographic images of cellular structures in a largely interactive way. Starting from a binary digitized image, the programs extract the line network (skeleton) of the structure and determine the graph representation that best models it. Provision is made for manually correcting defects such as incorrect node positions or dangling bonds. Then a suitable algorithm retrieves polygonal contours which define individual cells — local boundary curvatures are neglected for simplicity. Using elementary analytical geometry relations, a range of metric and topological parameters describing the population are then computed, organized into statistical distributions and graphically displayed.

  8. TiLIA: a software package for image analysis of firefly flash patterns.

    PubMed

    Konno, Junsuke; Hatta-Ohashi, Yoko; Akiyoshi, Ryutaro; Thancharoen, Anchana; Silalom, Somyot; Sakchoowong, Watana; Yiu, Vor; Ohba, Nobuyoshi; Suzuki, Hirobumi

    2016-05-01

    As flash signaling patterns of fireflies are species specific, signal-pattern analysis is important for understanding this system of communication. Here, we present time-lapse image analysis (TiLIA), a free open-source software package for signal and flight pattern analyses of fireflies that uses video-recorded image data. TiLIA enables flight path tracing of individual fireflies and provides frame-by-frame coordinates and light intensity data. As an example of TiLIA capabilities, we demonstrate flash pattern analysis of the fireflies Luciola cruciata and L. lateralis during courtship behavior.

  9. SOFI Simulation Tool: A Software Package for Simulating and Testing Super-Resolution Optical Fluctuation Imaging

    PubMed Central

    Sharipov, Azat; Geissbuehler, Stefan; Leutenegger, Marcel; Vandenberg, Wim; Dedecker, Peter; Hofkens, Johan; Lasser, Theo

    2016-01-01

    Super-resolution optical fluctuation imaging (SOFI) allows one to perform sub-diffraction fluorescence microscopy of living cells. By analyzing the acquired image sequence with an advanced correlation method, i.e. a high-order cross-cumulant analysis, super-resolution in all three spatial dimensions can be achieved. Here we introduce a software tool for a simple qualitative comparison of SOFI images under simulated conditions considering parameters of the microscope setup and essential properties of the biological sample. This tool incorporates SOFI and STORM algorithms, displays and describes the SOFI image processing steps in a tutorial-like fashion. Fast testing of various parameters simplifies the parameter optimization prior to experimental work. The performance of the simulation tool is demonstrated by comparing simulated results with experimentally acquired data. PMID:27583365

  10. SOFI Simulation Tool: A Software Package for Simulating and Testing Super-Resolution Optical Fluctuation Imaging.

    PubMed

    Girsault, Arik; Lukes, Tomas; Sharipov, Azat; Geissbuehler, Stefan; Leutenegger, Marcel; Vandenberg, Wim; Dedecker, Peter; Hofkens, Johan; Lasser, Theo

    2016-01-01

    Super-resolution optical fluctuation imaging (SOFI) allows one to perform sub-diffraction fluorescence microscopy of living cells. By analyzing the acquired image sequence with an advanced correlation method, i.e. a high-order cross-cumulant analysis, super-resolution in all three spatial dimensions can be achieved. Here we introduce a software tool for a simple qualitative comparison of SOFI images under simulated conditions considering parameters of the microscope setup and essential properties of the biological sample. This tool incorporates SOFI and STORM algorithms, displays and describes the SOFI image processing steps in a tutorial-like fashion. Fast testing of various parameters simplifies the parameter optimization prior to experimental work. The performance of the simulation tool is demonstrated by comparing simulated results with experimentally acquired data.

  11. SPLASSH: Open source software for camera-based high-speed, multispectral in-vivo optical image acquisition.

    PubMed

    Sun, Ryan; Bouchard, Matthew B; Hillman, Elizabeth M C

    2010-08-02

    Camera-based in-vivo optical imaging can provide detailed images of living tissue that reveal structure, function, and disease. High-speed, high resolution imaging can reveal dynamic events such as changes in blood flow and responses to stimulation. Despite these benefits, commercially available scientific cameras rarely include software that is suitable for in-vivo imaging applications, making this highly versatile form of optical imaging challenging and time-consuming to implement. To address this issue, we have developed a novel, open-source software package to control high-speed, multispectral optical imaging systems. The software integrates a number of modular functions through a custom graphical user interface (GUI) and provides extensive control over a wide range of inexpensive IEEE 1394 Firewire cameras. Multispectral illumination can be incorporated through the use of off-the-shelf light emitting diodes which the software synchronizes to image acquisition via a programmed microcontroller, allowing arbitrary high-speed illumination sequences. The complete software suite is available for free download. Here we describe the software's framework and provide details to guide users with development of this and similar software.

  12. Image 100 procedures manual development: Applications system library definition and Image 100 software definition

    NASA Technical Reports Server (NTRS)

    Guseman, L. F., Jr.; Decell, H. P., Jr.

    1975-01-01

    An outline for an Image 100 procedures manual for Earth Resources Program image analysis was developed which sets forth guidelines that provide a basis for the preparation and updating of an Image 100 Procedures Manual. The scope of the outline was limited to definition of general features of a procedures manual together with special features of an interactive system. Computer programs were identified which should be implemented as part of an applications oriented library for the system.

  13. Space Station Software Issues

    NASA Technical Reports Server (NTRS)

    Voigt, S. (Editor); Beskenis, S. (Editor)

    1985-01-01

    Issues in the development of software for the Space Station are discussed. Software acquisition and management, software development environment, standards, information system support for software developers, and a future software advisory board are addressed.

  14. The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable.

    PubMed

    Nickerson, David; Atalag, Koray; de Bono, Bernard; Geiger, Jörg; Goble, Carole; Hollmann, Susanne; Lonien, Joachim; Müller, Wolfgang; Regierer, Babette; Stanford, Natalie J; Golebiewski, Martin; Hunter, Peter

    2016-04-06

    Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome.

  15. The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable

    PubMed Central

    2016-01-01

    Reconstructing and understanding the Human Physiome virtually is a complex mathematical problem, and a highly demanding computational challenge. Mathematical models spanning from the molecular level through to whole populations of individuals must be integrated, then personalized. This requires interoperability with multiple disparate and geographically separated data sources, and myriad computational software tools. Extracting and producing knowledge from such sources, even when the databases and software are readily available, is a challenging task. Despite the difficulties, researchers must frequently perform these tasks so that available knowledge can be continually integrated into the common framework required to realize the Human Physiome. Software and infrastructures that support the communities that generate these, together with their underlying standards to format, describe and interlink the corresponding data and computer models, are pivotal to the Human Physiome being realized. They provide the foundations for integrating, exchanging and re-using data and models efficiently, and correctly, while also supporting the dissemination of growing knowledge in these forms. In this paper, we explore the standards, software tooling, repositories and infrastructures that support this work, and detail what makes them vital to realizing the Human Physiome. PMID:27051515

  16. Study on image processing of panoramic X-ray using deviation improvement software.

    PubMed

    Kim, Tae-Gon; Lee, Yang-Sun; Kim, Young-Pyo; Park, Yong-Pil; Cheon, Min-Woo

    2014-01-01

    Utilization of panoramic X-ray device is getting wider. Panoramic X-ray has low resolution than general X-ray device and it occurs to distortion by deviation of image synthesis. Due to structural problems, it has been used restrictively to identify of tooth structure, not for whole head. Therefore, it designed and produced panoramic X-ray device which is possible to diagnostic coverage can be extended and had to be adjusted interval control between X-ray generator and image processing for whole of Maxillofacia's diagnosis. Produced panoramic X-ray device is composed basically of short image synthesis. In addition, it was confirmed the results by used the device which was applied deviation of the brightness of the image, filter to improve the location of the deviation and interpolation method. In this study, it was used 13 images including the front. It occurs to brightness deviation, position deviation, and geometric correction when synthesis of image, but it had been solved by deviation improvement software and a change of CCD camera's scan line which is used for image acquisition. Therefore, it confirmed expansion possibility of utilization range to commonly used panoramic X-ray device.

  17. Consistent image presentation implemented using DICOM grayscale standard display function

    NASA Astrophysics Data System (ADS)

    Kump, Kenneth S.; Omernick, Jon; French, John

    2000-04-01

    In this paper, we evaluate our ability to achieve consistent image presentation across a wide range of output devices, focusing on digital x-ray radiography for chest applications. In particular we focus on dry versus wet printers of hardcopy prints. In this evaluation, we review the expected theoretical variability using the DICOM grayscale standard display function (GSDF). The GSDF maps DICOM presentation values to luminance values that are perceived by a human. We present our methodology for calibrating devices as evaluated on sixteen printers. Seven devices were selected for a human observer study to determine if there are perceptible differences in the presentation of a given image, focusing on differences between wet and dry processes. It was found that wet printers were preferred, however, there may be other logistical and practical reasons whey dry printers may be used.

  18. Development of an Open Source Image-Based Flow Modeling Software - SimVascular

    NASA Astrophysics Data System (ADS)

    Updegrove, Adam; Merkow, Jameson; Schiavazzi, Daniele; Wilson, Nathan; Marsden, Alison; Shadden, Shawn

    2014-11-01

    SimVascular (www.simvascular.org) is currently the only comprehensive software package that provides a complete pipeline from medical image data segmentation to patient specific blood flow simulation. This software and its derivatives have been used in hundreds of conference abstracts and peer-reviewed journal articles, as well as the foundation of medical startups. SimVascular was initially released in August 2007, yet major challenges and deterrents for new adopters were the requirement of licensing three expensive commercial libraries utilized by the software, a complicated build process, and a lack of documentation, support and organized maintenance. In the past year, the SimVascular team has made significant progress to integrate open source alternatives for the linear solver, solid modeling, and mesh generation commercial libraries required by the original public release. In addition, the build system, available distributions, and graphical user interface have been significantly enhanced. Finally, the software has been updated to enable users to directly run simulations using models and boundary condition values, included in the Vascular Model Repository (vascularmodel.org). In this presentation we will briefly overview the capabilities of the new SimVascular 2.0 release. National Science Foundation.

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

    PubMed Central

    Maier, Andreas; Hofmann, Hannes G.; Berger, Martin; Fischer, Peter; Schwemmer, Chris; Wu, Haibo; Müller, Kerstin; Hornegger, Joachim; Choi, Jang-Hwan; Riess, Christian; Keil, Andreas; Fahrig, Rebecca

    2013-01-01

    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 with 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

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

    SciTech Connect

    Maier, Andreas; Choi, Jang-Hwan; Riess, Christian; Keil, Andreas; Fahrig, Rebecca; Hofmann, Hannes G.; Berger, Martin; Fischer, Peter; Schwemmer, Chris; Wu, Haibo; Müller, Kerstin; Hornegger, Joachim

    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 with 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

  1. CAVASS: a computer-assisted visualization and analysis software system - image processing aspects

    NASA Astrophysics Data System (ADS)

    Udupa, Jayaram K.; Grevera, George J.; Odhner, Dewey; Zhuge, Ying; Souza, Andre; Mishra, Shipra; Iwanaga, Tad

    2007-03-01

    The development of the concepts within 3DVIEWNIX and of the software system 3DVIEWNIX itself dates back to the 1970s. Since then, a series of software packages for Computer Assisted Visualization and Analysis (CAVA) of images came out from our group, 3DVIEWNIX released in 1993, being the most recent, and all were distributed with source code. CAVASS, an open source system, is the latest in this series, and represents the next major incarnation of 3DVIEWNIX. It incorporates four groups of operations: IMAGE PROCESSING (including ROI, interpolation, filtering, segmentation, registration, morphological, and algebraic operations), VISUALIZATION (including slice display, reslicing, MIP, surface rendering, and volume rendering), MANIPULATION (for modifying structures and surgery simulation), ANALYSIS (various ways of extracting quantitative information). CAVASS is designed to work on all platforms. Its key features are: (1) most major CAVA operations incorporated; (2) very efficient algorithms and their highly efficient implementations; (3) parallelized algorithms for computationally intensive operations; (4) parallel implementation via distributed computing on a cluster of PCs; (5) interface to other systems such as CAD/CAM software, ITK, and statistical packages; (6) easy to use GUI. In this paper, we focus on the image processing operations and compare the performance of CAVASS with that of ITK. Our conclusions based on assessing performance by utilizing a regular (6 MB), large (241 MB), and a super (873 MB) 3D image data set are as follows: CAVASS is considerably more efficient than ITK, especially in those operations which are computationally intensive. It can handle considerably larger data sets than ITK. It is easy and ready to use in applications since it provides an easy to use GUI. The users can easily build a cluster from ordinary inexpensive PCs and reap the full power of CAVASS inexpensively compared to expensive multiprocessing systems which are less

  2. Intracoronary optical coherence tomography: Clinical and research applications and intravascular imaging software overview.

    PubMed

    Tenekecioglu, Erhan; Albuquerque, Felipe N; Sotomi, Yohei; Zeng, Yaping; Suwannasom, Pannipa; Tateishi, Hiroki; Cavalcante, Rafael; Ishibashi, Yuki; Nakatani, Shimpei; Abdelghani, Mohammad; Dijkstra, Jouke; Bourantas, Christos; Collet, Carlos; Karanasos, Antonios; Radu, Maria; Wang, Ancong; Muramatsu, Takashi; Landmesser, Ulf; Okamura, Takayuki; Regar, Evelyn; Räber, Lorenz; Guagliumi, Giulio; Pyo, Robert T; Onuma, Yoshinobu; Serruys, Patrick W

    2017-01-21

    By providing valuable information about the coronary artery wall and lumen, intravascular imaging may aid in optimizing interventional procedure results and thereby could improve clinical outcomes following percutaneous coronary intervention (PCI). Intravascular optical coherence tomography (OCT) is a light-based technology with a tissue penetration of approximately 1 to 3 mm and provides near histological resolution. It has emerged as a technological breakthrough in intravascular imaging with multiple clinical and research applications. OCT provides detailed visualization of the vessel following PCI and provides accurate assessment of post-procedural stent performance including detection of edge dissection, stent struts apposition, tissue prolapse, and healing parameters. Additionally, it can provide accurate characterization of plaque morphology and provides key information to optimize post-procedural outcomes. This manuscript aims to review the current clinical and research applications of intracoronary OCT and summarize the analytic OCT imaging software packages currently available. © 2017 Wiley Periodicals, Inc.

  3. The standardization of super resolution optical microscopic images based on DICOM

    NASA Astrophysics Data System (ADS)

    Xia, Wei; Gao, Xin

    2015-03-01

    Super resolution optical microscopy allows the capture of images with a higher resolution than the diffraction limit. However, due to the lack of a standard format, the processing, visualization, transfer, and exchange of Super Resolution Optical Microscope (SROM) images are inconvenient. In this work, we present an approach to standardize the SROM images based on the Digital Imaging and Communication in Medicine (DICOM) standard. The SROM images and associated information are encapsulated and converted to DICOM images based on the Visible Light Microscopic Image Information Object Definition of DICOM. The new generated SROM images in DICOM format can be displayed, processed, transferred, and exchanged by using most medical image processing tools.

  4. The role of camera-bundled image management software in the consumer digital imaging value chain

    NASA Astrophysics Data System (ADS)

    Mueller, Milton; Mundkur, Anuradha; Balasubramanian, Ashok; Chirania, Virat

    2005-02-01

    This research was undertaken by the Convergence Center at the Syracuse University School of Information Studies (www.digital-convergence.info). Project ICONICA, the name for the research, focuses on the strategic implications of digital Images and the CONvergence of Image management and image CApture. Consumer imaging - the activity that we once called "photography" - is now recognized as in the throes of a digital transformation. At the end of 2003, market researchers estimated that about 30% of the households in the U.S. and 40% of the households in Japan owned digital cameras. In 2004, of the 86 million new cameras sold (excluding one-time use cameras), a majority (56%) were estimated to be digital cameras. Sales of photographic film, while still profitable, are declining precipitously.

  5. Evaluation of cassette-based digital radiography detectors using standardized image quality metrics: AAPM TG-150 Draft Image Detector Tests.

    PubMed

    Li, Guang; Greene, Travis C; Nishino, Thomas K; Willis, Charles E

    2016-09-08

    The purpose of this study was to evaluate several of the standardized image quality metrics proposed by the American Association of Physics in Medicine (AAPM) Task Group 150. The task group suggested region-of-interest (ROI)-based techniques to measure nonuniformity, minimum signal-to-noise ratio (SNR), number of anomalous pixels, and modulation transfer function (MTF). This study evaluated the effects of ROI size and layout on the image metrics by using four different ROI sets, assessed result uncertainty by repeating measurements, and compared results with two commercially available quality control tools, namely the Carestream DIRECTVIEW Total Quality Tool (TQT) and the GE Healthcare Quality Assurance Process (QAP). Seven Carestream DRX-1C (CsI) detectors on mobile DR systems and four GE FlashPad detectors in radiographic rooms were tested. Images were analyzed using MATLAB software that had been previously validated and reported. Our values for signal and SNR nonuniformity and MTF agree with values published by other investigators. Our results show that ROI size affects nonuniformity and minimum SNR measurements, but not detection of anomalous pixels. Exposure geometry affects all tested image metrics except for the MTF. TG-150 metrics in general agree with the TQT, but agree with the QAP only for local and global signal nonuniformity. The difference in SNR nonuniformity and MTF values between the TG-150 and QAP may be explained by differences in the calculation of noise and acquisition beam quality, respectively. TG-150's SNR nonuniformity metrics are also more sensitive to detector nonuniformity compared to the QAP. Our results suggest that fixed ROI size should be used for consistency because nonuniformity metrics depend on ROI size. Ideally, detector tests should be performed at the exact calibration position. If not feasible, a baseline should be established from the mean of several repeated measurements. Our study indicates that the TG-150 tests can be

  6. 76 FR 43724 - In the Matter of Certain Digital Imaging Devices and Related Software; Notice of Commission...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-21

    ... From the Federal Register Online via the Government Publishing Office INTERNATIONAL TRADE COMMISSION In the Matter of Certain Digital Imaging Devices and Related Software; Notice of Commission... related software by reason of infringement of various claims of United States Patent Nos. 6,031,964 and...

  7. Mississippi Company Using NASA Software Program to Provide Unique Imaging Service: DATASTAR Success Story

    NASA Technical Reports Server (NTRS)

    2001-01-01

    DATASTAR, Inc., of Picayune, Miss., has taken NASA's award-winning Earth Resources Laboratory Applications (ELAS) software program and evolved it to the point that the company is now providing a unique, spatial imagery service over the Internet. ELAS was developed in the early 80's to process satellite and airborne sensor imagery data of the Earth's surface into readable and useable information. While there are several software packages on the market that allow the manipulation of spatial data into useable products, this is usually a laborious task. The new program, called the DATASTAR Image Processing Exploitation, or DIPX, Delivery Service, is a subscription service available over the Internet that takes the work out of the equation and provides normalized geo-spatial data in the form of decision products.

  8. Features of the Upgraded Imaging for Hypersonic Experimental Aeroheating Testing (IHEAT) Software

    NASA Technical Reports Server (NTRS)

    Mason, Michelle L.; Rufer, Shann J.

    2016-01-01

    The Imaging for Hypersonic Experimental Aeroheating Testing (IHEAT) software is used at the NASA Langley Research Center to analyze global aeroheating data on wind tunnel models tested in the Langley Aerothermodynamics Laboratory. One-dimensional, semi-infinite heating data derived from IHEAT are used in the design of thermal protection systems for hypersonic vehicles that are exposed to severe aeroheating loads, such as reentry vehicles during descent and landing procedures. This software program originally was written in the PV-WAVE(Registered Trademark) programming language to analyze phosphor thermography data from the two-color, relative-intensity system developed at Langley. To increase the efficiency, functionality, and reliability of IHEAT, the program was migrated to MATLAB(Registered Trademark) syntax and compiled as a stand-alone executable file labeled version 4.0. New features of IHEAT 4.0 include the options to perform diagnostic checks of the accuracy of the acquired data during a wind tunnel test, to extract data along a specified multi-segment line following a feature such as a leading edge or a streamline, and to batch process all of the temporal frame data from a wind tunnel run. Results from IHEAT 4.0 were compared on a pixel level to the output images from the legacy software to validate the program. The absolute differences between the heat transfer data output from the two programs were on the order of 10(exp -5) to 10(exp -7). IHEAT 4.0 replaces the PV-WAVE(Registered Trademark) version as the production software for aeroheating experiments conducted in the hypersonic facilities at NASA Langley.

  9. Scalable, high-performance 3D imaging software platform: system architecture and application to virtual colonoscopy.

    PubMed

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

    2012-01-01

    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.

  10. A complete software application for automatic registration of x-ray mammography and magnetic resonance images

    SciTech Connect

    Solves-Llorens, J. A.; Rupérez, M. J. Monserrat, C.; Lloret, M.

    2014-08-15

    Purpose: This work presents a complete and automatic software application to aid radiologists in breast cancer diagnosis. The application is a fully automated method that performs a complete registration of magnetic resonance (MR) images and x-ray (XR) images in both directions (from MR to XR and from XR to MR) and for both x-ray mammograms, craniocaudal (CC), and mediolateral oblique (MLO). This new approximation allows radiologists to mark points in the MR images and, without any manual intervention, it provides their corresponding points in both types of XR mammograms and vice versa. Methods: The application automatically segments magnetic resonance images and x-ray images using the C-Means method and the Otsu method, respectively. It compresses the magnetic resonance images in both directions, CC and MLO, using a biomechanical model of the breast that distinguishes the specific biomechanical behavior of each one of its three tissues (skin, fat, and glandular tissue) separately. It makes a projection of both compressions and registers them with the original XR images using affine transformations and nonrigid registration methods. Results: The application has been validated by two expert radiologists. This was carried out through a quantitative validation on 14 data sets in which the Euclidean distance between points marked by the radiologists and the corresponding points obtained by the application were measured. The results showed a mean error of 4.2 ± 1.9 mm for the MRI to CC registration, 4.8 ± 1.3 mm for the MRI to MLO registration, and 4.1 ± 1.3 mm for the CC and MLO to MRI registration. Conclusions: A complete software application that automatically registers XR and MR images of the breast has been implemented. The application permits radiologists to estimate the position of a lesion that is suspected of being a tumor in an imaging modality based on its position in another different modality with a clinically acceptable error. The results show that the

  11. Reliability and reproducibility of macular segmentation using a custom-built optical coherence tomography retinal image analysis software

    NASA Astrophysics Data System (ADS)

    Cabrera Debuc, Delia; Somfai, Gábor Márk; Ranganathan, Sudarshan; Tátrai, Erika; Ferencz, Mária; Puliafito, Carmen A.

    2009-11-01

    We determine the reliability and reproducibility of retinal thickness measurements with a custom-built OCT retinal image analysis software (OCTRIMA). Ten eyes of five healthy subjects undergo repeated standard macular thickness map scan sessions by two experienced examiners using a Stratus OCT device. Automatic/semi automatic thickness quantification of the macula and intraretinal layers is performed using OCTRIMA software. Intraobserver, interobserver, and intervisit repeatability and reproducibility coefficients, and intraclass correlation coefficients (ICCs) per scan are calculated. Intraobserver, interobserver, and intervisit variability combined account for less than 5% of total variability for the total retinal thickness measurements and less than 7% for the intraretinal layers except the outer segment/ retinal pigment epithelium (RPE) junction. There is no significant difference between scans acquired by different observers or during different visits. The ICCs obtained for the intraobserver and intervisit variability tests are greater than 0.75 for the total retina and all intraretinal layers, except the inner nuclear layer intraobserver and interobserver test and the outer plexiform layer, intraobserver, interobserver, and intervisit test. Our results indicate that thickness measurements for the total retina and all intraretinal layers (except the outer segment/RPE junction) performed using OCTRIMA are highly repeatable and reproducible.

  12. Multiplanar transcranial ultrasound imaging: standards, landmarks and correlation with magnetic resonance imaging.

    PubMed

    Kern, Rolf; Perren, Fabienne; Kreisel, Stefan; Szabo, Kristina; Hennerici, Michael; Meairs, Stephen

    2005-03-01

    The purpose of this study was to define a standardized multiplanar approach for transcranial ultrasound (US) imaging of brain parenchyma based on matched data from 3-D US and 3-D magnetic resonance imaging (MRI). The potential and limitations of multiple insonation planes in transverse and coronal orientation were evaluated for the visualization of intracranial landmarks in 60 healthy individuals (18 to 83 years old, mean 41.4 years) with sufficient temporal bone windows. Landmarks regularly visualized even in moderate sonographic conditions with identification rates of >75% were mesencephalon, pons, third ventricle, lateral ventricles, falx, thalamus, basal ganglia, pineal gland and temporal lobe. Identification of medulla oblongata, fourth ventricle, cerebellar structures, hippocampus, insula, frontal, parietal and occipital lobes was more difficult (<75%). We hypothesize that multiplanar transcranial US images, with standardized specification of tilt angles and orientation, not only allow comparison with other neuroimaging modalities, but may also provide a more objective framework for US monitoring of cerebral disease than freehand scanning.

  13. A comparison of strain calculation using digital image correlation and finite element software

    NASA Astrophysics Data System (ADS)

    Iadicola, M.; Banerjee, D.

    2016-08-01

    Digital image correlation (DIC) data are being extensively used for many forming applications and for comparisons with finite element analysis (FEA) simulated results. The most challenging comparisons are often in the area of strain localizations just prior to material failure. While qualitative comparisons can be misleading, quantitative comparisons are difficult because of insufficient information about the type of strain output. In this work, strains computed from DIC displacements from a forming limit test are compared to those from three commercial FEA software. Quantitative differences in calculated strains are assessed to determine if the scale of variations seen between FEA and DIC calculated strains constitute real behavior or just calculation differences.

  14. HYPOTrace: image analysis software for measuring hypocotyl growth and shape demonstrated on Arabidopsis seedlings undergoing photomorphogenesis.

    PubMed

    Wang, Liya; Uilecan, Ioan Vlad; Assadi, Amir H; Kozmik, Christine A; Spalding, Edgar P

    2009-04-01

    Analysis of time series of images can quantify plant growth and development, including the effects of genetic mutations (phenotypes) that give information about gene function. Here is demonstrated a software application named HYPOTrace that automatically extracts growth and shape information from electronic gray-scale images of Arabidopsis (Arabidopsis thaliana) seedlings. Key to the method is the iterative application of adaptive local principal components analysis to extract a set of ordered midline points (medial axis) from images of the seedling hypocotyl. Pixel intensity is weighted to avoid the medial axis being diverted by the cotyledons in areas where the two come in contact. An intensity feature useful for terminating the midline at the hypocotyl apex was isolated in each image by subtracting the baseline with a robust local regression algorithm. Applying the algorithm to time series of images of Arabidopsis seedlings responding to light resulted in automatic quantification of hypocotyl growth rate, apical hook opening, and phototropic bending with high spatiotemporal resolution. These functions are demonstrated here on wild-type, cryptochrome1, and phototropin1 seedlings for the purpose of showing that HYPOTrace generated expected results and to show how much richer the machine-vision description is compared to methods more typical in plant biology. HYPOTrace is expected to benefit seedling development research, particularly in the photomorphogenesis field, by replacing many tedious, error-prone manual measurements with a precise, largely automated computational tool.

  15. Review of free software tools for image analysis of fluorescence cell micrographs.

    PubMed

    Wiesmann, V; Franz, D; Held, C; Münzenmayer, C; Palmisano, R; Wittenberg, T

    2015-01-01

    An increasing number of free software tools have been made available for the evaluation of fluorescence cell micrographs. The main users are biologists and related life scientists with no or little knowledge of image processing. In this review, we give an overview of available tools and guidelines about which tools the users should use to segment fluorescence micrographs. We selected 15 free tools and divided them into stand-alone, Matlab-based, ImageJ-based, free demo versions of commercial tools and data sharing tools. The review consists of two parts: First, we developed a criteria catalogue and rated the tools regarding structural requirements, functionality (flexibility, segmentation and image processing filters) and usability (documentation, data management, usability and visualization). Second, we performed an image processing case study with four representative fluorescence micrograph segmentation tasks with figure-ground and cell separation. The tools display a wide range of functionality and usability. In the image processing case study, we were able to perform figure-ground separation in all micrographs using mainly thresholding. Cell separation was not possible with most of the tools, because cell separation methods are provided only by a subset of the tools and are difficult to parametrize and to use. Most important is that the usability matches the functionality of a tool. To be usable, specialized tools with less functionality need to fulfill less usability criteria, whereas multipurpose tools need a well-structured menu and intuitive graphical user interface.

  16. High Performance Embedded Computing Software Initiative (HPEC-SI) Program Facilitation of VSIPL++ Standardization

    DTIC Science & Technology

    2008-04-01

    parallel VSIPL++, and other parallel computing systems. The cluster is a fifty five node Beowulf style cluster with 116 compute processors of varying types...consoles, which GTRI inserted into to the parallel software testbed. A computer that is used as a compute node in a Beowulf -style cluster requires a... Beowulf -style cluster. GTRI also participated in technical advisory planning for the HPEC-SI program. 5. References 1. Schwartz, D. A ., Judd, R. R

  17. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods.

    PubMed

    Ramus, Claire; Hovasse, Agnès; Marcellin, Marlène; Hesse, Anne-Marie; Mouton-Barbosa, Emmanuelle; Bouyssié, David; Vaca, Sebastian; Carapito, Christine; Chaoui, Karima; Bruley, Christophe; Garin, Jérôme; Cianférani, Sarah; Ferro, Myriam; Dorssaeler, Alain Van; Burlet-Schiltz, Odile; Schaeffer, Christine; Couté, Yohann; Gonzalez de Peredo, Anne

    2016-03-01

    This data article describes a controlled, spiked proteomic dataset for which the "ground truth" of variant proteins is known. It is based on the LC-MS analysis of samples composed of a fixed background of yeast lysate and different spiked amounts of the UPS1 mixture of 48 recombinant proteins. It can be used to objectively evaluate bioinformatic pipelines for label-free quantitative analysis, and their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. More specifically, it can be useful for tuning software tools parameters, but also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods. The raw MS files can be downloaded from ProteomeXchange with identifier PXD001819. Starting from some raw files of this dataset, we also provide here some processed data obtained through various bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in different workflows, to exemplify the use of such data in the context of software benchmarking, as discussed in details in the accompanying manuscript [1]. The experimental design used here for data processing takes advantage of the different spike levels introduced in the samples composing the dataset, and processed data are merged in a single file to facilitate the evaluation and illustration of software tools results for the detection of variant proteins with different absolute expression levels and fold change values.

  18. Comparison of software and human observers in reading images of the CDMAM test object to assess digital mammography systems

    NASA Astrophysics Data System (ADS)

    Young, Kenneth C.; Cook, James J. H.; Oduko, Jennifer M.; Bosmans, Hilde

    2006-03-01

    European Guidelines for quality control in digital mammography specify minimum and achievable standards of image quality in terms of threshold contrast, based on readings of images of the CDMAM test object by human observers. However this is time-consuming and has large inter-observer error. To overcome these problems a software program (CDCOM) is available to automatically read CDMAM images, but the optimal method of interpreting the output is not defined. This study evaluates methods of determining threshold contrast from the program, and compares these to human readings for a variety of mammography systems. The methods considered are (A) simple thresholding (B) psychometric curve fitting (C) smoothing and interpolation and (D) smoothing and psychometric curve fitting. Each method leads to similar threshold contrasts but with different reproducibility. Method (A) had relatively poor reproducibility with a standard error in threshold contrast of 18.1 +/- 0.7%. This was reduced to 8.4% by using a contrast-detail curve fitting procedure. Method (D) had the best reproducibility with an error of 6.7%, reducing to 5.1% with curve fitting. A panel of 3 human observers had an error of 4.4% reduced to 2.9 % by curve fitting. All automatic methods led to threshold contrasts that were lower than for humans. The ratio of human to program threshold contrasts varied with detail diameter and was 1.50 +/- .04 (sem) at 0.1mm and 1.82 +/- .06 at 0.25mm for method (D). There were good correlations between the threshold contrast determined by humans and the automated methods.

  19. User's Guide for the MapImage Reprojection Software Package, Version 1.01

    USGS Publications Warehouse

    Finn, Michael P.; Trent, Jason R.

    2004-01-01

    Scientists routinely accomplish small-scale geospatial modeling in the raster domain, using high-resolution datasets (such as 30-m data) for large parts of continents and low-resolution to high-resolution datasets for the entire globe. Recently, Usery and others (2003a) expanded on the previously limited empirical work with real geographic data by compiling and tabulating the accuracy of categorical areas in projected raster datasets of global extent. Geographers and applications programmers at the U.S. Geological Survey's (USGS) Mid-Continent Mapping Center (MCMC) undertook an effort to expand and evolve an internal USGS software package, MapImage, or mapimg, for raster map projection transformation (Usery and others, 2003a). Daniel R. Steinwand of Science Applications International Corporation, Earth Resources Observation Systems Data Center in Sioux Falls, S. Dak., originally developed mapimg for the USGS, basing it on the USGS's General Cartographic Transformation Package (GCTP). It operated as a command line program on the Unix operating system. Through efforts at MCMC, and in coordination with Mr. Steinwand, this program has been transformed from an application based on a command line into a software package based on a graphic user interface for Windows, Linux, and Unix machines. Usery and others (2003b) pointed out that many commercial software packages do not use exact projection equations and that even when exact projection equations are used, the software often results in error and sometimes does not complete the transformation for specific projections, at specific resampling resolutions, and for specific singularities. Direct implementation of point-to-point transformation with appropriate functions yields the variety of projections available in these software packages, but implementation with data other than points requires specific adaptation of the equations or prior preparation of the data to allow the transformation to succeed. Additional

  20. Hierarchical Image Segmentation of Remotely Sensed Data using Massively Parallel GNU-LINUX Software

    NASA Technical Reports Server (NTRS)

    Tilton, James C.

    2003-01-01

    A hierarchical set of image segmentations is a set of several image segmentations of the same image at different levels of detail in which the segmentations at coarser levels of detail can be produced from simple merges of regions at finer levels of detail. In [1], Tilton, et a1 describes an approach for producing hierarchical segmentations (called HSEG) and gave a progress report on exploiting these hierarchical segmentations for image information mining. The HSEG algorithm is a hybrid of region growing and constrained spectral clustering that produces a hierarchical set of image segmentations based on detected convergence points. In the main, HSEG employs the hierarchical stepwise optimization (HSWO) approach to region growing, which was described as early as 1989 by Beaulieu and Goldberg. The HSWO approach seeks to produce segmentations that are more optimized than those produced by more classic approaches to region growing (e.g. Horowitz and T. Pavlidis, [3]). In addition, HSEG optionally interjects between HSWO region growing iterations, merges between spatially non-adjacent regions (i.e., spectrally based merging or clustering) constrained by a threshold derived from the previous HSWO region growing iteration. While the addition of constrained spectral clustering improves the utility of the segmentation results, especially for larger images, it also significantly increases HSEG s computational requirements. To counteract this, a computationally efficient recursive, divide-and-conquer, implementation of HSEG (RHSEG) was devised, which includes special code to avoid processing artifacts caused by RHSEG s recursive subdivision of the image data. The recursive nature of RHSEG makes for a straightforward parallel implementation. This paper describes the HSEG algorithm, its recursive formulation (referred to as RHSEG), and the implementation of RHSEG using massively parallel GNU-LINUX software. Results with Landsat TM data are included comparing RHSEG with classic

  1. X-ray volumetric imaging in image-guided radiotherapy: The new standard in on-treatment imaging

    SciTech Connect

    McBain, Catherine A.; Henry, Ann M. . E-mail: catherine.mcbain@christie-tr.nwest.nhs.uk; Sykes, Jonathan; Amer, Ali; Marchant, Tom; Moore, Christopher M.; Davies, Julie; Stratford, Julia; McCarthy, Claire; Porritt, Bridget; Williams, Peter; Khoo, Vincent S.; Price, Pat

    2006-02-01

    Purpose: X-ray volumetric imaging (XVI) for the first time allows for the on-treatment acquisition of three-dimensional (3D) kV cone beam computed tomography (CT) images. Clinical imaging using the Synergy System (Elekta, Crawley, UK) commenced in July 2003. This study evaluated image quality and dose delivered and assessed clinical utility for treatment verification at a range of anatomic sites. Methods and Materials: Single XVIs were acquired from 30 patients undergoing radiotherapy for tumors at 10 different anatomic sites. Patients were imaged in their setup position. Radiation doses received were measured using TLDs on the skin surface. The utility of XVI in verifying target volume coverage was qualitatively assessed by experienced clinicians. Results: X-ray volumetric imaging acquisition was completed in the treatment position at all anatomic sites. At sites where a full gantry rotation was not possible, XVIs were reconstructed from projection images acquired from partial rotations. Soft-tissue definition of organ boundaries allowed direct assessment of 3D target volume coverage at all sites. Individual image quality depended on both imaging parameters and patient characteristics. Radiation dose ranged from 0.003 Gy in the head to 0.03 Gy in the pelvis. Conclusions: On-treatment XVI provided 3D verification images with soft-tissue definition at all anatomic sites at acceptably low radiation doses. This technology sets a new standard in treatment verification and will facilitate novel adaptive radiotherapy techniques.

  2. SNARK09 - a software package for reconstruction of 2D images from 1D projections.

    PubMed

    Klukowska, Joanna; Davidi, Ran; Herman, Gabor T

    2013-06-01

    The problem of reconstruction of slices and volumes from 1D and 2D projections has arisen in a large number of scientific fields (including computerized tomography, electron microscopy, X-ray microscopy, radiology, radio astronomy and holography). Many different methods (algorithms) have been suggested for its solution. In this paper we present a software package, SNARK09, for reconstruction of 2D images from their 1D projections. In the area of image reconstruction, researchers often desire to compare two or more reconstruction techniques and assess their relative merits. SNARK09 provides a uniform framework to implement algorithms and evaluate their performance. It has been designed to treat both parallel and divergent projection geometries and can either create test data (with or without noise) for use by reconstruction algorithms or use data collected by another software or a physical device. A number of frequently-used classical reconstruction algorithms are incorporated. The package provides a means for easy incorporation of new algorithms for their testing, comparison and evaluation. It comes with tools for statistical analysis of the results and ten worked examples.

  3. Developing a new software package for PSF estimation and fitting of adaptive optics images

    NASA Astrophysics Data System (ADS)

    Schreiber, Laura; Diolaiti, Emiliano; Sollima, Antonio; Arcidiacono, Carmelo; Bellazzini, Michele; Ciliegi, Paolo; Falomo, Renato; Foppiani, Italo; Greggio, Laura; Lanzoni, Barbara; Lombini, Matteo; Montegriffo, Paolo; Dalessandro, Emanuele; Massari, Davide

    2012-07-01

    Adaptive Optics (AO) images are characterized by structured Point Spread Function (PSF), with sharp core and extended halo, and by significant variations across the field of view. In order to enable the extraction of high-precision quantitative information and improve the scientific exploitation of AO data, efforts in the PSF modeling and in the integration of suitable models in a code for image analysis are needed. We present the current status of a study on the modeling of AO PSFs based on observational data taken with present telescopes (VLT and LBT). The methods under development include parametric models and hybrid (i.e. analytical / numerical) models adapted to various types of PSFs that can show up in AO images. The specific features of AO data, such as the mainly radial variation of the PSF with respect to the guide star position in single-reference AO, are taken into account as much as possible. The final objective of this project is the development of a flexible software package, based on the Starfinder code (Diolaiati et Al 2000), specifically dedicated to the PSF estimation and to the astrometric and photometric analysis of AO images with complex and spatially variable PSF.

  4. The wavelet/scalar quantization compression standard for digital fingerprint images

    SciTech Connect

    Bradley, J.N.; Brislawn, C.M.

    1994-04-01

    A new digital image compression standard has been adopted by the US Federal Bureau of Investigation for use on digitized gray-scale fingerprint images. The algorithm is based on adaptive uniform scalar quantization of a discrete wavelet transform image decomposition and is referred to as the wavelet/scalar quantization standard. The standard produces archival quality images at compression ratios of around 20:1 and will allow the FBI to replace their current database of paper fingerprint cards with digital imagery.

  5. An Effective On-line Polymer Characterization Technique by Using SALS Image Processing Software and Wavelet Analysis

    PubMed Central

    Xian, Guang-ming; Qu, Jin-ping; Zeng, Bi-qing

    2008-01-01

    This paper describes an effective on-line polymer characterization technique by using small-angle light-scattering (SALS) image processing software and wavelet analysis. The phenomenon of small-angle light scattering has been applied to give information about transparent structures on morphology. Real-time visualization of various scattered light image and light intensity matrices is performed by the optical image real-time processing software for SALS. The software can measure the signal intensity of light scattering images, draw the frequency-intensity curves and the amplitude-intensity curves to indicate the variation of the intensity of scattered light in different processing conditions, and estimate the parameters. The current study utilizes a one-dimensional wavelet to delete noise from the original SALS signal and estimate the variation trend of maximum intensity area of the scattered light. So, the system brought the qualitative analysis of the structural information of transparent film success. PMID:19229343

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

    NASA Astrophysics Data System (ADS)

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

    2006-03-01

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

  7. Software-based high-level synthesis design of FPGA beamformers for synthetic aperture imaging.

    PubMed

    Amaro, Joao; Yiu, Billy Y S; Falcao, Gabriel; Gomes, Marco A C; Yu, Alfred C H

    2015-05-01

    Field-programmable gate arrays (FPGAs) can potentially be configured as beamforming platforms for ultrasound imaging, but a long design time and skilled expertise in hardware programming are typically required. In this article, we present a novel approach to the efficient design of FPGA beamformers for synthetic aperture (SA) imaging via the use of software-based high-level synthesis techniques. Software kernels (coded in OpenCL) were first developed to stage-wise handle SA beamforming operations, and their corresponding FPGA logic circuitry was emulated through a high-level synthesis framework. After design space analysis, the fine-tuned OpenCL kernels were compiled into register transfer level descriptions to configure an FPGA as a beamformer module. The processing performance of this beamformer was assessed through a series of offline emulation experiments that sought to derive beamformed images from SA channel-domain raw data (40-MHz sampling rate, 12 bit resolution). With 128 channels, our FPGA-based SA beamformer can achieve 41 frames per second (fps) processing throughput (3.44 × 10(8) pixels per second for frame size of 256 × 256 pixels) at 31.5 W power consumption (1.30 fps/W power efficiency). It utilized 86.9% of the FPGA fabric and operated at a 196.5 MHz clock frequency (after optimization). Based on these findings, we anticipate that FPGA and high-level synthesis can together foster rapid prototyping of real-time ultrasound processor modules at low power consumption budgets.

  8. A Real-Time GPP Software-Defined Radio Testbed for the Physical Layer of Wireless Standards

    NASA Astrophysics Data System (ADS)

    Schiphorst, R.; Hoeksema, F. W.; Slump, C. H.

    2005-12-01

    We present our contribution to the general-purpose-processor-(GPP)-based radio. We describe a baseband software-defined radio testbed for the physical layer of wireless LAN standards. All physical layer functions have been successfully mapped on a Pentium 4 processor that performs these functions in real time. The testbed consists of a transmitter PC with a DAC board and a receiver PC with an ADC board. In our project, we have implemented two different types of standards on this testbed, a continuous-phase-modulation-based standard, Bluetooth, and an OFDM-based standard, HiperLAN/2. However, our testbed can easily be extended to other standards, because the only limitation in our testbed is the maximal channel bandwidth of 20 MHz and of course the processing capabilities of the used PC. The transmitter functions require at most 714 M cycles per second and the receiver functions need 1225 M cycles per second on a Pentium 4 processor. In addition, baseband experiments have been carried out successfully.

  9. Current status of magnetic resonance imaging (MRI) and ultrasonography fusion software platforms for guidance of prostate biopsies.

    PubMed

    Logan, Jennifer K; Rais-Bahrami, Soroush; Turkbey, Baris; Gomella, Andrew; Amalou, Hayet; Choyke, Peter L; Wood, Bradford J; Pinto, Peter A

    2014-11-01

    Prostate MRI is currently the best diagnostic imaging method for detecting PCa. Magnetic resonance imaging (MRI)/ultrasonography (US) fusion allows the sensitivity and specificity of MRI to be combined with the real-time capabilities of transrectal ultrasonography (TRUS). Multiple approaches and techniques exist for MRI/US fusion and include direct 'in bore' MRI biopsies, cognitive fusion, and MRI/US fusion via software-based image coregistration platforms.

  10. Pre-Hardware Optimization of Spacecraft Image Processing Software Algorithms and Hardware Implementation

    NASA Technical Reports Server (NTRS)

    Kizhner, Semion; Flatley, Thomas P.; Hestnes, Phyllis; Jentoft-Nilsen, Marit; Petrick, David J.; Day, John H. (Technical Monitor)

    2001-01-01

    Spacecraft telemetry rates have steadily increased over the last decade presenting a problem for real-time processing by ground facilities. This paper proposes a solution to a related problem for the Geostationary Operational Environmental Spacecraft (GOES-8) image processing application. Although large super-computer facilities are the obvious heritage solution, they are very costly, making it imperative to seek a feasible alternative engineering solution at a fraction of the cost. The solution is based on a Personal Computer (PC) platform and synergy of optimized software algorithms and re-configurable computing hardware technologies, such as Field Programmable Gate Arrays (FPGA) and Digital Signal Processing (DSP). It has been shown in [1] and [2] that this configuration can provide superior inexpensive performance for a chosen application on the ground station or on-board a spacecraft. However, since this technology is still maturing, intensive pre-hardware steps are necessary to achieve the benefits of hardware implementation. This paper describes these steps for the GOES-8 application, a software project developed using Interactive Data Language (IDL) (Trademark of Research Systems, Inc.) on a Workstation/UNIX platform. The solution involves converting the application to a PC/Windows/RC platform, selected mainly by the availability of low cost, adaptable high-speed RC hardware. In order for the hybrid system to run, the IDL software was modified to account for platform differences. It was interesting to examine the gains and losses in performance on the new platform, as well as unexpected observations before implementing hardware. After substantial pre-hardware optimization steps, the necessity of hardware implementation for bottleneck code in the PC environment became evident and solvable beginning with the methodology described in [1], [2], and implementing a novel methodology for this specific application [6]. The PC-RC interface bandwidth problem for the

  11. Automated software for CCD-image processing and detection of small Solar System bodies

    NASA Astrophysics Data System (ADS)

    Savanevych, V.; Bryukhovetskiy, A.; Sokovikova, N.; Bezkrovniy, M.; Khlamov, S.; Elenin, L.; Movsesian, I.; Dihtyar, M.

    2014-07-01

    Efficiency is a crucial factor in the discovery of near-Earth asteroids (NEA) and potentially-hazardous asteroids. Current asteroid surveys yield many images per night. It is no longer possible for the observer to quickly view these images in the the blinking mode. This cause a serious difficulty for large-aperture wide-field telescopes, capturing up to several tens of asteroids in one image. To achieve better asteroid-survey efficiency it is necessary to design and develop automated software for the frame processing. Currently the CoLiTec software solves the problem of the frame processing for asteroid surveys in the real mode. The automatically detected asteroids are subject to follow-up visual confirmation. The CoLiTec software is in use for the automated detection of asteroids in Andrushivka Astronomical Observatory, in the Russian remote observatory ISON-NM (Mayhill, New Mexico, USA), as well as in the observatory ISON-Kislovodsk and in ISON-Ussuriysk starting from the fall 2013. The CoLiTec led to the first automated asteroid and comet discoveries in the CIS (Commonwealth of Independent States) and Baltic countries. In 2012 (2011) 80 (86) % of observations and 74 (75) % of discoveries of asteroids in these countries were made using the CoLiTec. The comet C/2010 X1 (Elenin), discovered using the CoLiTec on December 10, 2010, was the first comet discovered by a CIS astronomer over the past 20 years. In total, out of 7 recently discovered in the CIS and Baltic countries comets 4 comets were discovered due to the CoLiTec, namely C/2010 X1 (Elenin), P/2011 NO1 (Elenin), C/2012 S1 (ISON), and P/2013 V3 (Nevski). About 500,000 CoLiTec-used measurements were reported to MPC, including over 1,500 preliminary discovered objects. These objects include 21 Jupiter Trojan asteroids, 4 NEAs and 1 Centaur. Three other discovered asteroids were reported via dedicated electronic MPC circulars. In 2012 the CoLiTec users were ranked as No. 10, 13, and 22 in the list of the most

  12. Clean Colon Software Program (CCSP), Proposal of a standardized Method to quantify Colon Cleansing During Colonoscopy: Preliminary Results

    PubMed Central

    Rosa-Rizzotto, Erik; Dupuis, Adrian; Guido, Ennio; Caroli, Diego; Monica, Fabio; Canova, Daniele; Cervellin, Erica; Marin, Renato; Trovato, Cristina; Crosta, Cristiano; Cocchio, Silvia; Baldo, Vincenzo; De Lazzari, Franca

    2015-01-01

    Background and study aims: Neoplastic lesions can be missed during colonoscopy, especially when cleansing is inadequate. Bowel preparation scales have significant limitations and no objective and standardized method currently exists to establish colon cleanliness during colonoscopy. The aims of our study are to create a software algorithm that is able to analyze bowel cleansing during colonoscopies and to compare it to a validate bowel preparation scale. Patients and methods: A software application (the Clean Colon Software Program, CCSP) was developed. Fifty colonoscopies were carried out and video-recorded. Each video was divided into 3 segments: cecum-hepatic flexure (1st Segment), hepatic flexure-descending colon (2nd Segment) and rectosigmoid segment (3rd Segment). Each segment was recorded twice, both before and after careful cleansing of the intestinal wall. A score from 0 (dirty) to 3 (clean) was then assigned by CCSP. All the videos were also viewed by four endoscopists and colon cleansing was established using the Boston Bowel Preparation Scale. Interclass correlation coefficient was then calculated between the endoscopists and the software. Results: The cleansing score of the prelavage colonoscopies was 1.56 ± 0.52 and the postlavage one was 2,08 ± 0,59 (P < 0.001) showing an approximate 33.3 % improvement in cleansing after lavage. Right colon segment prelavage (0.99 ± 0.69) was dirtier than left colon segment prelavage (2.07 ± 0.71). The overall interobserver agreement between the average cleansing score for the 4 endoscopists and the software pre-cleansing was 0.87 (95 % CI, 0.84 – 0.90) and post-cleansing was 0.86 (95 % CI, 0.83 – 0.89). Conclusions: The software is able to discriminate clean from non-clean colon tracts with high significance and is comparable to endoscopist evaluation. PMID:26528508

  13. Application of standard and advanced open source GIS software functionality for analysis of coordinates obtained by GNSS measurements

    NASA Astrophysics Data System (ADS)

    Ilieva, Tamara

    2016-04-01

    Currently there is wide variety of GNSS measurements used in the geodetic practice. The coordinates obtained by static, kinematic or precise point positioning GNSS measurements could be analyzed by using the standard functionality of any GIS software, but the open source ones give to the users an opportunity to make themselves advanced functionality. There is an option the coordinates obtained by measurements to be stored in spatial geodatabase and information for the precision and time of measurement to be added. The data could be visualized in different coordinate systems and projections and analyzed by applying different types of spatial analysis. The process also could be automated in high degree. An example with test data is prepared. It includes automated loading of files with coordinates obtained by GNSS measurements and additional information for the precision and the time of measurements. Standard and advanced open source GIS software functionality is used for automation of the analysis process. Also, graph theory is implemented for making time series of the data stored in the spatial geodatabase.

  14. A software tool for stitching two PET/CT body segments into a single whole-body image set.

    PubMed

    Chang, Tingting; Chang, Guoping; Clark, John W; Rohren, Eric M; Mawlawi, Osama R

    2012-05-10

    A whole-body PET/CT scan extending from the vertex of the head to the toes of the patient is not feasible on a number of commercially available PET/CT scanners due to a limitation in the extent of bed travel on these systems. In such cases, the PET scan has to be divided into two parts: one covering the upper body segment, while the other covering the lower body segment. The aim of this paper is to describe and evaluate, using phantom and patient studies, a software tool that was developed to stitch two body segments and output a single whole-body image set, thereby facilitating the interpretation of whole-body PET scans. A mathematical model was first developed to stitch images from two body segments using three landmarks. The model calculates the relative positions of the landmarks on the two segments and then generates a rigid transformation that aligns these landmarks on the two segments. A software tool was written to implement this model while correcting for radioactive decay between the two body segments, and output a single DICOM whole-body image set with all the necessary tags. One phantom, and six patient studies were conducted to evaluate the performance of the software. In these studies, six radio-opaque markers (BBs) were used as landmarks (three on each leg). All studies were acquired in two body segments with BBs placed in the overlap region of the two segments. The PET/CT images of each segment were then stitched using the software tool to create a single DICOM whole-body PET/CT image. Evaluation of the stitching tool was based on visual inspection, consistency of radiotracer uptake in the two segments, and ability to display the resultant DICOM image set on two independent workstations. The software tool successfully stitched the two segments of the phantom image, and generated a single whole-body DICOM PET/CT image set that had the correct alignment and activity concentration throughout the image. The stitched images were viewed by two independent

  15. Digital mapping of side-scan sonar data with the Woods Hole Image Processing System software

    USGS Publications Warehouse

    Paskevich, Valerie F.

    1992-01-01

    Since 1985, the Branch of Atlantic Marine Geology has been involved in collecting, processing and digitally mosaicking high and low resolution sidescan sonar data. In the past, processing and digital mosaicking has been accomplished with a dedicated, shore-based computer system. Recent development of a UNIX-based image-processing software system includes a series of task specific programs for pre-processing sidescan sonar data. To extend the capabilities of the UNIX-based programs, development of digital mapping techniques have been developed. This report describes the initial development of an automated digital mapping procedure. Included is a description of the programs and steps required to complete the digital mosaicking on a UNIXbased computer system, and a comparison of techniques that the user may wish to select.

  16. Comparison between three methods to value lower tear meniscus measured by image software

    NASA Astrophysics Data System (ADS)

    García-Resúa, Carlos; Pena-Verdeal, Hugo; Lira, Madalena; Oliveira, M. Elisabete Real; Giráldez, María. Jesús; Yebra-Pimentel, Eva

    2013-11-01

    To measure different parameters of lower tear meniscus height (TMH) by using photography with open software of measurement. TMH was addressed from lower eyelid to the top of the meniscus (absolute TMH) and to the brightest meniscus reflex (reflex TMH). 121 young healthy subjects were included in the study. The lower tear meniscus was videotaped by a digital camera attached to a slit lamp. Three videos were recorded in central meniscus portion on three different methods: slit lamp without fluorescein instillation, slit lamp with fluorescein instillation and TearscopeTM without fluorescein instillation. Then, a masked observed obtained an image from each video and measured TMH by using open source software of measurement based on Java (NIH ImageJ). Absolute central (TMH-CA), absolute with fluorescein (TMH-F) and absolute using the Tearscope (TMH-Tc) were compared each other as well as reflex central (TMH-CR) and reflex Tearscope (TMH-TcR). Mean +/- S.D. values of TMH-CA, TMH-CR, TMH-F, TMH-Tc and TMH-TcR of 0.209 +/- 0.049, 0.139 +/- 0.031, 0.222 +/- 0.058, 0.175 +/- 0.045 and 0.109 +/- 0.029 mm, respectively were found. Paired t-test was performed for the relationship between TMH-CA - TMH-CR, TMH-CA - TMH-F, TMH-CA - TMH-Tc, TMH-F - TMH-Tc, TMH-Tc - TMH-TcR and TMH-CR - TMH-TcR. In all cases, it was found a significant difference between both variables (all p < 0.008). This study showed a useful tool to objectively measure TMH by photography. Eye care professionals should maintain the same TMH parameter in the follow-up visits, due to the difference between them.

  17. SU-E-J-264: Comparison of Two Commercially Available Software Platforms for Deformable Image Registration

    SciTech Connect

    Tuohy, R; Stathakis, S; Mavroidis, P; Bosse, C; Papanikolaou, N

    2014-06-01

    Purpose: To evaluate and compare the deformable image registration algorithms available in the Velocity (Velocity Medical Solutions, Atlanta, GA) and RayStation (RaySearch Americas, Inc., Garden city NY). Methods: Ten consecutive patient cone beam CTs (CBCT) for each fraction were collected. The CBCTs along with the simulation CT were exported to the Velocity and the RayStation software. Each CBCT was registered using deformable image registration to the simulation CT and the resulting deformable vector matrix was generated. Each registration was visually inspected by a physicist and the prescribing physician. The volumes of the critical organs were calculated for each deformable CT and used for comparison. Results: The resulting deformable registrations revealed differences between the two algorithms. These differences were realized when the organs at risk were contoured on each deformed CBCT. Differences in the order of 10% ±30% in volume were observed for bladder, 17 ±21% for rectum and 16±10% for sigmoid. The prostate and PTV volume differences were in the order of 3±5%. The volumetric differences observed had a respective impact on the DVHs of all organs at risk. Differences of 8–10% in the mean dose were observed for all organs above. Conclusion: Deformable registration is a powerful tool that aids in the definition of critical structures and is often used for the evaluation of daily dose delivered to the patient. It should be noted that extended QA should be performed before clinical implementation of the software and the users should be aware of advantages and limitations of the methods.

  18. Evaluation of cassette-based digital radiography detectors using standardized image quality metrics: AAPM TG-150 Draft Image Detector Tests.

    PubMed

    Li, Guang; Greene, Travis C; Nishino, Thomas K; Willis, Charles E

    2016-09-01

    The purpose of this study was to evaluate several of the standardized image quality metrics proposed by the American Association of Physics in Medicine (AAPM) Task Group 150. The task group suggested region-of-interest (ROI)-based techniques to measure nonuniformity, minimum signal-to-noise ratio (SNR), number of anomalous pixels, and modulation transfer function (MTF). This study evaluated the effects of ROI size and layout on the image metrics by using four different ROI sets, assessed result uncertainty by repeating measurements, and compared results with two commercially available quality control tools, namely the Carestream DIRECTVIEW Total Quality Tool (TQT) and the GE Healthcare Quality Assurance Process (QAP). Seven Carestream DRX-1C (CsI) detectors on mobile DR systems and four GE FlashPad detectors in radiographic rooms were tested. Images were analyzed using MATLAB software that had been previously validated and reported. Our values for signal and SNR nonuniformity and MTF agree with values published by other investigators. Our results show that ROI size affects nonuniformity and minimum SNR measurements, but not detection of anomalous pixels. Exposure geometry affects all tested image metrics except for the MTF. TG-150 metrics in general agree with the TQT, but agree with the QAP only for local and global signal nonuniformity. The difference in SNR nonuniformity and MTF values between the TG-150 and QAP may be explained by differences in the calculation of noise and acquisition beam quality, respectively. TG-150's SNR nonuniformity metrics are also more sensitive to detector nonuniformity compared to the QAP. Our results suggest that fixed ROI size should be used for consistency because nonuniformity metrics depend on ROI size. Ideally, detector tests should be performed at the exact calibration position. If not feasible, a baseline should be established from the mean of several repeated measurements. Our study indicates that the TG-150 tests can be

  19. Fundus image fusion in EYEPLAN software: An evaluation of a novel technique for ocular melanoma radiation treatment planning

    SciTech Connect

    Daftari, Inder K.; Mishra, Kavita K.; O'Brien, Joan M.; and others

    2010-10-15

    Purpose: The purpose of this study is to evaluate a novel approach for treatment planning using digital fundus image fusion in EYEPLAN for proton beam radiation therapy (PBRT) planning for ocular melanoma. The authors used a prototype version of EYEPLAN software, which allows for digital registration of high-resolution fundus photographs. The authors examined the improvement in tumor localization by replanning with the addition of fundus photo superimposition in patients with macular area tumors. Methods: The new version of EYEPLAN (v3.05) software allows for the registration of fundus photographs as a background image. This is then used in conjunction with clinical examination, tantalum marker clips, surgeon's mapping, and ultrasound to draw the tumor contour accurately. In order to determine if the fundus image superimposition helps in tumor delineation and treatment planning, the authors identified 79 patients with choroidal melanoma in the macular location that were treated with PBRT. All patients were treated to a dose of 56 GyE in four fractions. The authors reviewed and replanned all 79 macular melanoma cases with superimposition of pretreatment and post-treatment fundus imaging in the new EYEPLAN software. For patients with no local failure, the authors analyzed whether fundus photograph fusion accurately depicted and confirmed tumor volumes as outlined in the original treatment plan. For patients with local failure, the authors determined whether the addition of the fundus photograph might have benefited in terms of more accurate tumor volume delineation. Results: The mean follow-up of patients was 33.6{+-}23 months. Tumor growth was seen in six eyes of the 79 macular lesions. All six patients were marginal failures or tumor miss in the region of dose fall-off, including one patient with both in-field recurrence as well as marginal. Among the six recurrences, three were managed by enucleation and one underwent retreatment with proton therapy. Three

  20. WE-G-BRD-07: Automated MR Image Standardization and Auto-Contouring Strategy for MRI-Based Adaptive Brachytherapy for Cervix Cancer

    SciTech Connect

    Saleh, H Al; Erickson, B; Paulson, E

    2015-06-15

    Purpose: MRI-based adaptive brachytherapy (ABT) is an emerging treatment modality for patients with gynecological tumors. However, MR image intensity non-uniformities (IINU) can vary from fraction to fraction, complicating image interpretation and auto-contouring accuracy. We demonstrate here an automated MR image standardization and auto-contouring strategy for MRI-based ABT of cervix cancer. Methods: MR image standardization consisted of: 1) IINU correction using the MNI N3 algorithm, 2) noise filtering using anisotropic diffusion, and 3) signal intensity normalization using the volumetric median. This post-processing chain was implemented as a series of custom Matlab and Java extensions in MIM (v6.4.5, MIM Software) and was applied to 3D T2 SPACE images of six patients undergoing MRI-based ABT at 3T. Coefficients of variation (CV=σ/µ) were calculated for both original and standardized images and compared using Mann-Whitney tests. Patient-specific cumulative MR atlases of bladder, rectum, and sigmoid contours were constructed throughout ABT, using original and standardized MR images from all previous ABT fractions. Auto-contouring was performed in MIM two ways: 1) best-match of one atlas image to the daily MR image, 2) multi-match of all previous fraction atlas images to the daily MR image. Dice’s Similarity Coefficients (DSCs) were calculated for auto-generated contours relative to reference contours for both original and standardized MR images and compared using Mann-Whitney tests. Results: Significant improvements in CV were detected following MR image standardization (p=0.0043), demonstrating an improvement in MR image uniformity. DSCs consistently increased for auto-contoured bladder, rectum, and sigmoid following MR image standardization, with the highest DSCs detected when the combination of MR image standardization and multi-match cumulative atlas-based auto-contouring was utilized. Conclusion: MR image standardization significantly improves MR image

  1. A flexible software architecture for scalable real-time image and video processing applications

    NASA Astrophysics Data System (ADS)

    Usamentiaga, Rubén; Molleda, Julio; García, Daniel F.; Bulnes, Francisco G.

    2012-06-01

    Real-time image and video processing applications require skilled architects, and recent trends in the hardware platform make the design and implementation of these applications increasingly complex. Many frameworks and libraries have been proposed or commercialized to simplify the design and tuning of real-time image processing applications. However, they tend to lack flexibility because they are normally oriented towards particular types of applications, or they impose specific data processing models such as the pipeline. Other issues include large memory footprints, difficulty for reuse and inefficient execution on multicore processors. This paper presents a novel software architecture for real-time image and video processing applications which addresses these issues. The architecture is divided into three layers: the platform abstraction layer, the messaging layer, and the application layer. The platform abstraction layer provides a high level application programming interface for the rest of the architecture. The messaging layer provides a message passing interface based on a dynamic publish/subscribe pattern. A topic-based filtering in which messages are published to topics is used to route the messages from the publishers to the subscribers interested in a particular type of messages. The application layer provides a repository for reusable application modules designed for real-time image and video processing applications. These modules, which include acquisition, visualization, communication, user interface and data processing modules, take advantage of the power of other well-known libraries such as OpenCV, Intel IPP, or CUDA. Finally, we present different prototypes and applications to show the possibilities of the proposed architecture.

  2. Free digital image analysis software helps to resolve equivocal scores in HER2 immunohistochemistry.

    PubMed

    Helin, Henrik O; Tuominen, Vilppu J; Ylinen, Onni; Helin, Heikki J; Isola, Jorma

    2016-02-01

    Evaluation of human epidermal growth factor receptor 2 (HER2) immunohistochemistry (IHC) is subject to interobserver variation and lack of reproducibility. Digital image analysis (DIA) has been shown to improve the consistency and accuracy of the evaluation and its use is encouraged in current testing guidelines. We studied whether digital image analysis using a free software application (ImmunoMembrane) can assist in interpreting HER2 IHC in equivocal 2+ cases. We also compared digital photomicrographs with whole-slide images (WSI) as material for ImmunoMembrane DIA. We stained 750 surgical resection specimens of invasive breast cancers immunohistochemically for HER2 and analysed staining with ImmunoMembrane. The ImmunoMembrane DIA scores were compared with the originally responsible pathologists' visual scores, a researcher's visual scores and in situ hybridisation (ISH) results. The originally responsible pathologists reported 9.1 % positive 3+ IHC scores, for the researcher this was 8.4 % and for ImmunoMembrane 9.5 %. Equivocal 2+ scores were 34 % for the pathologists, 43.7 % for the researcher and 10.1 % for ImmunoMembrane. Negative 0/1+ scores were 57.6 % for the pathologists, 46.8 % for the researcher and 80.8 % for ImmunoMembrane. There were six false positive cases, which were classified as 3+ by ImmunoMembrane and negative by ISH. Six cases were false negative defined as 0/1+ by IHC and positive by ISH. ImmunoMembrane DIA using digital photomicrographs and WSI showed almost perfect agreement. In conclusion, digital image analysis by ImmunoMembrane can help to resolve a majority of equivocal 2+ cases in HER2 IHC, which reduces the need for ISH testing.

  3. Standardized platform for coregistration of nonconcurrent diffuse optical and magnetic resonance breast images obtained in different geometries.

    PubMed

    Azar, Fred S; Lee, Kijoon; Khamene, Ali; Choe, Regine; Corlu, Alper; Konecky, Soren D; Sauer, Frank; Yodh, Arjun G

    2007-01-01

    We present a novel methodology for combining breast image data obtained at different times, in different geometries, and by different techniques. We combine data based on diffuse optical tomography (DOT) and magnetic resonance imaging (MRI). The software platform integrates advanced multimodal registration and segmentation algorithms, requires minimal user experience, and employs computationally efficient techniques. The resulting superposed 3-D tomographs facilitate tissue analyses based on structural and functional data derived from both modalities, and readily permit enhancement of DOT data reconstruction using MRI-derived a-priori structural information. We demonstrate the multimodal registration method using a simulated phantom, and we present initial patient studies that confirm that tumorous regions in a patient breast found by both imaging modalities exhibit significantly higher total hemoglobin concentration (THC) than surrounding normal tissues. The average THC in the tumorous regions is one to three standard deviations larger than the overall breast average THC for all patients.

  4. Calculation of residence times and radiation doses using the standard PC software Excel.

    PubMed

    Herzog, H; Zilken, H; Niederbremer, A; Friedrich, W; Müller-Gärtner, H W

    1997-12-01

    We developed a program which aims to facilitate the calculation of radiation doses to single organs and the whole body. IMEDOSE uses Excel to include calculations, graphical displays, and interactions with the user in a single general-purpose PC software tool. To start the procedure the input data are copied into a spreadsheet. They must represent percentage uptake values of several organs derived from measurements in animals or humans. To extrapolate these data up to seven half-lives of the radionuclide, fitting to one or two exponentional functions is included and can be checked by the user. By means of the approximate time-activity information the cumulated activity or residence times are calculated. Finally these data are combined with the absorbed fraction doses (S-values) given by MIRD pamphlet No. 11 to yield radiation doses, the effective dose equivalent and the effective dose. These results are presented in a final table. Interactions are realized with push-buttons and drop-down menus. Calculations use the Visual Basic tool of Excel. In order to test our program, biodistribution data of fluorine-18 fluorodeoxyglucose were taken from the literature (Meija et al., J Nucl Med 1991; 32:699-706). For a 70-kg adult the resulting radiation doses of all target organs listed in MIRD 11 were different from the ICRP 53 values by 1%+/-18% on the average. When the residence times were introduced into MIRDOSE3 (Stabin, J Nucl Med 1996; 37:538-546) the mean difference between our results and those of MIRDOSE3 was -3%+/-6%. Both outcomes indicate the validity of the present approach.

  5. SU-E-I-13: Evaluation of Metal Artifact Reduction (MAR) Software On Computed Tomography (CT) Images

    SciTech Connect

    Huang, V; Kohli, K

    2015-06-15

    Purpose: A new commercially available metal artifact reduction (MAR) software in computed tomography (CT) imaging was evaluated with phantoms in the presence of metals. The goal was to assess the ability of the software to restore the CT number in the vicinity of the metals without impacting the image quality. Methods: A Catphan 504 was scanned with a GE Optima RT 580 CT scanner (GE Healthcare, Milwaukee, WI) and the images were reconstructed with and without the MAR software. Both datasets were analyzed with Image Owl QA software (Image Owl Inc, Greenwich, NY). CT number sensitometry, MTF, low contrast, uniformity, noise and spatial accuracy were compared for scans with and without MAR software. In addition, an in-house made phantom was scanned with and without a stainless steel insert at three different locations. The accuracy of the CT number and metal insert dimension were investigated as well. Results: Comparisons between scans with and without MAR algorithm on the Catphan phantom demonstrate similar results for image quality. However, noise was slightly higher for the MAR algorithm. Evaluation of the CT number at various locations of the in-house made phantom was also performed. The baseline HU, obtained from the scan without metal insert, was compared to scans with the stainless steel insert at 3 different locations. The HU difference between the baseline scan versus metal scan was improved when the MAR algorithm was applied. In addition, the physical diameter of the stainless steel rod was over-estimated by the MAR algorithm by 0.9 mm. Conclusion: This work indicates with the presence of metal in CT scans, the MAR algorithm is capable of providing a more accurate CT number without compromising the overall image quality. Future work will include the dosimetric impact on the MAR algorithm.

  6. 3.0 Tesla magnetic resonance imaging: A new standard in liver imaging?

    PubMed

    Girometti, Rossano

    2015-07-28

    An ever-increasing number of 3.0 Tesla (T) magnets are installed worldwide. Moving from the standard of 1.5 T to higher field strength implies a number of potential advantage and drawbacks, requiring careful optimization of imaging protocols or implementation of novel hardware components. Clinical practice and literature review suggest that state-of-the-art 3.0 T is equivalent to 1.5 T in the assessment of focal liver lesions and diffuse liver disease. Therefore, further technical improvements are needed in order to fully exploit the potential of higher field strength.

  7. 3.0 Tesla magnetic resonance imaging: A new standard in liver imaging?

    PubMed Central

    Girometti, Rossano

    2015-01-01

    An ever-increasing number of 3.0 Tesla (T) magnets are installed worldwide. Moving from the standard of 1.5 T to higher field strength implies a number of potential advantage and drawbacks, requiring careful optimization of imaging protocols or implementation of novel hardware components. Clinical practice and literature review suggest that state-of-the-art 3.0 T is equivalent to 1.5 T in the assessment of focal liver lesions and diffuse liver disease. Therefore, further technical improvements are needed in order to fully exploit the potential of higher field strength. PMID:26244063

  8. WCPS: An Open Geospatial Consortium Standard Applied to Flight Hardware/Software

    NASA Astrophysics Data System (ADS)

    Cappelaere, P. G.; Mandl, D.; Stanley, J.; Frye, S.; Baumann, P.

    2009-12-01

    The Open GeoSpatial Consortium Web Coverage Processing Service (WCPS) has the potential to allow advanced users to define processing algorithms using the web environment and seamlessly provide the capability to upload them directly to the satellite for autonomous execution using smart agent technology. The Open Geospatial Consortium recently announced the adoption of a specification for a Web Coverage Processing Service on Mar 25, 2009. This effort has been spearheaded by Dr. Peter Baumann, Jacobs University, Bremen, Germany. The WCPS specifies a coverage processing language allowing clients to send processing requests for evaluation to a server. NASA has been taking the next step by wrapping the user-defined requests into dynamic agents that can be uploaded to a spacecraft for onboard processing. This could have a dramatic impact to the new decadal missions such as HyspIRI. Dynamic onboard classifiers are key to providing level 2 products in near-realtime directly to end-users on the ground. This capability, currently implemented on the Hyspiri pathfinder testbed using the NASA SpaceCube, will be demonstrated on EO-1, a NASA Hyperspectral/Multispectral imager, as the next capability for agile autonomous science experiments.

  9. Caltech/JPL Conference on Image Processing Technology, Data Sources and Software for Commercial and Scientific Applications

    NASA Technical Reports Server (NTRS)

    Redmann, G. H.

    1976-01-01

    Recent advances in image processing and new applications are presented to the user community to stimulate the development and transfer of this technology to industrial and commercial applications. The Proceedings contains 37 papers and abstracts, including many illustrations (some in color) and provides a single reference source for the user community regarding the ordering and obtaining of NASA-developed image-processing software and science data.

  10. Cloud computing geospatial application for water resources based on free and open source software and open standards - a prototype

    NASA Astrophysics Data System (ADS)

    Delipetrev, Blagoj

    2016-04-01

    Presently, most of the existing software is desktop-based, designed to work on a single computer, which represents a major limitation in many ways, starting from limited computer processing, storage power, accessibility, availability, etc. The only feasible solution lies in the web and cloud. This abstract presents research and development of a cloud computing geospatial application for water resources based on free and open source software and open standards using hybrid deployment model of public - private cloud, running on two separate virtual machines (VMs). The first one (VM1) is running on Amazon web services (AWS) and the second one (VM2) is running on a Xen cloud platform. The presented cloud application is developed using free and open source software, open standards and prototype code. The cloud application presents a framework how to develop specialized cloud geospatial application that needs only a web browser to be used. This cloud application is the ultimate collaboration geospatial platform because multiple users across the globe with internet connection and browser can jointly model geospatial objects, enter attribute data and information, execute algorithms, and visualize results. The presented cloud application is: available all the time, accessible from everywhere, it is scalable, works in a distributed computer environment, it creates a real-time multiuser collaboration platform, the programing languages code and components are interoperable, and it is flexible in including additional components. The cloud geospatial application is implemented as a specialized water resources application with three web services for 1) data infrastructure (DI), 2) support for water resources modelling (WRM), 3) user management. The web services are running on two VMs that are communicating over the internet providing services to users. The application was tested on the Zletovica river basin case study with concurrent multiple users. The application is a state

  11. An image analysis pipeline for the semi-automated analysis of clinical fMRI images based on freely available software.

    PubMed

    Karmonik, Christof; York, Michele; Grossman, Robert; Kakkar, Ekta; Patel, Krutina; Haykal, Hani; King, David

    2010-03-01

    The technique of functional Magnetic Resonance Imaging (fMRI) has evolved in the last 15 years from a research concept into a clinically relevant medical procedure. In this study, an efficient, semi-automated and cost-effective solution for the analysis of fMRI images acquired in a clinical setting is presented relying heavily on open source software. The core of the pipeline is the software Analysis of Functional NeuroImages (AFNI, National Institute of Mental Health (NIMH)) combined with K-PACS and ImageJ. Its application is illustrated with clinical fMRI exams and with a research study involving comparing subjects diagnosed with Parkinson's disease and age-matched controls.

  12. eWaterCycle: Building an operational global Hydrological forecasting system based on standards and open source software

    NASA Astrophysics Data System (ADS)

    Drost, Niels; Bierkens, Marc; Donchyts, Gennadii; van de Giesen, Nick; Hummel, Stef; Hut, Rolf; Kockx, Arno; van Meersbergen, Maarten; Sutanudjaja, Edwin; Verlaan, Martin; Weerts, Albrecht; Winsemius, Hessel

    2015-04-01

    At EGU 2015, the eWaterCycle project (www.ewatercycle.org) will launch an operational high-resolution Hydrological global model, including 14 day ensemble forecasts. Within the eWaterCycle project we aim to use standards and open source software as much as possible. This ensures the sustainability of the software created, and the ability to swap out components as newer technologies and solutions become available. It also allows us to build the system much faster than would otherwise be the case. At the heart of the eWaterCycle system is the PCRGLOB-WB Global Hydrological model (www.globalhydrology.nl) developed at Utrecht University. Version 2.0 of this model is implemented in Python, and models a wide range of Hydrological processes at 10 x 10km (and potentially higher) resolution. To assimilate near-real time satellite data into the model, and run an ensemble forecast we use the OpenDA system (www.openda.org). This allows us to make use of different data assimilation techniques without the need to implement these from scratch. As a data assimilation technique we currently use (variant of) an Ensemble Kalman Filter, specifically optimized for High Performance Computing environments. Coupling of the model with the DA is done with the Basic Model Interface (BMI), developed in the framework of the Community Surface Dynamics Modeling System (CSDMS) (csdms.colorado.edu). We have added support for BMI to PCRGLOB-WB, and developed a BMI adapter for OpenDA, allowing OpenDA to use any BMI compatible model. We currently use multiple different BMI models with OpenDA, already showing the benefits of using this standard. Throughout the system, all file based input and output is done via NetCDF files. We use several standard tools to be used for pre- and post-processing data. Finally we use ncWMS, an NetCDF based implementation of the Web Map Service (WMS) protocol to serve the forecasting result. We have build a 3D web application based on Cesium.js to visualize the output. In

  13. FBI wavelet/scalar quantization standard for gray-scale fingerprint image compression

    NASA Astrophysics Data System (ADS)

    Bradley, Jonathan N.; Brislawn, Christopher M.; Hopper, Thomas

    1993-08-01

    The FBI has recently adopted a standard for the compression of digitized 8-bit gray-scale fingerprint images. The standard is based on scalar quantization of a 64-subband discrete wavelet transform decomposition of the images, followed by Huffman coding. Novel features of the algorithm include the use of symmetric boundary conditions for transforming finite- length signals and a subband decomposition tailored for fingerprint images scanned at 500 dpi. The standard is intended for use in conjunction with ANSI/NBS-CLS 1-1993, American National Standard Data Format for the Interchange of Fingerprint Information, and the FBI's Integrated Automated Fingerprint Identification System.

  14. The FBI wavelet/scalar quantization standard for gray-scale fingerprint image compression

    SciTech Connect

    Bradley, J.N.; Brislawn, C.M. ); Hopper, T. )

    1993-01-01

    The FBI has recently adopted a standard for the compression of digitized 8-bit gray-scale fingerprint images. The standard is based on scalar quantization of a 64-subband discrete wavelet transform decomposition of the images, followed by Huffman coding. Novel features of the algorithm include the use of symmetric boundary conditions for transforming finite-length signals and a subband decomposition tailored for fingerprint images scanned at 500 dpi. The standard is intended for use in conjunction with ANSI/NBS-CLS 1-1993, American National Standard Data Format for the Interchange of Fingerprint Information, and the FBI's Integrated Automated Fingerprint Identification System.

  15. The FBI wavelet/scalar quantization standard for gray-scale fingerprint image compression

    SciTech Connect

    Bradley, J.N.; Brislawn, C.M.; Hopper, T.

    1993-05-01

    The FBI has recently adopted a standard for the compression of digitized 8-bit gray-scale fingerprint images. The standard is based on scalar quantization of a 64-subband discrete wavelet transform decomposition of the images, followed by Huffman coding. Novel features of the algorithm include the use of symmetric boundary conditions for transforming finite-length signals and a subband decomposition tailored for fingerprint images scanned at 500 dpi. The standard is intended for use in conjunction with ANSI/NBS-CLS 1-1993, American National Standard Data Format for the Interchange of Fingerprint Information, and the FBI`s Integrated Automated Fingerprint Identification System.

  16. Applying and extending ISO/TC42 digital camera resolution standards to mobile imaging products

    NASA Astrophysics Data System (ADS)

    Williams, Don; Burns, Peter D.

    2007-01-01

    There are no fundamental differences between today's mobile telephone cameras and consumer digital still cameras that suggest many existing ISO imaging performance standards do not apply. To the extent that they have lenses, color filter arrays, detectors, apertures, image processing, and are hand held, there really are no operational or architectural differences. Despite this, there are currently differences in the levels of imaging performance. These are driven by physical and economic constraints, and image-capture conditions. Several ISO standards for resolution, well established for digital consumer digital cameras, require care when applied to the current generation of cell phone cameras. In particular, accommodation of optical flare, shading non-uniformity and distortion are recommended. We offer proposals for the application of existing ISO imaging resolution performance standards to mobile imaging products, and suggestions for extending performance standards to the characteristic behavior of camera phones.

  17. 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.

  18. 3D reconstruction of SEM images by use of optical photogrammetry software.

    PubMed

    Eulitz, Mona; Reiss, Gebhard

    2015-08-01

    Reconstruction of the three-dimensional (3D) surface of an object to be examined is widely used for structure analysis in science and many biological questions require information about their true 3D structure. For Scanning Electron Microscopy (SEM) there has been no efficient non-destructive solution for reconstruction of the surface morphology to date. The well-known method of recording stereo pair images generates a 3D stereoscope reconstruction of a section, but not of the complete sample surface. We present a simple and non-destructive method of 3D surface reconstruction from SEM samples based on the principles of optical close range photogrammetry. In optical close range photogrammetry a series of overlapping photos is used to generate a 3D model of the surface of an object. We adapted this method to the special SEM requirements. Instead of moving a detector around the object, the object itself was rotated. A series of overlapping photos was stitched and converted into a 3D model using the software commonly used for optical photogrammetry. A rabbit kidney glomerulus was used to demonstrate the workflow of this adaption. The reconstruction produced a realistic and high-resolution 3D mesh model of the glomerular surface. The study showed that SEM micrographs are suitable for 3D reconstruction by optical photogrammetry. This new approach is a simple and useful method of 3D surface reconstruction and suitable for various applications in research and teaching.

  19. ORBS: A data reduction software for the imaging Fourier transform spectrometers SpIOMM and SITELLE

    NASA Astrophysics Data System (ADS)

    Martin, T.; Drissen, L.; Joncas, G.

    2012-09-01

    SpIOMM (Spectromètre-Imageur de l'Observatoire du Mont Mégantic) is still the only operational astronomical Imaging Fourier Transform Spectrometer (IFTS) capable of obtaining the visible spectrum of every source of light in a field of view of 12 arc-minutes. Even if it has been designed to work with both outputs of the Michelson interferometer, up to now only one output has been used. Here we present ORBS (Outils de Réduction Binoculaire pour SpIOMM/SITELLE), the reduction software we designed in order to take advantage of the two output data. ORBS will also be used to reduce the data of SITELLE (Spectromètre-Imageur pour l' Étude en Long et en Large des raies d' Émissions) { the direct successor of SpIOMM, which will be in operation at the Canada-France- Hawaii Telescope (CFHT) in early 2013. SITELLE will deliver larger data cubes than SpIOMM (up to 2 cubes of 34 Go each). We thus have made a strong effort in optimizing its performance efficiency in terms of speed and memory usage in order to ensure the best compliance with the quality characteristics discussed with the CFHT team. As a result ORBS is now capable of reducing 68 Go of data in less than 20 hours using only 5 Go of random-access memory (RAM).

  20. I-SPINE: a software package for advances in image-guided and minimally invasive spine procedures

    NASA Astrophysics Data System (ADS)

    Choi, Jae Jeong; Cleary, Kevin R.; Zeng, Jianchao; Gary, Kevin A.; Freedman, Matthew T.; Watson, Vance; Lindisch, David; Mun, Seong K.

    2000-05-01

    While image guidance is now routinely used in the brain in the form of frameless stereotaxy, it is beginning to be more widely used in other clinical areas such as the spine. At Georgetown University Medical Center, we are developing a program to provide advanced visualization and image guidance for minimally invasive spine procedures. This is a collaboration between an engineering-based research group and physicians from the radiology, neurosurgery, and orthopaedics departments. A major component of this work is the ISIS Center Spine Procedures Imaging and Navigation Engine, which is a software package under development as the base platform for technical advances.

  1. Army technology development. IBIS query. Software to support the Image Based Information System (IBIS) expansion for mapping, charting and geodesy

    NASA Technical Reports Server (NTRS)

    Friedman, S. Z.; Walker, R. E.; Aitken, R. B.

    1986-01-01

    The Image Based Information System (IBIS) has been under development at the Jet Propulsion Laboratory (JPL) since 1975. It is a collection of more than 90 programs that enable processing of image, graphical, tabular data for spatial analysis. IBIS can be utilized to create comprehensive geographic data bases. From these data, an analyst can study various attributes describing characteristics of a given study area. Even complex combinations of disparate data types can be synthesized to obtain a new perspective on spatial phenomena. In 1984, new query software was developed enabling direct Boolean queries of IBIS data bases through the submission of easily understood expressions. An improved syntax methodology, a data dictionary, and display software simplified the analysts' tasks associated with building, executing, and subsequently displaying the results of a query. The primary purpose of this report is to describe the features and capabilities of the new query software. A secondary purpose of this report is to compare this new query software to the query software developed previously (Friedman, 1982). With respect to this topic, the relative merits and drawbacks of both approaches are covered.

  2. Standards of ultrasound imaging of the adrenal glands.

    PubMed

    Słapa, Rafał Z; Jakubowski, Wiesław S; Dobruch-Sobczak, Katarzyna; Kasperlik-Załuska, Anna A

    2015-12-01

    Adrenal glands are paired endocrine glands located over the upper renal poles. Adrenal pathologies have various clinical presentations. They can coexist with the hyperfunction of individual cortical zones or the medulla, insufficiency of the adrenal cortex or retained normal hormonal function. The most common adrenal masses are tumors incidentally detected in imaging examinations (ultrasound, tomography, magnetic resonance imaging), referred to as incidentalomas. They include a range of histopathological entities but cortical adenomas without hormonal hyperfunction are the most common. Each abdominal ultrasound scan of a child or adult should include the assessment of the suprarenal areas. If a previously non-reported, incidental solid focal lesion exceeding 1 cm (incidentaloma) is detected in the suprarenal area, computed tomography or magnetic resonance imaging should be conducted to confirm its presence and for differentiation and the tumor functional status should be determined. Ultrasound imaging is also used to monitor adrenal incidentaloma that is not eligible for a surgery. The paper presents recommendations concerning the performance and assessment of ultrasound examinations of the adrenal glands and their pathological lesions. The article includes new ultrasound techniques, such as tissue harmonic imaging, spatial compound imaging, three-dimensional ultrasound, elastography, contrast-enhanced ultrasound and parametric imaging. The guidelines presented above are consistent with the recommendations of the Polish Ultrasound Society.

  3. Thoughts on standardization of parameters for image evaluation

    NASA Technical Reports Server (NTRS)

    Billingsley, F. C.

    1976-01-01

    Images received for image processing and analysis are obtained from a wide variety of sources and with a wide variety of sensors. Because it is desirable to have image processing algorithms be as universally applicable as possible, they should be designed, where possible, to be insensitive to the parametric variations of the source material. Where this is not possible, these variations must be taken into account. Therefore, it is necessary to consider what parameters may be defined in common across a suite of image types. Objective parameters or measurements of images which, in the proper combinations, may serve as surrogates for real images may be pixel-specific, location dependent, or combinations thereof. Parameters which have proven useful in defining the characteristics of images include the gray scale linearity, granularity of the quantization, spectral content, geometrical fidelity, resolution of the system expressed as either the point spread function or the modulation transfer function, and the spatial frequency content and characteristics of the data itself.

  4. IRCAMDR: IRCAM3 Data Reduction Software

    NASA Astrophysics Data System (ADS)

    Aspin, Colin; McCaughrean, Mark; Bridger, Alan B.; Baines, Dave; Beard, Steven; Chan, S.; Giddings, Jack; Hartley, K. F.; Horsfield, A. P.; Kelly, B. D.; Emerson, J. P.; Currie, Malcolm J.; Economou, Frossie

    2014-06-01

    The UKIRT IRCAM3 data reduction and analysis software package, IRCAMDR (formerly ircam_clred) analyzes and displays any 2D data image stored in the standard Starlink (ascl:1110.012) NDF data format. It reduces and analyzes IRCAM1/2 data images of 62x58 pixels and IRCAM3 images of 256x256 size. Most of the applications will work on NDF images of any physical (pixel) dimensions, for example, 1024x1024 CCD images can be processed.

  5. Analyses of requirements for computer control and data processing experiment subsystems: Image data processing system (IDAPS) software description (7094 version), volume 2

    NASA Technical Reports Server (NTRS)

    1973-01-01

    A description of each of the software modules of the Image Data Processing System (IDAPS) is presented. The changes in the software modules are the result of additions to the application software of the system and an upgrade of the IBM 7094 Mod(1) computer to a 1301 disk storage configuration. Necessary information about IDAPS sofware is supplied to the computer programmer who desires to make changes in the software system or who desires to use portions of the software outside of the IDAPS system. Each software module is documented with: module name, purpose, usage, common block(s) description, method (algorithm of subroutine) flow diagram (if needed), subroutines called, and storage requirements.

  6. The 'Densitometric Image Analysis Software' and its application to determine stepwise equilibrium constants from electrophoretic mobility shift assays.

    PubMed

    van Oeffelen, Liesbeth; Peeters, Eveline; Nguyen Le Minh, Phu; Charlier, Daniël

    2014-01-01

    Current software applications for densitometric analysis, such as ImageJ, QuantityOne (BioRad) and the Intelligent or Advanced Quantifier (Bio Image) do not allow to take the non-linearity of autoradiographic films into account during calibration. As a consequence, quantification of autoradiographs is often regarded as problematic, and phosphorimaging is the preferred alternative. However, the non-linear behaviour of autoradiographs can be described mathematically, so it can be accounted for. Therefore, the 'Densitometric Image Analysis Software' has been developed, which allows to quantify electrophoretic bands in autoradiographs, as well as in gels and phosphorimages, while providing optimized band selection support to the user. Moreover, the program can determine protein-DNA binding constants from Electrophoretic Mobility Shift Assays (EMSAs). For this purpose, the software calculates a chosen stepwise equilibrium constant for each migration lane within the EMSA, and estimates the errors due to non-uniformity of the background noise, smear caused by complex dissociation or denaturation of double-stranded DNA, and technical errors such as pipetting inaccuracies. Thereby, the program helps the user to optimize experimental parameters and to choose the best lanes for estimating an average equilibrium constant. This process can reduce the inaccuracy of equilibrium constants from the usual factor of 2 to about 20%, which is particularly useful when determining position weight matrices and cooperative binding constants to predict genomic binding sites. The MATLAB source code, platform-dependent software and installation instructions are available via the website http://micr.vub.ac.be.

  7. Parameter-based estimation of CT dose index and image quality using an in-house android™-based software

    NASA Astrophysics Data System (ADS)

    Mubarok, S.; Lubis, L. E.; Pawiro, S. A.

    2016-03-01

    Compromise between radiation dose and image quality is essential in the use of CT imaging. CT dose index (CTDI) is currently the primary dosimetric formalisms in CT scan, while the low and high contrast resolutions are aspects indicating the image quality. This study was aimed to estimate CTDIvol and image quality measures through a range of exposure parameters variation. CTDI measurements were performed using PMMA (polymethyl methacrylate) phantom of 16 cm diameter, while the image quality test was conducted by using catphan ® 600. CTDI measurements were carried out according to IAEA TRS 457 protocol using axial scan mode, under varied parameters of tube voltage, collimation or slice thickness, and tube current. Image quality test was conducted accordingly under the same exposure parameters with CTDI measurements. An Android™ based software was also result of this study. The software was designed to estimate the value of CTDIvol with maximum difference compared to actual CTDIvol measurement of 8.97%. Image quality can also be estimated through CNR parameter with maximum difference to actual CNR measurement of 21.65%.

  8. ImageMiner: a software system for comparative analysis of tissue microarrays using content-based image retrieval, high-performance computing, and grid technology

    PubMed Central

    Foran, David J; Yang, Lin; Hu, Jun; Goodell, Lauri A; Reiss, Michael; Wang, Fusheng; Kurc, Tahsin; Pan, Tony; Sharma, Ashish; Saltz, Joel H

    2011-01-01

    Objective and design The design and implementation of ImageMiner, a software platform for performing comparative analysis of expression patterns in imaged microscopy specimens such as tissue microarrays (TMAs), is described. ImageMiner is a federated system of services that provides a reliable set of analytical and data management capabilities for investigative research applications in pathology. It provides a library of image processing methods, including automated registration, segmentation, feature extraction, and classification, all of which have been tailored, in these studies, to support TMA analysis. The system is designed to leverage high-performance computing machines so that investigators can rapidly analyze large ensembles of imaged TMA specimens. To support deployment in collaborative, multi-institutional projects, ImageMiner features grid-enabled, service-based components so that multiple instances of ImageMiner can be accessed remotely and federated. Results The experimental evaluation shows that: (1) ImageMiner is able to support reliable detection and feature extraction of tumor regions within imaged tissues; (2) images and analysis results managed in ImageMiner can be searched for and retrieved on the basis of image-based features, classification information, and any correlated clinical data, including any metadata that have been generated to describe the specified tissue and TMA; and (3) the system is able to reduce computation time of analyses by exploiting computing clusters, which facilitates analysis of larger sets of tissue samples. PMID:21606133

  9. Stereoscopic adapter based system using HMD and image processing software for supporting inner ear operations performed using operating microscope

    NASA Astrophysics Data System (ADS)

    Leśniewski, Marcin; Kujawińska, Malgorzata; Kucharski, Tomasz; Niemczyk, Kazimierz

    2006-02-01

    Recently surgery requires extensive support from imaging technologies in order to increase effectiveness and safety of operations. One of important tasks is to enhance visualisation of quasi-phase (transparent) 3D structures. In this paper authors present a few of practical hardware solutions using of operational stereoscopic microscope with two image acquisition channels, stereoscopic adapter and Helmet Mounted Display (HMD) for stereoscopic visualization of operational field "in real time". Special attention is paid to the development of opto- mechanical unit. The authors focus on searching cheap, accurate and ergonomic solutions. A few proposals are analyzed: typical stereoscopic adapter with two image acquisition channels equipped with developed software for image low contrast enhancement for stereoscopic observation in stereoscopic HMD of operational field, visual - picture adapter (real operational view through microscope channels or processed operational field images observation in "real time").

  10. Software safety

    NASA Technical Reports Server (NTRS)

    Leveson, Nancy

    1987-01-01

    Software safety and its relationship to other qualities are discussed. It is shown that standard reliability and fault tolerance techniques will not solve the safety problem for the present. A new attitude requires: looking at what you do NOT want software to do along with what you want it to do; and assuming things will go wrong. New procedures and changes to entire software development process are necessary: special software safety analysis techniques are needed; and design techniques, especially eliminating complexity, can be very helpful.

  11. New Instruments for Survey: on Line Softwares for 3d Recontruction from Images

    NASA Astrophysics Data System (ADS)

    Fratus de Balestrini, E.; Guerra, F.

    2011-09-01

    3d scanning technologies had a significant development and have been widely used in documentation of cultural, architectural and archeological heritages. Modern methods of three-dimensional acquiring and modeling allow to represent an object through a digital model that combines visual potentialities of images (normally used for documentation) to the accuracy of the survey, becoming at the same time support for the visualization that for metric evaluation of any artefact that have an historical or artistic interest, opening up new possibilities for cultural heritage's fruition, cataloging and study. Despite this development, because of the small catchment area and the 3D laser scanner's sophisticated technologies, the cost of these instruments is very high and beyond the reach of most operators in the field of cultural heritages. This is the reason why they have appeared low-cost technologies or even free, allowing anyone to approach the issues of acquisition and 3D modeling, providing tools that allow to create three-dimensional models in a simple and economical way. The research, conducted by the Laboratory of Photogrammetry of the University IUAV of Venice, of which we present here some results, is intended to figure out whether, with Arc3D, it is possible to obtain results that can be somehow comparable, in therms of overall quality, to those of the laser scanner, and/or whether it is possible to integrate them. They were carried out a series of tests on certain types of objects, models made with Arc3D, from raster images, were compared with those obtained using the point clouds from laser scanner. We have also analyzed the conditions for an optimal use of Arc3D: environmental conditions (lighting), acquisition tools (digital cameras) and type and size of objects. After performing the tests described above, we analyzed the patterns generated by Arc3D to check what other graphic representations can be obtained from them: orthophotos and drawings. The research

  12. First experiences with the implementation of the European standard EN 62304 on medical device software for the quality assurance of a radiotherapy unit

    PubMed Central

    2014-01-01

    Background According to the latest amendment of the Medical Device Directive standalone software qualifies as a medical device when intended by the manufacturer to be used for medical purposes. In this context, the EN 62304 standard is applicable which defines the life-cycle requirements for the development and maintenance of medical device software. A pilot project was launched to acquire skills in implementing this standard in a hospital-based environment (in-house manufacture). Methods The EN 62304 standard outlines minimum requirements for each stage of the software life-cycle, defines the activities and tasks to be performed and scales documentation and testing according to its criticality. The required processes were established for the pre-existent decision-support software FlashDumpComparator (FDC) used during the quality assurance of treatment-relevant beam parameters. As the EN 62304 standard implicates compliance with the EN ISO 14971 standard on the application of risk management to medical devices, a risk analysis was carried out to identify potential hazards and reduce the associated risks to acceptable levels. Results The EN 62304 standard is difficult to implement without proper tools, thus open-source software was selected and integrated into a dedicated development platform. The control measures yielded by the risk analysis were independently implemented and verified, and a script-based test automation was retrofitted to reduce the associated test effort. After all documents facilitating the traceability of the specified requirements to the corresponding tests and of the control measures to the proof of execution were generated, the FDC was released as an accessory to the HIT facility. Conclusions The implementation of the EN 62304 standard was time-consuming, and a learning curve had to be overcome during the first iterations of the associated processes, but many process descriptions and all software tools can be re-utilized in follow-up projects

  13. DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research

    PubMed Central

    Clunie, David; Ulrich, Ethan; Bauer, Christian; Wahle, Andreas; Brown, Bartley; Onken, Michael; Riesmeier, Jörg; Pieper, Steve; Kikinis, Ron; Buatti, John; Beichel, Reinhard R.

    2016-01-01

    Background. Imaging biomarkers hold tremendous promise for precision medicine clinical applications. Development of such biomarkers relies heavily on image post-processing tools for automated image quantitation. Their deployment in the context of clinical research necessitates interoperability with the clinical systems. Comparison with the established outcomes and evaluation tasks motivate integration of the clinical and imaging data, and the use of standardized approaches to support annotation and sharing of the analysis results and semantics. We developed the methodology and tools to support these tasks in Positron Emission Tomography and Computed Tomography (PET/CT) quantitative imaging (QI) biomarker development applied to head and neck cancer (HNC) treatment response assessment, using the Digital Imaging and Communications in Medicine (DICOM®) international standard and free open-source software. Methods. Quantitative analysis of PET/CT imaging data collected on patients undergoing treatment for HNC was conducted. Processing steps included Standardized Uptake Value (SUV) normalization of the images, segmentation of the tumor using manual and semi-automatic approaches, automatic segmentation of the reference regions, and extraction of the volumetric segmentation-based measurements. Suitable components of the DICOM standard were identified to model the various types of data produced by the analysis. A developer toolkit of conversion routines and an Application Programming Interface (API) were contributed and applied to create a standards-based representation of the data. Results. DICOM Real World Value Mapping, Segmentation and Structured Reporting objects were utilized for standards-compliant representation of the PET/CT QI analysis results and relevant clinical data. A number of correction proposals to the standard were developed. The open-source DICOM toolkit (DCMTK) was improved to simplify the task of DICOM encoding by introducing new API abstractions

  14. DICOM for quantitative imaging biomarker development: a standards based approach to sharing clinical data and structured PET/CT analysis results in head and neck cancer research.

    PubMed

    Fedorov, Andriy; Clunie, David; Ulrich, Ethan; Bauer, Christian; Wahle, Andreas; Brown, Bartley; Onken, Michael; Riesmeier, Jörg; Pieper, Steve; Kikinis, Ron; Buatti, John; Beichel, Reinhard R

    2016-01-01

    Background. Imaging biomarkers hold tremendous promise for precision medicine clinical applications. Development of such biomarkers relies heavily on image post-processing tools for automated image quantitation. Their deployment in the context of clinical research necessitates interoperability with the clinical systems. Comparison with the established outcomes and evaluation tasks motivate integration of the clinical and imaging data, and the use of standardized approaches to support annotation and sharing of the analysis results and semantics. We developed the methodology and tools to support these tasks in Positron Emission Tomography and Computed Tomography (PET/CT) quantitative imaging (QI) biomarker development applied to head and neck cancer (HNC) treatment response assessment, using the Digital Imaging and Communications in Medicine (DICOM(®)) international standard and free open-source software. Methods. Quantitative analysis of PET/CT imaging data collected on patients undergoing treatment for HNC was conducted. Processing steps included Standardized Uptake Value (SUV) normalization of the images, segmentation of the tumor using manual and semi-automatic approaches, automatic segmentation of the reference regions, and extraction of the volumetric segmentation-based measurements. Suitable components of the DICOM standard were identified to model the various types of data produced by the analysis. A developer toolkit of conversion routines and an Application Programming Interface (API) were contributed and applied to create a standards-based representation of the data. Results. DICOM Real World Value Mapping, Segmentation and Structured Reporting objects were utilized for standards-compliant representation of the PET/CT QI analysis results and relevant clinical data. A number of correction proposals to the standard were developed. The open-source DICOM toolkit (DCMTK) was improved to simplify the task of DICOM encoding by introducing new API abstractions

  15. Osteolytica: An automated image analysis software package that rapidly measures cancer-induced osteolytic lesions in in vivo models with greater reproducibility compared to other commonly used methods☆

    PubMed Central

    Evans, H.R.; Karmakharm, T.; Lawson, M.A.; Walker, R.E.; Harris, W.; Fellows, C.; Huggins, I.D.; Richmond, P.; Chantry, A.D.

    2016-01-01

    Methods currently used to analyse osteolytic lesions caused by malignancies such as multiple myeloma and metastatic breast cancer vary from basic 2-D X-ray analysis to 2-D images of micro-CT datasets analysed with non-specialised image software such as ImageJ. However, these methods have significant limitations. They do not capture 3-D data, they are time-consuming and they often suffer from inter-user variability. We therefore sought to develop a rapid and reproducible method to analyse 3-D osteolytic lesions in mice with cancer-induced bone disease. To this end, we have developed Osteolytica, an image analysis software method featuring an easy to use, step-by-step interface to measure lytic bone lesions. Osteolytica utilises novel graphics card acceleration (parallel computing) and 3-D rendering to provide rapid reconstruction and analysis of osteolytic lesions. To evaluate the use of Osteolytica we analysed tibial micro-CT datasets from murine models of cancer-induced bone disease and compared the results to those obtained using a standard ImageJ analysis method. Firstly, to assess inter-user variability we deployed four independent researchers to analyse tibial datasets from the U266-NSG murine model of myeloma. Using ImageJ, inter-user variability between the bones was substantial (± 19.6%), in contrast to using Osteolytica, which demonstrated minimal variability (± 0.5%). Secondly, tibial datasets from U266-bearing NSG mice or BALB/c mice injected with the metastatic breast cancer cell line 4T1 were compared to tibial datasets from aged and sex-matched non-tumour control mice. Analyses by both Osteolytica and ImageJ showed significant increases in bone lesion area in tumour-bearing mice compared to control mice. These results confirm that Osteolytica performs as well as the current 2-D ImageJ osteolytic lesion analysis method. However, Osteolytica is advantageous in that it analyses over the entirety of the bone volume (as opposed to selected 2-D images

  16. [Design of the 2D-FFT image reconstruction software based on Matlab].

    PubMed

    Xu, Hong-yu; Wang, Hong-zhi

    2008-09-01

    This paper presents a Matlab's implementation for 2D-FFT image reconstruction algorithm of magnetic resonance imaging, with the universal COM component that Windows system can identify. This allows to segregate the 2D-FFT image reconstruction algorithm from the business magnetic resonance imaging closed system, providing the ability for initial data processing before reconstruction, which would be important for improving the image quality, diagnostic value and image post-processing.

  17. Image presentation in digital radiology: perspectives on the emerging DICOM display function standard and its application.

    PubMed

    Blume, H; Hemminger, B M

    1997-01-01

    DICOM (Digital Imaging and Communications in Medicine) Working Group XI, formerly called ACR/NEMA (American College of Radiology/National Electrical Manufacturers' Association) Working Group XI, is currently developing a display function standard. The main objective of the standard is to define mathematically a display function for all image presentation systems. As a secondary objective, the standard aims at providing similarity in gray-scale perception for a given image between display systems of different luminance and at facilitating efficient utilization of the available digital input levels of a display system. The design of the display function incorporates the concept of perceptual linearization. The proposed standard applies to monochrome image presentation devices such as cathode ray tube monitor-display controller systems and digital laser image printers. The standard does not eliminate the use of application-specific display functions but rather ensures their effectiveness. Neither does the standard guarantee equal information transfer between image presentation devices with different physical properties; it does, however, from the basis for applying image processing to compensate for such differences.

  18. Analysis of nuclear organization with TANGO, software for high-throughput quantitative analysis of 3D fluorescence microscopy images.

    PubMed

    Ollion, Jean; Cochennec, Julien; Loll, François; Escudé, Christophe; Boudier, Thomas

    2015-01-01

    The cell nucleus is a highly organized cellular organelle that contains the genome. An important step to understand the relationships between genome positioning and genome functions is to extract quantitative data from three-dimensional (3D) fluorescence imaging. However, such approaches are limited by the requirement for processing and analyzing large sets of images. Here we present a practical approach using TANGO (Tools for Analysis of Nuclear Genome Organization), an image analysis tool dedicated to the study of nuclear architecture. TANGO is a generic tool able to process large sets of images, allowing quantitative study of nuclear organization. In this chapter a practical description of the software is drawn in order to give an overview of its different concepts and functionalities. This description is illustrated with a precise example that can be performed step-by-step on experimental data provided on the website http://biophysique.mnhn.fr/tango/HomePage.

  19. Development and Evaluation of an Open-Source Software Package “CGITA” for Quantifying Tumor Heterogeneity with Molecular Images

    PubMed Central

    Fang, Yu-Hua Dean; Lin, Chien-Yu; Shih, Meng-Jung; Wang, Hung-Ming; Ho, Tsung-Ying; Liao, Chun-Ta; Yen, Tzu-Chen

    2014-01-01

    Background. The quantification of tumor heterogeneity with molecular images, by analyzing the local or global variation in the spatial arrangements of pixel intensity with texture analysis, possesses a great clinical potential for treatment planning and prognosis. To address the lack of available software for computing the tumor heterogeneity on the public domain, we develop a software package, namely, Chang-Gung Image Texture Analysis (CGITA) toolbox, and provide it to the research community as a free, open-source project. Methods. With a user-friendly graphical interface, CGITA provides users with an easy way to compute more than seventy heterogeneity indices. To test and demonstrate the usefulness of CGITA, we used a small cohort of eighteen locally advanced oral cavity (ORC) cancer patients treated with definitive radiotherapies. Results. In our case study of ORC data, we found that more than ten of the current implemented heterogeneity indices outperformed SUVmean for outcome prediction in the ROC analysis with a higher area under curve (AUC). Heterogeneity indices provide a better area under the curve up to 0.9 than the SUVmean and TLG (0.6 and 0.52, resp.). Conclusions. CGITA is a free and open-source software package to quantify tumor heterogeneity from molecular images. CGITA is available for free for academic use at http://code.google.com/p/cgita. PMID:24757667

  20. Interference-free ultrasound imaging during HIFU therapy, using software tools

    NASA Technical Reports Server (NTRS)

    Vaezy, Shahram (Inventor); Held, Robert (Inventor); Sikdar, Siddhartha (Inventor); Managuli, Ravi (Inventor); Zderic, Vesna (Inventor)

    2010-01-01

    Disclosed herein is a method for obtaining a composite interference-free ultrasound image when non-imaging ultrasound waves would otherwise interfere with ultrasound imaging. A conventional ultrasound imaging system is used to collect frames of ultrasound image data in the presence of non-imaging ultrasound waves, such as high-intensity focused ultrasound (HIFU). The frames are directed to a processor that analyzes the frames to identify portions of the frame that are interference-free. Interference-free portions of a plurality of different ultrasound image frames are combined to generate a single composite interference-free ultrasound image that is displayed to a user. In this approach, a frequency of the non-imaging ultrasound waves is offset relative to a frequency of the ultrasound imaging waves, such that the interference introduced by the non-imaging ultrasound waves appears in a different portion of the frames.

  1. Sandia software guidelines: Software quality planning

    SciTech Connect

    Not Available

    1987-08-01

    This volume is one in a series of Sandia Software Guidelines intended for use in producing quality software within Sandia National Laboratories. In consonance with the IEEE Standard for Software Quality Assurance Plans, this volume identifies procedures to follow in producing a Software Quality Assurance Plan for an organization or a project, and provides an example project SQA plan. 2 figs., 4 tabs.

  2. Image intensity standardization in 3D rotational angiography and its application to vascular segmentation

    NASA Astrophysics Data System (ADS)

    Bogunović, Hrvoje; Radaelli, Alessandro G.; De Craene, Mathieu; Delgado, David; Frangi, Alejandro F.

    2008-03-01

    Knowledge-based vascular segmentation methods typically rely on a pre-built training set of segmented images, which is used to estimate the probability of each voxel to belong to a particular tissue. In 3D Rotational Angiography (3DRA) the same tissue can correspond to different intensity ranges depending on the imaging device, settings and contrast injection protocol. As a result, pre-built training sets do not apply to all images and the best segmentation results are often obtained when the training set is built specifically for each individual image. We present an Image Intensity Standardization (IIS) method designed to ensure a correspondence between specific tissues and intensity ranges common to every image that undergoes the standardization process. The method applies a piecewise linear transformation to the image that aligns the intensity histogram to the histogram taken as reference. The reference histogram has been selected from a high quality image not containing artificial objects such as coils or stents. This is a pre-processing step that allows employing a training set built on a limited number of standardized images for the segmentation of standardized images which were not part of the training set. The effectiveness of the presented IIS technique in combination with a well-validated knowledge-based vasculature segmentation method is quantified on a variety of 3DRA images depicting cerebral arteries and intracranial aneurysms. The proposed IIS method offers a solution to the standardization of tissue classes in routine medical images and effectively improves automation and usability of knowledge-based vascular segmentation algorithms.

  3. SU-E-J-42: Customized Deformable Image Registration Using Open-Source Software SlicerRT

    SciTech Connect

    Gaitan, J Cifuentes; Chin, L; Pignol, J; Kirby, N; Pouliot, J; Lasso, A; Pinter, C; Fichtinger, G

    2014-06-01

    Purpose: SlicerRT is a flexible platform that allows the user to incorporate the necessary images registration and processing tools to improve clinical workflow. This work validates the accuracy and the versatility of the deformable image registration algorithm of the free open-source software SlicerRT using a deformable physical pelvic phantom versus available commercial image fusion algorithms. Methods: Optical camera images of nonradiopaque markers implanted in an anatomical pelvic phantom were used to measure the ground-truth deformation and evaluate the theoretical deformations for several DIR algorithms. To perform the registration, full and empty bladder computed tomography (CT) images of the phantom were obtained and used as fixed and moving images, respectively. The DIR module, found in SlicerRT, used a B-spline deformable image registration with multiple optimization parameters that allowed customization of the registration including a regularization term that controlled the amount of local voxel displacement. The virtual deformation field at the center of the phantom was obtained and compared to the experimental ground-truth values. The parameters of SlicerRT were then varied to improve spatial accuracy. To quantify image similarity, the mean absolute difference (MAD) parameter using Hounsfield units was calculated. In addition, the Dice coefficient of the contoured rectum was evaluated to validate the strength of the algorithm to transfer anatomical contours. Results: Overall, SlicerRT achieved one of the lowest MAD values across the algorithm spectrum, but slightly smaller mean spatial errors in comparison to MIM software (MIM). On the other hand, SlicerRT created higher mean spatial errors than Velocity Medical Solutions (VEL), although obtaining an improvement on the DICE to 0.91. The large spatial errors were attributed to the poor contrast in the prostate bladder interface of the phantom. Conclusion: Based phantom validation, SlicerRT is capable of

  4. Nuquantus: Machine learning software for the characterization and quantification of cell nuclei in complex immunofluorescent tissue images

    PubMed Central

    Gross, Polina; Honnorat, Nicolas; Varol, Erdem; Wallner, Markus; Trappanese, Danielle M.; Sharp, Thomas E.; Starosta, Timothy; Duran, Jason M.; Koller, Sarah; Davatzikos, Christos; Houser, Steven R.

    2016-01-01

    Determination of fundamental mechanisms of disease often hinges on histopathology visualization and quantitative image analysis. Currently, the analysis of multi-channel fluorescence tissue images is primarily achieved by manual measurements of tissue cellular content and sub-cellular compartments. Since the current manual methodology for image analysis is a tedious and subjective approach, there is clearly a need for an automated analytical technique to process large-scale image datasets. Here, we introduce Nuquantus (Nuclei quantification utility software) - a novel machine learning-based analytical method, which identifies, quantifies and classifies nuclei based on cells of interest in composite fluorescent tissue images, in which cell borders are not visible. Nuquantus is an adaptive framework that learns the morphological attributes of intact tissue in the presence of anatomical variability and pathological processes. Nuquantus allowed us to robustly perform quantitative image analysis on remodeling cardiac tissue after myocardial infarction. Nuquantus reliably classifies cardiomyocyte versus non-cardiomyocyte nuclei and detects cell proliferation, as well as cell death in different cell classes. Broadly, Nuquantus provides innovative computerized methodology to analyze complex tissue images that significantly facilitates image analysis and minimizes human bias. PMID:27005843

  5. Nuquantus: Machine learning software for the characterization and quantification of cell nuclei in complex immunofluorescent tissue images.

    PubMed

    Gross, Polina; Honnorat, Nicolas; Varol, Erdem; Wallner, Markus; Trappanese, Danielle M; Sharp, Thomas E; Starosta, Timothy; Duran, Jason M; Koller, Sarah; Davatzikos, Christos; Houser, Steven R

    2016-03-23

    Determination of fundamental mechanisms of disease often hinges on histopathology visualization and quantitative image analysis. Currently, the analysis of multi-channel fluorescence tissue images is primarily achieved by manual measurements of tissue cellular content and sub-cellular compartments. Since the current manual methodology for image analysis is a tedious and subjective approach, there is clearly a need for an automated analytical technique to process large-scale image datasets. Here, we introduce Nuquantus (Nuclei quantification utility software) - a novel machine learning-based analytical method, which identifies, quantifies and classifies nuclei based on cells of interest in composite fluorescent tissue images, in which cell borders are not visible. Nuquantus is an adaptive framework that learns the morphological attributes of intact tissue in the presence of anatomical variability and pathological processes. Nuquantus allowed us to robustly perform quantitative image analysis on remodeling cardiac tissue after myocardial infarction. Nuquantus reliably classifies cardiomyocyte versus non-cardiomyocyte nuclei and detects cell proliferation, as well as cell death in different cell classes. Broadly, Nuquantus provides innovative computerized methodology to analyze complex tissue images that significantly facilitates image analysis and minimizes human bias.

  6. Nuquantus: Machine learning software for the characterization and quantification of cell nuclei in complex immunofluorescent tissue images

    NASA Astrophysics Data System (ADS)

    Gross, Polina; Honnorat, Nicolas; Varol, Erdem; Wallner, Markus; Trappanese, Danielle M.; Sharp, Thomas E.; Starosta, Timothy; Duran, Jason M.; Koller, Sarah; Davatzikos, Christos; Houser, Steven R.

    2016-03-01

    Determination of fundamental mechanisms of disease often hinges on histopathology visualization and quantitative image analysis. Currently, the analysis of multi-channel fluorescence tissue images is primarily achieved by manual measurements of tissue cellular content and sub-cellular compartments. Since the current manual methodology for image analysis is a tedious and subjective approach, there is clearly a need for an automated analytical technique to process large-scale image datasets. Here, we introduce Nuquantus (Nuclei quantification utility software) - a novel machine learning-based analytical method, which identifies, quantifies and classifies nuclei based on cells of interest in composite fluorescent tissue images, in which cell borders are not visible. Nuquantus is an adaptive framework that learns the morphological attributes of intact tissue in the presence of anatomical variability and pathological processes. Nuquantus allowed us to robustly perform quantitative image analysis on remodeling cardiac tissue after myocardial infarction. Nuquantus reliably classifies cardiomyocyte versus non-cardiomyocyte nuclei and detects cell proliferation, as well as cell death in different cell classes. Broadly, Nuquantus provides innovative computerized methodology to analyze complex tissue images that significantly facilitates image analysis and minimizes human bias.

  7. Image processing of standard grading scales for objective assessment of contact lens wear complications

    NASA Astrophysics Data System (ADS)

    Perez-Cabre, Elisabet; Millan, Maria S.; Abril, Hector C.; Otxoa, E.

    2004-10-01

    Ocular complications in contact lens wearers are usually graded by specialists using visual inspection and comparing with established standards. The standard grading scales consist of either a set of illustrations or photographs ordered from a normal situation to a severe complication. In this work, an objective assessment of contact lens wear complications is intended by applying different image processing techniques to two standard grading scales (Efron and CCLRU grading scales). In particular, conjunctival hyperemia and papillary conjunctivitis are considered. Given a set of standard illustrations or pictures for each considered ocular disorder, image preprocessing is needed to compare equivalent areas. Histogram analysis allows segmenting vessel and background pixel populations, which are used to determine the most relevant features in the measurement of contact lens effects. Features such as color, total area of vessels and vessel length are used to evaluate bulbar and lid redness. The procedure to obtain an automatic grading method by digital image analysis of standard grading scales is described.

  8. Software workflow for the automatic tagging of medieval manuscript images (SWATI)

    NASA Astrophysics Data System (ADS)

    Chandna, Swati; Tonne, Danah; Jejkal, Thomas; Stotzka, Rainer; Krause, Celia; Vanscheidt, Philipp; Busch, Hannah; Prabhune, Ajinkya

    2015-01-01

    Digital methods, tools and algorithms are gaining in importance for the analysis of digitized manuscript collections in the arts and humanities. One example is the BMBF-funded research project "eCodicology" which aims to design, evaluate and optimize algorithms for the automatic identification of macro- and micro-structural layout features of medieval manuscripts. The main goal of this research project is to provide better insights into high-dimensional datasets of medieval manuscripts for humanities scholars. The heterogeneous nature and size of the humanities data and the need to create a database of automatically extracted reproducible features for better statistical and visual analysis are the main challenges in designing a workflow for the arts and humanities. This paper presents a concept of a workflow for the automatic tagging of medieval manuscripts. As a starting point, the workflow uses medieval manuscripts digitized within the scope of the project Virtual Scriptorium St. Matthias". Firstly, these digitized manuscripts are ingested into a data repository. Secondly, specific algorithms are adapted or designed for the identification of macro- and micro-structural layout elements like page size, writing space, number of lines etc. And lastly, a statistical analysis and scientific evaluation of the manuscripts groups are performed. The workflow is designed generically to process large amounts of data automatically with any desired algorithm for feature extraction. As a result, a database of objectified and reproducible features is created which helps to analyze and visualize hidden relationships of around 170,000 pages. The workflow shows the potential of automatic image analysis by enabling the processing of a single page in less than a minute. Furthermore, the accuracy tests of the workflow on a small set of manuscripts with respect to features like page size and text areas show that automatic and manual analysis are comparable. The usage of a computer

  9. [Standardizing a protocol of magnetic resonance imaging of temporomandibular joints. Part I].

    PubMed

    Bulanova, T V

    2004-01-01

    The paper presents the standard of a procedure for magnetic resonance imaging of temporomandibular joints, which has been used to examine 275 patients. It describes the study projections, that are most significant for visualization, and scanning protocols. Illustrations of magnetic resonance imaging of the structures of the intact temporomandibular joint are presented.

  10. Development of image quality assurance measures of the ExacTrac localization system using commercially available image evaluation software and hardware for image-guided radiotherapy.

    PubMed

    Stanley, Dennis N; Papanikolaou, Nikos; Gutierrez, Alonso N

    2014-11-01

    Quality assurance (QA) of the image quality for image-guided localization systems is crucial to ensure accurate visualization and localization of target volumes. In this study, a methodology was developed to assess and evaluate the constancy of the high-contrast spatial resolution, dose, energy, contrast, and geometrical accuracy of the BrainLAB ExacTrac system. An in-house fixation device was constructed to hold the QCkV-1 phantom firmly and reproducibly against the face of the flat panel detectors. Two image sets per detector were acquired using ExacTrac preset console settings over a period of three months. The image sets were analyzed in PIPSpro and the following metrics were recorded: high-contrast spatial resolution (f30,f40,f50 (lp/mm)), noise, and contrast-to-noise ratio. Geometrical image accuracy was evaluated by assessing the length between to predetermined points of the QCkV-1 phantom. Dose and kVp were recorded using the Unfors RaySafe Xi R/F Detector. The kVp and dose were evaluated for the following: Cranial Standard (CS) (80 kV,80 mA,80 ms), Thorax Standard (TS) (120 kV,160 mA,160 ms), Abdomen Standard (AS) (120 kV,160 mA,130 ms), and Pelvis Standard (PS) (120 kV,160 mA,160 ms). With regard to high-contrast spatial resolution, the mean values of the f30 (lp/mm), f40 (lp/mm) and f50 (lp/mm) for the left detector were 1.39±0.04,1.24±0.05, and 1.09±0.04, respectively, while for the right detector they were 1.38±0.04,1.22±0.05, and 1.09±0.05, respectively. Mean CNRs for the left and right detectors were 148±3 and 143±4, respectively. For geometrical accuracy, both detectors had a measured image length of the QCkV-1 of 57.9±0.5mm. The left detector showed dose measurements of 20.4±0.2μGy(CS), 191.8±0.7μGy(TS), 154.2±0.7μGy(AS), and 192.2±0.6μGy(PS), while the right detector showed 20.3±0.3μGy(CS), 189.7±0.8μGy(TS), 151.0±0.7μGy(AS), and 189.7±0.8μGy(PS), respectively. For X-ray energy, the left detector (right X-ray tube) had

  11. Development of image quality assurance measures of the ExacTrac localization system using commercially available image evaluation software and hardware for image-guided radiotherapy.

    PubMed

    Stanley, Dennis N; Papanikolaou, Nikos; Gutiérrez, Alonso N

    2014-11-08

    Quality assurance (QA) of the image quality for image-guided localization systems is crucial to ensure accurate visualization and localization of target volumes. In this study, a methodology was developed to assess and evaluate the constancy of the high-contrast spatial resolution, dose, energy, contrast, and geometrical accuracy of the BrainLAB ExacTrac system. An in-house fixation device was constructed to hold the QCkV-1 phantom firmly and reproducibly against the face of the flat panel detectors. Two image sets per detector were acquired using ExacTrac preset console settings over a period of three months. The image sets were analyzed in PIPSpro and the following metrics were recorded: high-contrast spatial resolution (f30, f40, f50 (lp/mm)), noise, and contrast-to-noise ratio. Geometrical image accu- racy was evaluated by assessing the length between to predetermined points of the QCkV-1 phantom. Dose and kVp were recorded using the Unfors RaySafe Xi R/F Detector. The kVp and dose were evaluated for the following: Cranial Standard (CS) (80 kV,80 mA,80 ms), Thorax Standard (TS) (120 kV,160 mA,160 ms), Abdomen Standard (AS) (120 kV,160 mA,130 ms), and Pelvis Standard (PS) (120 kV,160 mA,160 ms). With regard to high-contrast spatial resolution, the mean values of the f30 (lp/mm), f40 (lp/mm) and f50 (lp/mm) for the left detector were 1.39 ± 0.04, 1.24 ± 0.05, and 1.09 ± 0.04, respectively, while for the right detector they were 1.38 ± 0.04, 1.22 ± 0.05, and 1.09 ± 0.05, respectively. Mean CNRs for the left and right detectors were 148 ± 3 and 143 ± 4, respectively. For geometrical accuracy, both detectors had a measured image length of the QCkV-1 of 57.9 ± 0.5 mm. The left detector showed dose measurements of 20.4 ± 0.2 μGy (CS), 191.8 ± 0.7 μGy (TS), 154.2 ± 0.7 μGy (AS), and 192.2 ± 0.6 μGy (PS), while the right detector showed 20.3 ± 0.3 μGy (CS), 189.7 ± 0.8 μGy (TS), 151.0 ± 0.7 μGy (AS), and 189.7 ± 0.8 μGy (PS), respectively. For X

  12. Automatic Detection of Mitosis and Nuclei From Cytogenetic Images by CellProfiler Software for Mitotic Index Estimation.

    PubMed

    González, Jorge Ernesto; Radl, Analía; Romero, Ivonne; Barquinero, Joan Francesc; García, Omar; Di Giorgio, Marina

    2016-12-01

    Mitotic Index (MI) estimation expressed as percentage of mitosis plays an important role as quality control endpoint. To this end, MI is applied to check the lot of media and reagents to be used throughout the assay and also to check cellular viability after blood sample shipping, indicating satisfactory/unsatisfactory conditions for the progression of cell culture. The objective of this paper was to apply the CellProfiler open-source software for automatic detection of mitotic and nuclei figures from digitized images of cultured human lymphocytes for MI assessment, and to compare its performance to that performed through semi-automatic and visual detection. Lymphocytes were irradiated and cultured for mitosis detection. Sets of images from cultures were analyzed visually and findings were compared with those using CellProfiler software. The CellProfiler pipeline includes the detection of nuclei and mitosis with 80% sensitivity and more than 99% specificity. We conclude that CellProfiler is a reliable tool for counting mitosis and nuclei from cytogenetic images, saves considerable time compared to manual operation and reduces the variability derived from the scoring criteria of different scorers. The CellProfiler automated pipeline achieves good agreement with visual counting workflow, i.e. it allows fully automated mitotic and nuclei scoring in cytogenetic images yielding reliable information with minimal user intervention.

  13. Development of image and information management system for Korean standard brain

    NASA Astrophysics Data System (ADS)

    Chung, Soon Cheol; Choi, Do Young; Tack, Gye Rae; Sohn, Jin Hun

    2004-04-01

    The purpose of this study is to establish a reference for image acquisition for completing a standard brain for diverse Korean population, and to develop database management system that saves and manages acquired brain images and personal information of subjects. 3D MP-RAGE (Magnetization Prepared Rapid Gradient Echo) technique which has excellent Signal to Noise Ratio (SNR) and Contrast to Noise Ratio (CNR) as well as reduces image acquisition time was selected for anatomical image acquisition, and parameter values were obtained for the optimal image acquisition. Using these standards, image data of 121 young adults (early twenties) were obtained and stored in the system. System was designed to obtain, save, and manage not only anatomical image data but also subjects' basic demographic factors, medical history, handedness inventory, state-trait anxiety inventory, A-type personality inventory, self-assessment depression inventory, mini-mental state examination, intelligence test, and results of personality test via a survey questionnaire. Additionally this system was designed to have functions of saving, inserting, deleting, searching, and printing image data and personal information of subjects, and to have accessibility to them as well as automatic connection setup with ODBC. This newly developed system may have major contribution to the completion of a standard brain for diverse Korean population since it can save and manage their image data and personal information.

  14. New solutions for standardization, monitoring and quality management of fluorescence-based imaging systems (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Royon, Arnaud; Papon, Gautier

    2016-03-01

    Fluorescence microscopes have become ubiquitous in life sciences laboratories, including those focused on pharmaceuticals, diagnosis, and forensics. For the past few years, the need for both performance guarantees and quantifiable results has driven development in this area. However, the lack of appropriate standards and reference materials makes it difficult or impossible to compare the results of two fluorescence microscopes, or to measure performance fluctuations of one microscope over time. Therefore, the operation of fluorescence microscopes is not monitored as often as their use warrants - an issue that is recognized by both systems manufacturers and national metrology institutes. We have developed a new process that enables the etching of long-term stable fluorescent patterns with sub-micrometer sizes in three dimensions inside glass. In this paper, we present, based on this new process, a fluorescent multi-dimensional ruler and a dedicated software that are suitable for monitoring and quality management of fluorescence-based imaging systems (wide-field, confocal, multiphoton, high content machines). In addition to fluorescence, the same patterns exhibit bright- and dark-field contrast, DIC, and phase contrast, which make them also relevant to monitor these types of microscopes. Non-exhaustively, this new solution enables the measurement of: The stage repositioning accuracy; The illumination and detection homogeneities; The field flatness; The detectors' characteristics; The lateral and axial spatial resolutions; The spectral response (spectrum, intensity and lifetime) of the system. Thanks to the stability of the patterns, microscope performance assessment can be carried out as well in a daily basis as in the long term.

  15. Using image analysis to develop reference standards for the video trashmeter

    NASA Astrophysics Data System (ADS)

    Thibodeaux, Devron P.; Evans, Janice P.

    1995-01-01

    Results of research to develop a reference method for calibrating standard dot image tiles and cotton trash boxes are reported. The tiles and trash boxes are produced by the Agricultural Marketing Service for use in standardizing HVI Video Trashmeters. The reference method involves use of a highly sensitive image analysis system (the Quantimet 970) to measure the number and percent area fraction of particle images produced on the replica tiles or of real trash particles placed on the surface of cotton incased in plastic boxes. Calibration data for a set of tiles and boxes is presented. The effects of magnification (system resolution) and detection threshold are investigated as related to measurement accuracy.

  16. 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).

  17. NeuroGam Software Analysis in Epilepsy Diagnosis Using 99mTc-ECD Brain Perfusion SPECT Imaging.

    PubMed

    Fu, Peng; Zhang, Fang; Gao, Jianqing; Jing, Jianmin; Pan, Liping; Li, Dongxue; Wei, Lingge

    2015-09-20

    BACKGROUND The aim of this study was to explore the value of NeuroGam software in diagnosis of epilepsy by 99Tcm-ethyl cysteinate dimer (ECD) brain imaging. MATERIAL AND METHODS NeuroGam was used to analyze 52 cases of clinically proven epilepsy by 99Tcm-ECD brain imaging. The results were compared with EEG and MRI, and the positive rates and localization to epileptic foci were analyzed. RESULTS NeuroGam analysis showed that 42 of 52 epilepsy cases were abnormal. 99Tcm-ECD brain imaging revealed a positive rate of 80.8% (42/52), with 36 out of 42 patients (85.7%) clearly showing an abnormal area. Both were higher than that of brain perfusion SPECT, with a consistency of 64.5% (34/52) using these 2 methods. Decreased regional cerebral blood flow (rCBF) was observed in frontal (18), temporal (20), and parietal lobes (2). Decreased rCBF was seen in frontal and temporal lobes in 4 out of 36 patients, and in temporal and parietal lobes of 2 out of 36 patients. NeuroGam further showed that the abnormal area was located in a different functional area of the brain. EEG abnormalities were detected in 29 out of 52 patients (55.8%) with 16 cases (55.2%) clearly showing an abnormal area. MRI abnormalities were detected in 17 out of 43 cases (39.5%), including 9 cases (52.9%) clearly showing an abnormal area. The consistency of NeuroGam software analysis, and EEG and MRI were 48.1% (25/52) and 34.9% (15/43), respectively. CONCLUSIONS NeuroGam software analysis offers a higher sensitivity in detecting epilepsy than EEG or MRI. It is a powerful tool in 99Tcm-ECD brain imaging.

  18. Filtering Chromatic Aberration for Wide Acceptance Angle Electrostatic Lenses II--Experimental Evaluation and Software-Based Imaging Energy Analyzer.

    PubMed

    Fazekas, Ádám; Daimon, Hiroshi; Matsuda, Hiroyuki; Tóth, László

    2016-03-01

    Here, the experimental results of the method of filtering the effect of chromatic aberration for wide acceptance angle electrostatic lens-based system are described. This method can eliminate the effect of chromatic aberration from the images of a measured spectral image sequence by determining and removing the effect of higher and lower kinetic energy electrons on each different energy image, which leads to significant improvement of image and spectral quality. The method is based on the numerical solution of a large system of linear equations and equivalent with a multivariate strongly nonlinear deconvolution method. A matrix whose elements describe the strongly nonlinear chromatic aberration-related transmission function of the lens system acts on the vector of the ordered pixels of the distortion free spectral image sequence, and produces the vector of the ordered pixels of the measured spectral image sequence. Since the method can be applied not only on 2D real- and $k$ -space diffraction images, but also along a third dimension of the image sequence that is along the optical or in the 3D parameter space, the energy axis, it functions as a software-based imaging energy analyzer (SBIEA). It can also be applied in cases of light or other type of optics for different optical aberrations and distortions. In case of electron optics, the SBIEA method makes possible the spectral imaging without the application of any other energy filter. It is notable that this method also eliminates the disturbing background significantly in the present investigated case of reflection electron energy loss spectra. It eliminates the instrumental effects and makes possible to measure the real physical processes better.

  19. SU-E-J-104: Evaluation of Accuracy for Various Deformable Image Registrations with Virtual Deformation QA Software

    SciTech Connect

    Han, S; Kim, K; Kim, M; Jung, H; Ji, Y; Choi, S; Park, S

    2015-06-15

    Purpose: The accuracy of deformable image registration (DIR) has a significant dosimetric impact in radiation treatment planning. We evaluated accuracy of various DIR algorithms using virtual deformation QA software (ImSimQA, Oncology System Limited, UK). Methods: The reference image (Iref) and volume (Vref) was first generated with IMSIMQA software. We deformed Iref with axial movement of deformation point and Vref depending on the type of deformation that are the deformation1 is to increase the Vref (relaxation) and the deformation 2 is to decrease the Vref (contraction) .The deformed image (Idef) and volume (Vdef) were inversely deformed to Iref and Vref using DIR algorithms. As a Result, we acquired deformed image (Iid) and volume (Vid). The DIR algorithms were optical flow (HS, IOF) and demons (MD, FD) of the DIRART. The image similarity evaluation between Iref and Iid was calculated by Normalized Mutual Information (NMI) and Normalized Cross Correlation (NCC). The value of Dice Similarity Coefficient (DSC) was used for evaluation of volume similarity. Results: When moving distance of deformation point was 4 mm, the value of NMI was above 1.81 and NCC was above 0.99 in all DIR algorithms. Since the degree of deformation was increased, the degree of image similarity was decreased. When the Vref increased or decreased about 12%, the difference between Vref and Vid was within ±5% regardless of the type of deformation. The value of DSC was above 0.95 in deformation1 except for the MD algorithm. In case of deformation 2, that of DSC was above 0.95 in all DIR algorithms. Conclusion: The Idef and Vdef have not been completely restored to Iref and Vref and the accuracy of DIR algorithms was different depending on the degree of deformation. Hence, the performance of DIR algorithms should be verified for the desired applications.

  20. Mission planning for Shuttle Imaging Radar-C (SIR-C) with a real-time interactive planning software

    NASA Technical Reports Server (NTRS)

    Potts, Su K.

    1993-01-01

    The Shuttle Imaging Radar-C (SIR-C) mission will operate from the payload bay of the space shuttle for 8 days, gathering Synthetic Aperture Radar (SAR) data over specific sites on the Earth. The short duration of the mission and the requirement for realtime planning offer challenges in mission planning and in the design of the Planning and Analysis Subsystem (PAS). The PAS generates shuttle ephemerides and mission planning data and provides an interactive real-time tool for quick mission replanning. It offers a multi-user and multiprocessing environment, and it is able to keep multiple versions of the mission timeline data while maintaining data integrity and security. Its flexible design allows one software to provide different menu options based on the user's operational function, and makes it easy to tailor the software for other Earth orbiting missions.

  1. Standardization of size, shape and internal structure of spinal cord images: comparison of three transformation methods.

    PubMed

    Fujiki, Yasuhisa; Yokota, Shigefumi; Okada, Yasumasa; Oku, Yoshitaka; Tamura, Yoshiyasu; Ishiguro, Makio; Miwakeichi, Fumikazu

    2013-01-01

    Functional fluorescence imaging has been widely applied to analyze spatio-temporal patterns of cellular dynamics in the brain and spinal cord. However, it is difficult to integrate spatial information obtained from imaging data in specific regions of interest across multiple samples, due to large variability in the size, shape and internal structure of samples. To solve this problem, we attempted to standardize transversely sectioned spinal cord images focusing on the laminar structure in the gray matter. We employed three standardization methods, the affine transformation (AT), the angle-dependent transformation (ADT) and the combination of these two methods (AT+ADT). The ADT is a novel non-linear transformation method developed in this study to adjust an individual image onto the template image in the polar coordinate system. We next compared the accuracy of these three standardization methods. We evaluated two indices, i.e., the spatial distribution of pixels that are not categorized to any layer and the error ratio by the leave-one-out cross validation method. In this study, we used neuron-specific marker (NeuN)-stained histological images of transversely sectioned cervical spinal cord slices (21 images obtained from 4 rats) to create the standard atlas and also to serve for benchmark tests. We found that the AT+ADT outperformed other two methods, though the accuracy of each method varied depending on the layer. This novel image standardization technique would be applicable to optical recording such as voltage-sensitive dye imaging, and will enable statistical evaluations of neural activation across multiple samples.

  2. Software Based Supernova Recognition

    NASA Astrophysics Data System (ADS)

    Walters, Stephen M.

    2014-05-01

    This paper describes software for detecting Supernova (SN) in images. The software can operate in real-time to discover SN while data is being collected so the instrumentation can immediately be re-tasked to perform spectroscopy or photometry of a discovery. Because the instrumentation captures two images per minute, the realtime budget is constrained to 30 seconds per target, a challenging goal. Using a set of two to four images, the program creates a "Reference" (REF) image and a "New" (NEW) image where all images are used in both NEW and REF but any SN survives the combination process only in the NEW image. This process produces good quality images having similar noise characteristics but without artifacts that might be interpreted as SN. The images are then adjusted for seeing and brightness differences using a variant of Tomaney and Crotts method of Point Spread Function (PSF) matching after which REF is subtracted from NEW to produce a Difference (DIF) image. A Classifier is then trained on a grid of artificial SN to estimate the statistical properties of four attributes and used in a process to mask false positives that can be clearly identified as such. Further training to avoid any remaining false positives sets the range, in standard deviations for each attribute, that the Classifier will accept as a valid SN. This training enables the Classifier to discriminate between SN and most subtraction residue. Lastly, the DIF image is scanned and measured by the Classifier to find locations where all four properties fall within their acceptance ranges. If multiple locations are found, the one best conforming to the training estimates is chosen. This location is then declared as a Candidate SN, the instrumentation re-tasked and the operator notified.

  3. Standardized quantitative measurements of wrist cartilage in healthy humans using 3T magnetic resonance imaging

    PubMed Central

    Zink, Jean-Vincent; Souteyrand, Philippe; Guis, Sandrine; Chagnaud, Christophe; Fur, Yann Le; Militianu, Daniela; Mattei, Jean-Pierre; Rozenbaum, Michael; Rosner, Itzhak; Guye, Maxime; Bernard, Monique; Bendahan, David

    2015-01-01

    AIM: To quantify the wrist cartilage cross-sectional area in humans from a 3D magnetic resonance imaging (MRI) dataset and to assess the corresponding reproducibility. METHODS: The study was conducted in 14 healthy volunteers (6 females and 8 males) between 30 and 58 years old and devoid of articular pain. Subjects were asked to lie down in the supine position with the right hand positioned above the pelvic region on top of a home-built rigid platform attached to the scanner bed. The wrist was wrapped with a flexible surface coil. MRI investigations were performed at 3T (Verio-Siemens) using volume interpolated breath hold examination (VIBE) and dual echo steady state (DESS) MRI sequences. Cartilage cross sectional area (CSA) was measured on a slice of interest selected from a 3D dataset of the entire carpus and metacarpal-phalangeal areas on the basis of anatomical criteria using conventional image processing radiology software. Cartilage cross-sectional areas between opposite bones in the carpal region were manually selected and quantified using a thresholding method. RESULTS: Cartilage CSA measurements performed on a selected predefined slice were 292.4 ± 39 mm2 using the VIBE sequence and slightly lower, 270.4 ± 50.6 mm2, with the DESS sequence. The inter (14.1%) and intra (2.4%) subject variability was similar for both MRI methods. The coefficients of variation computed for the repeated measurements were also comparable for the VIBE (2.4%) and the DESS (4.8%) sequences. The carpus length averaged over the group was 37.5 ± 2.8 mm with a 7.45% between-subjects coefficient of variation. Of note, wrist cartilage CSA measured with either the VIBE or the DESS sequences was linearly related to the carpal bone length. The variability between subjects was significantly reduced to 8.4% when the CSA was normalized with respect to the carpal bone length. CONCLUSION: The ratio between wrist cartilage CSA and carpal bone length is a highly reproducible standardized

  4. SpotMetrics: An Open-Source Image-Analysis Software Plugin for Automatic Chromatophore Detection and Measurement

    PubMed Central

    Hadjisolomou, Stavros P.; El-Haddad, George

    2017-01-01

    Coleoid cephalopods (squid, octopus, and sepia) are renowned for their elaborate body patterning capabilities, which are employed for camouflage or communication. The specific chromatic appearance of a cephalopod, at any given moment, is a direct result of the combined action of their intradermal pigmented chromatophore organs and reflecting cells. Therefore, a lot can be learned about the cephalopod coloration system by video recording and analyzing the activation of individual chromatophores in time. The fact that adult cephalopods have small chromatophores, up to several hundred thousand in number, makes measurement and analysis over several seconds a difficult task. However, current advancements in videography enable high-resolution and high framerate recording, which can be used to record chromatophore activity in more detail and accuracy in both space and time domains. In turn, the additional pixel information and extra frames per video from such recordings result in large video files of several gigabytes, even when the recording spans only few minutes. We created a software plugin, “SpotMetrics,” that can automatically analyze high resolution, high framerate video of chromatophore organ activation in time. This image analysis software can track hundreds of individual chromatophores over several hundred frames to provide measurements of size and color. This software may also be used to measure differences in chromatophore activation during different behaviors which will contribute to our understanding of the cephalopod sensorimotor integration system. In addition, this software can potentially be utilized to detect numbers of round objects and size changes in time, such as eye pupil size or number of bacteria in a sample. Thus, we are making this software plugin freely available as open-source because we believe it will be of benefit to other colleagues both in the cephalopod biology field and also within other disciplines. PMID:28298896

  5. SpotMetrics: An Open-Source Image-Analysis Software Plugin for Automatic Chromatophore Detection and Measurement.

    PubMed

    Hadjisolomou, Stavros P; El-Haddad, George

    2017-01-01

    Coleoid cephalopods (squid, octopus, and sepia) are renowned for their elaborate body patterning capabilities, which are employed for camouflage or communication. The specific chromatic appearance of a cephalopod, at any given moment, is a direct result of the combined action of their intradermal pigmented chromatophore organs and reflecting cells. Therefore, a lot can be learned about the cephalopod coloration system by video recording and analyzing the activation of individual chromatophores in time. The fact that adult cephalopods have small chromatophores, up to several hundred thousand in number, makes measurement and analysis over several seconds a difficult task. However, current advancements in videography enable high-resolution and high framerate recording, which can be used to record chromatophore activity in more detail and accuracy in both space and time domains. In turn, the additional pixel information and extra frames per video from such recordings result in large video files of several gigabytes, even when the recording spans only few minutes. We created a software plugin, "SpotMetrics," that can automatically analyze high resolution, high framerate video of chromatophore organ activation in time. This image analysis software can track hundreds of individual chromatophores over several hundred frames to provide measurements of size and color. This software may also be used to measure differences in chromatophore activation during different behaviors which will contribute to our understanding of the cephalopod sensorimotor integration system. In addition, this software can potentially be utilized to detect numbers of round objects and size changes in time, such as eye pupil size or number of bacteria in a sample. Thus, we are making this software plugin freely available as open-source because we believe it will be of benefit to other colleagues both in the cephalopod biology field and also within other disciplines.

  6. Integration of bio- and geoscience data with the ODM2 standards and software ecosystem for the CZOData and BiG CZ Data projects

    NASA Astrophysics Data System (ADS)

    Aufdenkampe, A. K.; Mayorga, E.; Horsburgh, J. S.; Lehnert, K. A.; Zaslavsky, I.

    2015-12-01

    We have developed a family of solutions to the challenges of integrating diverse data from of biological and geological (BiG) disciplines for Critical Zone (CZ) science. These standards and software solutions have been developed around the new Observations Data Model version 2.0 (ODM2, http://ODM2.org), which was designed as a profile of the Open Geospatial Consortium's (OGC) Observations and Measurements (O&M) standard. The ODM2 standards and software ecosystem has at it's core an information model that balances specificity with flexibility to powerfully and equally serve the needs of multiple dataset types, from multivariate sensor-generated time series to geochemical measurements of specimen hierarchies to multi-dimensional spectral data to biodiversity observations. ODM2 has been adopted as the information model guiding the next generation of cyberinfrastructure development for the Interdisciplinary Earth Data Alliance (http://www.iedadata.org/) and the CUAHSI Water Data Center (https://www.cuahsi.org/wdc). Here we present several components of the ODM2 standards and software ecosystem that were developed specifically to help CZ scientists and their data managers to share and manage data through the national Critical Zone Observatory data integration project (CZOData, http://criticalzone.org/national/data/) and the bio integration with geo for critical zone science data project (BiG CZ Data, http://bigcz.org/). These include the ODM2 Controlled Vocabulary system (http://vocabulary.odm2.org), the YAML Observation Data Archive & exchange (YODA) File Format (https://github.com/ODM2/YODA-File) and the BiG CZ Toolbox, which will combine easy-to-install ODM2 databases (https://github.com/ODM2/ODM2) with a variety of graphical software packages for data management such as ODMTools (https://github.com/ODM2/ODMToolsPython) and the ODM2 Streaming Data Loader (https://github.com/ODM2/ODM2StreamingDataLoader).

  7. ImaSim, a software tool for basic education of medical x-ray imaging in radiotherapy and radiology

    NASA Astrophysics Data System (ADS)

    Landry, Guillaume; deBlois, François; Verhaegen, Frank

    2013-11-01

    Introduction: X-ray imaging is an important part of medicine and plays a crucial role in radiotherapy. Education in this field is mostly limited to textbook teaching due to equipment restrictions. A novel simulation tool, ImaSim, for teaching the fundamentals of the x-ray imaging process based on ray-tracing is presented in this work. ImaSim is used interactively via a graphical user interface (GUI). Materials and methods: The software package covers the main x-ray based medical modalities: planar kilo voltage (kV), planar (portal) mega voltage (MV), fan beam computed tomography (CT) and cone beam CT (CBCT) imaging. The user can modify the photon source, object to be imaged and imaging setup with three-dimensional editors. Objects are currently obtained by combining blocks with variable shapes. The imaging of three-dimensional voxelized geometries is currently not implemented, but can be added in a later release. The program follows a ray-tracing approach, ignoring photon scatter in its current implementation. Simulations of a phantom CT scan were generated in ImaSim and were compared to measured data in terms of CT number accuracy. Spatial variations in the photon fluence and mean energy from an x-ray tube caused by the heel effect were estimated from ImaSim and Monte Carlo simulations and compared. Results: In this paper we describe ImaSim and provide two examples of its capabilities. CT numbers were found to agree within 36 Hounsfield Units (HU) for bone, which corresponds to a 2% attenuation coefficient difference. ImaSim reproduced the heel effect reasonably well when compared to Monte Carlo simulations. Discussion: An x-ray imaging simulation tool is made available for teaching and research purposes. ImaSim provides a means to facilitate the teaching of medical x-ray imaging.

  8. Panoramic Images Mapping Tools Integrated Within the ESRI ArcGIS Software

    NASA Astrophysics Data System (ADS)

    Guo, Jiao; Zhong, Ruofei; Zeng, Fanyang

    2014-03-01

    There is a general study on panoramic images which are presented along with appearance of the Google street map. Despite 360 degree viewing of street, we can realize more applications over panoramic images. This paper developed a toolkits plugged in ArcGIS, which can view panoramic photographs at street level directly from ArcMap and measure and capture all visible elements as frontages, trees and bridges. We use a series of panoramic images adjoined with absolute coordinate through GPS and IMU. There are two methods in this paper to measure object from these panoramic images: one is to intersect object position through a stereogram; the other one is multichip matching involved more than three images which all cover the object. While someone wants to measure objects from these panoramic images, each two panoramic images which both contain the object can be chosen to display on ArcMap. Then we calculate correlation coefficient of the two chosen panoramic images so as to calculate the coordinate of object. Our study test different patterns of panoramic pairs and compare the results of measurement to the real value of objects so as to offer the best choosing suggestion. The article has mainly elaborated the principles of calculating correlation coefficient and multichip matching.

  9. Software-based turbulence mitigation of short exposure image data with motion detection and background segmentation

    NASA Astrophysics Data System (ADS)

    Huebner, Claudia S.

    2011-11-01

    The degree of image degradation due to atmospheric turbulence is particularly severe when imaging over long horizontal paths since the turbulence is strongest close to the ground. The most pronounced effects include image blurring and image dancing and in case of strong turbulence image distortion as well. To mitigate these effects a number of methods from the field of image processing have been proposed most of which aim exclusively at the restoration of static scenes. But there is also an increasing interest in advancing turbulence mitigation to encompass moving objects as well. Therefore, in this paper a procedure is described that employs block-matching for the segmentation of static scene elements and moving objects such that image restoration can be carried out for both separately. This way motion blurring is taken into account in addition to atmospheric blurring, effectively reducing motion artefacts and improving the overall restoration result. Motion-compensated averaging with subsequent blind deconvolution is used for the actual image restoration.

  10. Super-resolution for everybody: An image processing workflow to obtain high-resolution images with a standard confocal microscope.

    PubMed

    Lam, France; Cladière, Damien; Guillaume, Cyndélia; Wassmann, Katja; Bolte, Susanne

    2017-02-15

    In the presented work we aimed at improving confocal imaging to obtain highest possible resolution in thick biological samples, such as the mouse oocyte. We therefore developed an image processing workflow that allows improving the lateral and axial resolution of a standard confocal microscope. Our workflow comprises refractive index matching, the optimization of microscope hardware parameters and image restoration by deconvolution. We compare two different deconvolution algorithms, evaluate the necessity of denoising and establish the optimal image restoration procedure. We validate our workflow by imaging sub resolution fluorescent beads and measuring the maximum lateral and axial resolution of the confocal system. Subsequently, we apply the parameters to the imaging and data restoration of fluorescently labelled meiotic spindles of mouse oocytes. We measure a resolution increase of approximately 2-fold in the lateral and 3-fold in the axial direction throughout a depth of 60μm. This demonstrates that with our optimized workflow we reach a resolution that is comparable to 3D-SIM-imaging, but with better depth penetration for confocal images of beads and the biological sample.

  11. Robotic 3D scanner as an alternative to standard modalities of medical imaging.

    PubMed

    Chromy, Adam; Zalud, Ludek

    2014-01-01

    There are special medical cases, where standard medical imaging modalities are able to offer sufficient results, but not in the optimal way. It means, that desired results are produced with unnecessarily high expenses, with redundant informations or with needless demands on patient. This paper deals with one special case, where information useful for examination is the body surface only, inner sight into the body is needless. New specialized medical imaging device is developed for this situation. In the Introduction section, analysis of presently used medical imaging modalities is presented, which declares, that no available imaging device is best fitting for mentioned purposes. In the next section, development of the new specialized medical imaging device is presented, and its principles and functions are described. Then, the parameters of new device are compared with present ones. It brings significant advantages comparing to present imaging systems.

  12. Simultaneous iterative reconstruction technique software for spectral-spatial EPR imaging

    NASA Astrophysics Data System (ADS)

    Spitzbarth, Martin; Drescher, Malte

    2015-08-01

    Continuous wave electron paramagnetic resonance imaging (EPRI) experiments often suffer from low signal to noise ratio. The increase in spectrometer time required to acquire data of sufficient quality to allow further analysis can be counteracted in part by more processing effort during the image reconstruction step. We suggest a simultaneous iterative reconstruction algorithm (SIRT) for reconstruction of continuous wave EPRI experimental data as an alternative to the widely applied filtered back projection algorithm (FBP). We show experimental and numerical test data of 2d spatial images and spectral-spatial images. We find that for low signal to noise ratio and spectral-spatial images that are limited by the maximum magnetic field gradient strength SIRT is more suitable than FBP.

  13. User's Guide for MapIMG 2: Map Image Re-projection Software Package

    USGS Publications Warehouse

    Finn, Michael P.; Trent, Jason R.; Buehler, Robert A.

    2006-01-01

    BACKGROUND Scientists routinely accomplish small-scale geospatial modeling in the raster domain, using high-resolution datasets for large parts of continents and low-resolution to high-resolution datasets for the entire globe. Direct implementation of point-to-point transformation with appropriate functions yields the variety of projections available in commercial software packages, but implementation with data other than points requires specific adaptation of the transformation equations or prior preparation of the data to allow the transformation to succeed. It seems that some of these packages use the U.S. Geological Survey's (USGS) General Cartographic Transformation Package (GCTP) or similar point transformations without adaptation to the specific characteristics of raster data (Usery and others, 2003a). Usery and others (2003b) compiled and tabulated the accuracy of categorical areas in projected raster datasets of global extent. Based on the shortcomings identified in these studies, geographers and applications programmers at the USGS expanded and evolved a USGS software package, MapIMG, for raster map projection transformation (Finn and Trent, 2004). Daniel R. Steinwand of Science Applications International Corporation, National Center for Earth Resources Observation and Science, originally developed MapIMG for the USGS, basing it on GCTP. Through previous and continuing efforts at the USGS' National Geospatial Technical Operations Center, this program has been transformed from an application based on command line input into a software package based on a graphical user interface for Windows, Linux, and other UNIX machines.

  14. Image Format Conversion to DICOM and Lookup Table Conversion to Presentation Value of the Japanese Society of Radiological Technology (JSRT) Standard Digital Image Database.

    PubMed

    Yanagita, Satoshi; Imahana, Masato; Suwa, Kazuaki; Sugimura, Hitomi; Nishiki, Masayuki

    Japanese Society of Radiological Technology (JSRT) standard digital image database contains many useful cases of chest X-ray images, and has been used in many state-of-the-art researches. However, the pixel values of all the images are simply digitized as relative density values by utilizing a scanned film digitizer. As a result, the pixel values are completely different from the standardized display system input value of digital imaging and communications in medicine (DICOM), called presentation value (P-value), which can maintain a visual consistency when observing images using different display luminance. Therefore, we converted all the images from JSRT standard digital image database to DICOM format followed by the conversion of the pixel values to P-value using an original program developed by ourselves. Consequently, JSRT standard digital image database has been modified so that the visual consistency of images is maintained among different luminance displays.

  15. Review and Implementation of the Emerging CCSDS Recommended Standard for Multispectral and Hyperspectral Lossless Image Coding

    NASA Technical Reports Server (NTRS)

    Sanchez, Jose Enrique; Auge, Estanislau; Santalo, Josep; Blanes, Ian; Serra-Sagrista, Joan; Kiely, Aaron

    2011-01-01

    A new standard for image coding is being developed by the MHDC working group of the CCSDS, targeting onboard compression of multi- and hyper-spectral imagery captured by aircraft and satellites. The proposed standard is based on the "Fast Lossless" adaptive linear predictive compressor, and is adapted to better overcome issues of onboard scenarios. In this paper, we present a review of the state of the art in this field, and provide an experimental comparison of the coding performance of the emerging standard in relation to other state-of-the-art coding techniques. Our own independent implementation of the MHDC Recommended Standard, as well as of some of the other techniques, has been used to provide extensive results over the vast corpus of test images from the CCSDS-MHDC.

  16. Reduction of blocking effects for the JPEG baseline image compression standard

    NASA Technical Reports Server (NTRS)

    Zweigle, Gregary C.; Bamberger, Roberto H.

    1992-01-01

    Transform coding has been chosen for still image compression in the Joint Photographic Experts Group (JPEG) standard. Although transform coding performs superior to many other image compression methods and has fast algorithms for implementation, it is limited by a blocking effect at low bit rates. The blocking effect is inherent in all nonoverlapping transforms. This paper presents a technique for reducing blocking while remaining compatible with the JPEG standard. Simulations show that the system results in subjective performance improvements, sacrificing only a marginal increase in bit rate.

  17. Multiparametric Cell Cycle Analysis Using the Operetta High-Content Imager and Harmony Software with PhenoLOGIC.

    PubMed

    Massey, Andrew J

    2015-01-01

    High-content imaging is a powerful tool for determining cell phenotypes at the single cell level. Characterising the effect of small molecules on cell cycle distribution is important for understanding their mechanism of action especially in oncology drug discovery but also for understanding potential toxicology liabilities. Here, a high-throughput phenotypic assay utilising the PerkinElmer Operetta high-content imager and Harmony software to determine cell cycle distribution is described. PhenoLOGIC, a machine learning algorithm within Harmony software was employed to robustly separate single cells from cell clumps. DNA content, EdU incorporation and pHH3 (S10) expression levels were subsequently utilised to separate cells into the various phases of the cell cycle. The assay is amenable to multiplexing with an additional pharmacodynamic marker to assess cell cycle changes within a specific cellular sub-population. Using this approach, the cell cycle distribution of γH2AX positive nuclei was determined following treatment with DNA damaging agents. Likewise, the assay can be multiplexed with Ki67 to determine the fraction of quiescent cells and with BrdU dual labelling to determine S-phase duration. This methodology therefore provides a relatively cheap, quick and high-throughput phenotypic method for determining accurate cell cycle distribution for small molecule mechanism of action and drug toxicity studies.

  18. A new substitution-diffusion based image cipher using chaotic standard and logistic maps

    NASA Astrophysics Data System (ADS)

    Patidar, Vinod; Pareek, N. K.; Sud, K. K.

    2009-07-01

    In this paper, we propose a new loss-less symmetric image cipher based on the widely used substitution-diffusion architecture which utilizes chaotic standard and logistic maps. It is specifically designed for the coloured images, which are 3D arrays of data streams. The initial condition, system parameter of the chaotic standard map and number of iterations together constitute the secret key of the algorithm. The first round of substitution/confusion is achieved with the help of intermediate XORing keys calculated from the secret key. Then two rounds of diffusion namely the horizontal and vertical diffusions are completed by mixing the properties of horizontally and vertically adjacent pixels, respectively. In the fourth round, a robust substitution/confusion is accomplished by generating an intermediate chaotic key stream (CKS) image in a novel manner with the help of chaotic standard and logistic maps. The security and performance of the proposed image encryption technique has been analyzed thoroughly using various statistical analysis, key sensitivity analysis, differential analysis, key space analysis, speed analysis, etc. Results of the various types of analysis are encouraging and suggest that the proposed image encryption technique is able to manage the trade offs between the security and speed and hence suitable for the real-time secure image and video communication applications.

  19. Software Update.

    ERIC Educational Resources Information Center

    Currents, 2000

    2000-01-01

    A chart of 40 alumni-development database systems provides information on vendor/Web site, address, contact/phone, software name, price range, minimum suggested workstation/suggested server, standard reports/reporting tools, minimum/maximum record capacity, and number of installed sites/client type. (DB)

  20. Measurement of ground displacement from optical satellite image correlation using the free open-source software MicMac

    NASA Astrophysics Data System (ADS)

    Rosu, Ana-Maria; Pierrot-Deseilligny, Marc; Delorme, Arthur; Binet, Renaud; Klinger, Yann

    2015-02-01

    Image correlation is one of the most efficient techniques to determine horizontal ground displacements due to earthquakes, landslides, ice flows or sand dune migrations. Analyzing these deformations allows a better understanding of the causes and mechanisms of the events. By using sub-pixel correlation on before- and after-event ortho-images obtained from high resolution satellite images it is possible to compute the displacement field with high planimetric resolution. In this paper, we focus on measuring the ground displacements due to seismotectonic events. The three sub-pixel correlators used are: COSI-Corr - developed by Caltech, a free, closed-source correlator, dependent on commercial software (ENVI) and widely used by the geoscience community for measuring ground displacement; Medicis - developed by CNES, also a closed-source correlator capable of measuring this type of deformation; and MicMac - developed by IGN, the free open-source correlator we study and tune for measuring fine ground displacements. We measured horizontal ground deformation using these three correlators on SPOT images in three study cases: the 2001 Kokoxili earthquake, the 2005 dyke intrusion in the Afar depression and the 2008 Yutian earthquake.

  1. Application of Technical Measures and Software in Constructing Photorealistic 3D Models of Historical Building Using Ground-Based and Aerial (UAV) Digital Images

    NASA Astrophysics Data System (ADS)

    Zarnowski, Aleksander; Banaszek, Anna; Banaszek, Sebastian

    2015-12-01

    Preparing digital documentation of historical buildings is a form of protecting cultural heritage. Recently there have been several intensive studies using non-metric digital images to construct realistic 3D models of historical buildings. Increasingly often, non-metric digital images are obtained with unmanned aerial vehicles (UAV). Technologies and methods of UAV flights are quite different from traditional photogrammetric approaches. The lack of technical guidelines for using drones inhibits the process of implementing new methods of data acquisition. This paper presents the results of experiments in the use of digital images in the construction of photo-realistic 3D model of a historical building (Raphaelsohns' Sawmill in Olsztyn). The aim of the study at the first stage was to determine the meteorological and technical conditions for the acquisition of aerial and ground-based photographs. At the next stage, the technology of 3D modelling was developed using only ground-based or only aerial non-metric digital images. At the last stage of the study, an experiment was conducted to assess the possibility of 3D modelling with the comprehensive use of aerial (UAV) and ground-based digital photographs in terms of their labour intensity and precision of development. Data integration and automatic photo-realistic 3D construction of the models was done with Pix4Dmapper and Agisoft PhotoScan software Analyses have shown that when certain parameters established in an experiment are kept, the process of developing the stock-taking documentation for a historical building moves from the standards of analogue to digital technology with considerably reduced cost.

  2. Data reduction software for the Mid-Infrared E-ELT Imager and Spectrograph (METIS) for the European Extremely Large Telescope (E-ELT)

    NASA Astrophysics Data System (ADS)

    Mach, Michael; Köhler, Rainer; Czoske, Oliver; Leschinski, Kieran; Zeilinger, Werner W.; Kausch, Wolfgang; Ratzka, Thorsten; Leitzinger, Martin; Greimel, Robert; Przybilla, Norbert; Schaffenroth, Veronika; Güdel, Manuel; Brandl, Bernhard R.

    2016-07-01

    We present the current status of the design of the science data reduction pipeline and the corresponding dataflow system for METIS. It will be one of the first three instruments for the E-ELT and work at wavelengths between 3-19 μm (L/M/N/Q1 bands). We will deliver software which is compliant to standards of the European Southern Observatory (ESO), and will employ state of the art techniques to produce science grade data, master calibration frames, quality control parameters and to handle instrument effects. The Instrument currently offers a wealth of observing modes that are listed in this paper. Data reduction for a ground based instrument at these wavelengths is particularly challenging because of the massive influence of thermal radiation from various sources. We will give a comprehensive overview of the data ow system for the imaging modes that the instrument offers and discuss a single recipe versus a multi recipe approach for the different observing modes for imaging.

  3. Automatic magnification determination of electron cryomicroscopy images using apoferritin as a standard.

    PubMed

    Wasilewski, Sebastian; Karelina, Darya; Berriman, John A; Rosenthal, Peter B

    2012-10-01

    Interpretation of the structural information in cryomicroscopy images recorded on film or CCD camera requires a precise knowledge of the electron microscope parameters that affect image features such as magnification and defocus. Magnification must be determined in order to combine data from different images in a three-dimensional reconstruction and to accurately scale reconstructions for fitting with atomic resolution models. A method is described for estimating the absolute magnification of an electron micrograph of a frozen-hydrated specimen using horse spleen apoferritin as a standard. Apoferritin is a widely available protein complex of known structure that may be included with the specimen of interest and imaged under conditions identical to those used for imaging other biological specimens by cryomicroscopy. The sum of the structure factor intensities of images of randomly-oriented apoferritin particles shows three low resolution peaks to 25Å that arise from the hollow ball structure of apoferritin. Comparison of peak positions of the experimental intensities with structure factor intensities of an atomic model of apoferritin determined by X-ray crystallography provides a scale factor for estimating the absolute magnification of the micrograph. We compare the magnification estimate using apoferritin to that obtained with tobacco mosaic virus, another common magnification standard for cryomicroscopy. We verify the precision of the method by acquiring images with a systematic variation of magnification.

  4. Dual-energy CT with virtual monochromatic images and metal artifact reduction software for reducing metallic dental artifacts.

    PubMed

    Cha, Jihoon; Kim, Hyung-Jin; Kim, Sung Tae; Kim, Yi Kyung; Kim, Ha Youn; Park, Gyeong Min

    2017-01-01

    Background Metallic dental prostheses may degrade image quality on head and neck computed tomography (CT). However, there is little information available on the use of dual-energy CT (DECT) and metal artifact reduction software (MARS) in the head and neck regions to reduce metallic dental artifacts. Purpose To assess the usefulness of DECT with virtual monochromatic imaging and MARS to reduce metallic dental artifacts. Material and Methods DECT was performed using fast kilovoltage (kV)-switching between 80-kV and 140-kV in 20 patients with metallic dental prostheses. CT data were reconstructed with and without MARS, and with synthesized monochromatic energy in the range of 40-140-kiloelectron volt (keV). For quantitative analysis, the artifact index of the tongue, buccal, and parotid areas was calculated for each scan. For qualitative analysis, two radiologists evaluated 70-keV and 100-keV images with and without MARS for tongue, buccal, parotid areas, and metallic denture. The locations and characteristics of the MARS-related artifacts, if any, were also recorded. Results DECT with MARS markedly reduced metallic dental artifacts and improved image quality in the buccal area ( P < 0.001) and the tongue ( P < 0.001), but not in the parotid area. The margin and internal architecture of the metallic dentures were more clearly delineated with MARS ( P < 0.001) and in the higher-energy images than in the lower-energy images ( P = 0.042). MARS-related artifacts most commonly occurred in the deep center of the neck. Conclusion DECT with MARS can reduce metallic dental artifacts and improve delineation of the metallic prosthesis and periprosthetic region.

  5. Analysis of image sharpness reproducibility on a novel engineered micro-CT scanner with variable geometry and embedded recalibration software.

    PubMed

    Panetta, D; Belcari, N; Del Guerra, A; Bartolomei, A; Salvadori, P A

    2012-04-01

    This study investigates the reproducibility of the reconstructed image sharpness, after modifications of the geometry setup, for a variable magnification micro-CT (μCT) scanner. All the measurements were performed on a novel engineered μCT scanner for in vivo imaging of small animals (Xalt), which has been recently built at the Institute of Clinical Physiology of the National Research Council (IFC-CNR, Pisa, Italy), in partnership with the University of Pisa. The Xalt scanner is equipped with an integrated software for on-line geometric recalibration, which will be used throughout the experiments. In order to evaluate the losses of image quality due to modifications of the geometry setup, we have made 22 consecutive acquisitions by changing alternatively the system geometry between two different setups (Large FoV - LF, and High Resolution - HR). For each acquisition, the tomographic images have been reconstructed before and after the on-line geometric recalibration. For each reconstruction, the image sharpness was evaluated using two different figures of merit: (i) the percentage contrast on a small bar pattern of fixed frequency (f = 5.5 lp/mm for the LF setup and f = 10 lp/mm for the HR setup) and (ii) the image entropy. We have found that, due to the small-scale mechanical uncertainty (in the order of the voxel size), a recalibration is necessary for each geometric setup after repositioning of the system's components; the resolution losses due to the lack of recalibration are worse for the HR setup (voxel size = 18.4 μm). The integrated on-line recalibration algorithm of the Xalt scanner allowed to perform the recalibration quickly, by restoring the spatial resolution of the system to the reference resolution obtained after the initial (off-line) calibration.

  6. Familiarity effects in the construction of facial-composite images using modern software systems.

    PubMed

    Frowd, Charlie D; Skelton, Faye C; Butt, Neelam; Hassan, Amal; Fields, Stephen; Hancock, Peter J B

    2011-12-01

    We investigate the effect of target familiarity on the construction of facial composites, as used by law enforcement to locate criminal suspects. Two popular software construction methods were investigated. Participants were shown a target face that was either familiar or unfamiliar to them and constructed a composite of it from memory using a typical 'feature' system, involving selection of individual facial features, or one of the newer 'holistic' types, involving repeated selection and breeding from arrays of whole faces. This study found that composites constructed of a familiar face were named more successfully than composites of an unfamiliar face; also, naming of composites of internal and external features was equivalent for construction of unfamiliar targets, but internal features were better named than the external features for familiar targets. These findings applied to both systems, although benefit emerged for the holistic type due to more accurate construction of internal features and evidence for a whole-face advantage. STATEMENT OF RELEVANCE: This work is of relevance to practitioners who construct facial composites with witnesses to and victims of crime, as well as for software designers to help them improve the effectiveness of their composite systems.

  7. Seismic reflection imaging of underground cavities using open-source software

    SciTech Connect

    Mellors, R J

    2011-12-20

    The Comprehensive Nuclear Test Ban Treaty (CTBT) includes provisions for an on-site inspection (OSI), which allows the use of specific techniques to detect underground anomalies including cavities and rubble zones. One permitted technique is active seismic surveys such as seismic refraction or reflection. The purpose of this report is to conduct some simple modeling to evaluate the potential use of seismic reflection in detecting cavities and to test the use of open-source software in modeling possible scenarios. It should be noted that OSI inspections are conducted under specific constraints regarding duration and logistics. These constraints are likely to significantly impact active seismic surveying, as a seismic survey typically requires considerable equipment, effort, and expertise. For the purposes of this study, which is a first-order feasibility study, these issues will not be considered. This report provides a brief description of the seismic reflection method along with some commonly used software packages. This is followed by an outline of a simple processing stream based on a synthetic model, along with results from a set of models representing underground cavities. A set of scripts used to generate the models are presented in an appendix. We do not consider detection of underground facilities in this work and the geologic setting used in these tests is an extremely simple one.

  8. Motion correction of PET brain images through deconvolution: I. Theoretical development and analysis in software simulations

    NASA Astrophysics Data System (ADS)

    Faber, T. L.; Raghunath, N.; Tudorascu, D.; Votaw, J. R.

    2009-02-01

    Image quality is significantly degraded even by small amounts of patient motion in very high-resolution PET scanners. Existing correction methods that use known patient motion obtained from tracking devices either require multi-frame acquisitions, detailed knowledge of the scanner, or specialized reconstruction algorithms. A deconvolution algorithm has been developed that alleviates these drawbacks by using the reconstructed image to estimate the original non-blurred image using maximum likelihood estimation maximization (MLEM) techniques. A high-resolution digital phantom was created by shape-based interpolation of the digital Hoffman brain phantom. Three different sets of 20 movements were applied to the phantom. For each frame of the motion, sinograms with attenuation and three levels of noise were simulated and then reconstructed using filtered backprojection. The average of the 20 frames was considered the motion blurred image, which was restored with the deconvolution algorithm. After correction, contrast increased from a mean of 2.0, 1.8 and 1.4 in the motion blurred images, for the three increasing amounts of movement, to a mean of 2.5, 2.4 and 2.2. Mean error was reduced by an average of 55% with motion correction. In conclusion, deconvolution can be used for correction of motion blur when subject motion is known.

  9. Space Station Software Recommendations

    NASA Technical Reports Server (NTRS)

    Voigt, S. (Editor)

    1985-01-01

    Four panels of invited experts and NASA representatives focused on the following topics: software management, software development environment, languages, and software standards. Each panel deliberated in private, held two open sessions with audience participation, and developed recommendations for the NASA Space Station Program. The major thrusts of the recommendations were as follows: (1) The software management plan should establish policies, responsibilities, and decision points for software acquisition; (2) NASA should furnish a uniform modular software support environment and require its use for all space station software acquired (or developed); (3) The language Ada should be selected for space station software, and NASA should begin to address issues related to the effective use of Ada; and (4) The space station software standards should be selected (based upon existing standards where possible), and an organization should be identified to promulgate and enforce them. These and related recommendations are described in detail in the conference proceedings.

  10. Integration of instrumentation and processing software of a laser speckle contrast imaging system

    NASA Astrophysics Data System (ADS)

    Carrick, Jacob J.

    Laser speckle contrast imaging (LSCI) has the potential to be a powerful tool in medicine, but more research in the field is required so it can be used properly. To help in the progression of Michigan Tech's research in the field, a graphical user interface (GUI) was designed in Matlab to control the instrumentation of the experiments as well as process the raw speckle images into contrast images while they are being acquired. The design of the system was successful and is currently being used by Michigan Tech's Biomedical Engineering department. This thesis describes the development of the LSCI GUI as well as offering a full introduction into the history, theory and applications of LSCI.

  11. Automated image mosaics by non-automated light microscopes: the MicroMos software tool.

    PubMed

    Piccinini, F; Bevilacqua, A; Lucarelli, E

    2013-12-01

    Light widefield microscopes and digital imaging are the basis for most of the analyses performed in every biological laboratory. In particular, the microscope's user is typically interested in acquiring high-detailed images for analysing observed cells and tissues, meanwhile being representative of a wide area to have reliable statistics. The microscopist has to choose between higher magnification factor and extension of the observed area, due to the finite size of the camera's field of view. To overcome the need of arrangement, mosaicing techniques have been developed in the past decades for increasing the camera's field of view by stitching together more images. Nevertheless, these approaches typically work in batch mode and rely on motorized microscopes. Or alternatively, the methods are conceived just to provide visually pleasant mosaics not suitable for quantitative analyses. This work presents a tool for building mosaics of images acquired with nonautomated light microscopes. The method proposed is based on visual information only and the mosaics are built by incrementally stitching couples of images, making the approach available also for online applications. Seams in the stitching regions as well as tonal inhomogeneities are corrected by compensating the vignetting effect. In the experiments performed, we tested different registration approaches, confirming that the translation model is not always the best, despite the fact that the motion of the sample holder of the microscope is apparently translational and typically considered as such. The method's implementation is freely distributed as an open source tool called MicroMos. Its usability makes building mosaics of microscope images at subpixel accuracy easier. Furthermore, optional parameters for building mosaics according to different strategies make MicroMos an easy and reliable tool to compare different registration approaches, warping models and tonal corrections.

  12. Hardware, software, and scanning issues encountered during small animal imaging of photodynamic therapy in the athymic nude rat

    NASA Astrophysics Data System (ADS)

    Cross, Nathan; Sharma, Rahul; Varghai, Davood; Spring-Robinson, Chandra; Oleinick, Nancy L.; Muzic, Raymond F., Jr.; Dean, David

    2007-02-01

    Small animal imaging devices are now commonly used to study gene activation and model the effects of potential therapies. We are attempting to develop a protocol that non-invasively tracks the affect of Pc 4-mediated photodynamic therapy (PDT) in a human glioma model using structural image data from micro-CT and/or micro-MR scanning and functional data from 18F-fluorodeoxy-glucose (18F-FDG) micro-PET imaging. Methods: Athymic nude rat U87-derived glioma was imaged by micro-PET and either micro-CT or micro-MR prior to Pc 4-PDT. Difficulty insuring animal anesthesia and anatomic position during the micro-PET, micro-CT, and micro-MR scans required adaptation of the scanning bed hardware. Following Pc 4-PDT the animals were again 18F-FDG micro-PET scanned, euthanized one day later, and their brains were explanted and prepared for H&E histology. Histology provided the gold standard for tumor location and necrosis. The tumor and surrounding brain functional and structural image data were then isolated and coregistered. Results: Surprisingly, both the non-PDT and PDT groups showed an increase in tumor functional activity when we expected this signal to disappear in the group receiving PDT. Co-registration of the functional and structural image data was done manually. Discussion: As expected, micro-MR imaging provided better structural discrimination of the brain tumor than micro-CT. Contrary to expectations, in our preliminary analysis 18F-FDG micro-PET imaging does not readily discriminate the U87 tumors that received Pc 4-PDT. We continue to investigate the utility of micro-PET and other methods of functional imaging to remotely detect the specificity and sensitivity of Pc 4-PDT in deeply placed tumors.

  13. Toolkits and Software for Developing Biomedical Image Processing and Analysis Applications

    NASA Astrophysics Data System (ADS)

    Wolf, Ivo

    Solutions in biomedical image processing and analysis usually consist of much more than a single method. Typically, a whole pipeline of algorithms is necessary, combined with visualization components to display and verify the results as well as possibilities to interact with the data. Therefore, successful research in biomedical image processing and analysis requires a solid base to start from. This is the case regardless whether the goal is the development of a new method (e.g., for segmentation) or to solve a specific task (e.g., computer-assisted planning of surgery).

  14. Image-guided tumor ablation: standardization of terminology and reporting criteria.

    PubMed

    Goldberg, S Nahum; Grassi, Clement J; Cardella, John F; Charboneau, J William; Dodd, Gerald D; Dupuy, Damian E; Gervais, Debra A; Gillams, Alice R; Kane, Robert A; Lee, Fred T; Livraghi, Tito; McGahan, John; Phillips, David A; Rhim, Hyunchul; Silverman, Stuart G; Solbiati, Luigi; Vogl, Thomas J; Wood, Bradford J; Vedantham, Suresh; Sacks, David

    2009-07-01

    The field of interventional oncology with use of image-guided tumor ablation requires standardization of terminology and reporting criteria to facilitate effective communication of ideas and appropriate comparison between treatments that use different technologies, such as chemical (ethanol or acetic acid) ablation, and thermal therapies, such as radiofrequency (RF), laser, microwave, ultrasound, and cryoablation. This document provides a framework that will hopefully facilitate the clearest communication between investigators and will provide the greatest flexibility in comparison between the many new, exciting, and emerging technologies. An appropriate vehicle for reporting the various aspects of image-guided ablation therapy, including classification of therapies and procedure terms, appropriate descriptors of imaging guidance, and terminology to define imaging and pathologic findings, are outlined. Methods for standardizing the reporting of follow-up findings and complications and other important aspects that require attention when reporting clinical results are addressed. It is the group's intention that adherence to the recommendations will facilitate achievement of the group's main objective: improved precision and communication in this field that lead to more accurate comparison of technologies and results and, ultimately, to improved patient outcomes. The intent of this standardization of terminology is to provide an appropriate vehicle for reporting the various aspects of image-guided ablation therapy.

  15. Standard resolution spectral domain optical coherence tomography in clinical ophthalmic imaging

    NASA Astrophysics Data System (ADS)

    Szkulmowska, Anna; Cyganek, Marta; Targowski, Piotr; Kowalczyk, Andrzej; Kaluzny, Jakub J.; Wojtkowski, Maciej; Fujimoto, James G.

    2005-04-01

    In this study we show clinical application of Spectral Optical Coherence Tomography (SOCT), which enables operation with 40 times higher speed than commercial Stratus OCT instrument. Using high speed SOCT instrument it is possible to collect more information and increase the quality of reconstructed cross-sectional retinal images. Two generations of compact and portable clinical SOCT instruments were constructed in Medical Physics Group at Nicolaus Copernicus University in Poland. The first SOCT instrument is a low-cost system operating with standard, 12 micrometer axial resolution and the second is high resolution system using combined superluminescent diodes light source, which enables imaging with 4.8 micrometer axial resolution. Both instruments have worked in Ophthalmology Clinic of Collegium Medicum in Bydgoszcz. During the study we have examined 44 patients with different pathologies of the retina including: Central Serous Chorioretinopathy (CSC), Choroidal Neovascularization (CNV), Pigment Epithelial Detachment (PED), Macular Hole, Epiretinal Membrane, Outer Retinal Infarction etc. All these pathologies were first diagnosed by classical methods (like fundus camera imaging and angiography) and then examined with the aid of SOCT system. In this contribution we present examples of SOCT cross-sectional retinal imaging of pathologic eyes measured with standard resolution. We also compare cross-sectional images of pathology obtained by standard and high resolution systems.

  16. Quantification of Abdominal Fat in Obese and Healthy Adolescents Using 3 Tesla Magnetic Resonance Imaging and Free Software for Image Analysis

    PubMed Central

    Eloi, Juliana Cristina; Epifanio, Matias; de Gonçalves, Marília Maia; Pellicioli, Augusto; Vieira, Patricia Froelich Giora; Dias, Henrique Bregolin; Bruscato, Neide; Soder, Ricardo Bernardi; Santana, João Carlos Batista; Mouzaki, Marialena; Baldisserotto, Matteo

    2017-01-01

    Background and Aims Computed tomography, which uses ionizing radiation and expensive software packages for analysis of scans, can be used to quantify abdominal fat. The objective of this study is to measure abdominal fat with 3T MRI using free software for image analysis and to correlate these findings with anthropometric and laboratory parameters in adolescents. Methods This prospective observational study included 24 overweight/obese and 33 healthy adolescents (mean age 16.55 years). All participants underwent abdominal MRI exams. Visceral and subcutaneous fat area and percentage were correlated with anthropometric parameters, lipid profile, glucose metabolism, and insulin resistance. Student’s t test and Mann-Whitney’s test was applied. Pearson’s chi-square test was used to compare proportions. To determine associations Pearson’s linear correlation or Spearman’s correlation were used. Results In both groups, waist circumference (WC) was associated with visceral fat area (P = 0.001 and P = 0.01 respectively), and triglycerides were associated with fat percentage (P = 0.046 and P = 0.071 respectively). In obese individuals, total cholesterol/HDL ratio was associated with visceral fat area (P = 0.03) and percentage (P = 0.09), and insulin and HOMA-IR were associated with visceral fat area (P = 0.001) and percentage (P = 0.005). Conclusions 3T MRI can provide reliable and good quality images for quantification of visceral and subcutaneous fat by using a free software package. The results demonstrate that WC is a good predictor of visceral fat in obese adolescents and visceral fat area is associated with total cholesterol/HDL ratio, insulin and HOMA-IR. PMID:28129354

  17. A standard test method based on point spread function for three-dimensional imaging system

    NASA Astrophysics Data System (ADS)

    Wen, Tao; Dong, Jinxin; Hu, Zhixiong; Cao, Zhenggang; Liu, Wenli; Wang, Jianlin

    2016-09-01

    Point spread function (PSF) theory has been demonstrated as proof of concept in evaluation of spatial resolution of three dimensional imaging technology like optical coherence tomography (OCT) and confocal microscopy. A robust test target and associated evaluation algorithm are in demand for keeping regular quality assurance and inter-comparison of such 3D imaging system performance. To achieve this goal, standard-size micro spheres were utilized to develop PSF phantoms. The OCT system was investigated with the microsphere PSF phantom. Differing from previous study, a statistical model comprising data from hundreds of scatterers was established to acquire the PSF distribution and variation. The research provided an effective method and a set of practical standard phantoms for evaluating resolution of three dimensional imaging modalities.

  18. eSlide suite: an open source software system for whole slide imaging.

    PubMed

    Della Mea, V; Bortolotti, N; Beltrami, C A

    2009-08-01

    This short report briefly describes the principles underlying the telepathology technique known as whole slide imaging, and the design and implementation of a system for acquisition and visualisation of digital slides. The developed system, including an acquisition module and a visualisation module, is available as an open source on the Internet, together with sample acquired slides.

  19. 3D Imaging for hand gesture recognition: Exploring the software-hardware interaction of current technologies

    NASA Astrophysics Data System (ADS)

    Periverzov, Frol; Ilieş, Horea T.

    2012-09-01

    Interaction with 3D information is one of the fundamental and most familiar tasks in virtually all areas of engineering and science. Several recent technological advances pave the way for developing hand gesture recognition capabilities available to all, which will lead to more intuitive and efficient 3D user interfaces (3DUI). These developments can unlock new levels of expression and productivity in all activities concerned with the creation and manipulation of virtual 3D shapes and, specifically, in engineering design. Building fully automated systems for tracking and interpreting hand gestures requires robust and efficient 3D imaging techniques as well as potent shape classifiers. We survey and explore current and emerging 3D imaging technologies, and focus, in particular, on those that can be used to build interfaces between the users' hands and the machine. The purpose of this paper is to categorize and highlight the relevant differences between these existing 3D imaging approaches in terms of the nature of the information provided, output data format, as well as the specific conditions under which these approaches yield reliable data. Furthermore we explore the impact of each of these approaches on the computational cost and reliability of the required image processing algorithms. Finally we highlight the main challenges and opportunities in developing natural user interfaces based on hand gestures, and conclude with some promising directions for future research. [Figure not available: see fulltext.

  20. DullRazor: a software approach to hair removal from images.

    PubMed

    Lee, T; Ng, V; Gallagher, R; Coldman, A; McLean, D

    1997-11-01

    Recently, there has been a growing number of studies applying image processing techniques to analyze melanocytic lesions for atypia and possible malignancy and for total-body mole mapping. However, such lesions can be partially obscured by body hairs. None of these studies has fully addressed the problem of human hairs occluding the imaged lesions. In our previous study we designed an automatic segmentation program to differentiate skin lesions from the normal healthy skin, and learned that the program performed well with most of the images, the exception being those with hairs, especially dark thick hairs, covering part of the lesions. These thick dark hairs confused the program, resulting in unsatisfactory segmentation results. In this paper, we present a method to remove hairs from an image using a pre-processing program we have called DullRazor. This pre-processing step enables the segmentation program to achieve satisfactory results. DullRazor can be downloaded as shareware from http:/(/)www.derm.ubc.ca.

  1. Advances in software for faster procedure and lower radiotracer dose myocardial perfusion imaging.

    PubMed

    Piccinelli, Marina; Garcia, Ernest V

    2015-01-01

    The American Society of Nuclear Cardiology has recently published documents that encourage laboratories to take all the appropriate steps to greatly decrease patient radiation dose and has set the goal of 50% of all myocardial perfusion studies performed with an associated radiation exposure of 9mSv by 2014. In the present work, a description of the major software techniques readily available to shorten procedure time and decrease injected activity is presented. Particularly new reconstruction methods and their ability to include means for resolution recovery and noise regularization are described. The use of these improved reconstruction algorithms results in a consistent reduction in acquisition time, injected activity and consequently in the radiation dose absorbed by the patient. The clinical implications to the use of these techniques are also described in terms of maintained and even improved study quality, accuracy and sensitivity for the detection of heart disease.

  2. Prediction of standard-dose brain PET image by using MRI and low-dose brain [{sup 18}F]FDG PET images

    SciTech Connect

    Kang, Jiayin; Gao, Yaozong; Shi, Feng; Lalush, David S.; Lin, Weili; Shen, Dinggang

    2015-09-15

    Purpose: Positron emission tomography (PET) is a nuclear medical imaging technology that produces 3D images reflecting tissue metabolic activity in human body. PET has been widely used in various clinical applications, such as in diagnosis of brain disorders. High-quality PET images play an essential role in diagnosing brain diseases/disorders. In practice, in order to obtain high-quality PET images, a standard-dose radionuclide (tracer) needs to be used and injected into a living body. As a result, it will inevitably increase the patient’s exposure to radiation. One solution to solve this problem is predicting standard-dose PET images using low-dose PET images. As yet, no previous studies with this approach have been reported. Accordingly, in this paper, the authors propose a regression forest based framework for predicting a standard-dose brain [{sup 18}F]FDG PET image by using a low-dose brain [{sup 18}F]FDG PET image and its corresponding magnetic resonance imaging (MRI) image. Methods: The authors employ a regression forest for predicting the standard-dose brain [{sup 18}F]FDG PET image by low-dose brain [{sup 18}F]FDG PET and MRI images. Specifically, the proposed method consists of two main steps. First, based on the segmented brain tissues (i.e., cerebrospinal fluid, gray matter, and white matter) in the MRI image, the authors extract features for each patch in the brain image from both low-dose PET and MRI images to build tissue-specific models that can be used to initially predict standard-dose brain [{sup 18}F]FDG PET images. Second, an iterative refinement strategy, via estimating the predicted image difference, is used to further improve the prediction accuracy. Results: The authors evaluated their algorithm on a brain dataset, consisting of 11 subjects with MRI, low-dose PET, and standard-dose PET images, using leave-one-out cross-validations. The proposed algorithm gives promising results with well-estimated standard-dose brain [{sup 18}F]FDG PET

  3. Delay and Standard Deviation Beamforming to Enhance Specular Reflections in Ultrasound Imaging.

    PubMed

    Bandaru, Raja Sekhar; Sornes, Anders Rasmus; Hermans, Jeroen; Samset, Eigil; D'hooge, Jan

    2016-12-01

    Although interventional devices, such as needles, guide wires, and catheters, are best visualized by X-ray, real-time volumetric echography could offer an attractive alternative as it avoids ionizing radiation; it provides good soft tissue contrast, and it is mobile and relatively cheap. Unfortunately, as echography is traditionally used to image soft tissue and blood flow, the appearance of interventional devices in conventional ultrasound images remains relatively poor, which is a major obstacle toward ultrasound-guided interventions. The objective of this paper was therefore to enhance the appearance of interventional devices in ultrasound images. Thereto, a modified ultrasound beamforming process using conventional-focused transmit beams is proposed that exploits the properties of received signals containing specular reflections (as arising from these devices). This new beamforming approach referred to as delay and standard deviation beamforming (DASD) was quantitatively tested using simulated as well as experimental data using a linear array transducer. Furthermore, the influence of different imaging settings (i.e., transmit focus, imaging depth, and scan angle) on the obtained image contrast was evaluated. The study showed that the image contrast of specular regions improved by 5-30 dB using DASD beamforming compared with traditional delay and sum (DAS) beamforming. The highest gain in contrast was observed when the interventional device was tilted away from being orthogonal to the transmit beam, which is a major limitation in standard DAS imaging. As such, the proposed beamforming methodology can offer an improved visualization of interventional devices in the ultrasound image with potential implications for ultrasound-guided interventions.

  4. Delay and Standard Deviation beamforming to enhance specular reflections in Ultrasound Imaging.

    PubMed

    Bandaru, Raja Sekhar; Sornes, Anders; Hermans, Jeroen; Samset, Eigil; D'hooge, Jan

    2016-09-27

    Although interventional devices such as needles, guide wires and catheters are best visualized by X-ray, real-time volumetric echography could offer an attractive alternative as it avoids ionizing radiation; it provides good soft tissue contrast and it is mobile and relatively cheap. Unfortunately, as echography is traditionally used to image soft tissue and blood flow, the appearance of interventional devices in conventional ultrasound images remains relatively poor which is a major obstacle towards ultrasound-guided interventions. The objective of the current study was therefore to enhance the appearance of interventional devices in ultrasound images. Thereto a modified ultrasound beamforming process using conventional focused transmit beams is proposed that exploits the properties of received signals containing specular reflections (as arising from these devices). This new beamforming approach referred to as Delay and Standard Deviation beamforming (DASD) was quantitatively tested using simulated as well as experimental data using a linear array transducer. Furthermore, the influence of different imaging settings (i.e. transmit focus, imaging depth and scan angle) on the obtained image contrast was evaluated. The study showed that the image contrast of specular regions improved by 5 to 30dB using DASD beamforming compared to traditional delay and sum (DAS) beamforming. The highest gain in contrast was observed when the interventional device was tilted away from being orthogonal to the transmit beam, which is a major limitation in standard DAS imaging. As such, the proposed beamforming methodology can offer an improved visualization of interventional devices in the ultrasound image with potential implications for ultrasound-guided interventions.

  5. Consensus recommendations for a standardized Brain Tumor Imaging Protocol in clinical trials

    PubMed Central

    Ellingson, Benjamin M.; Bendszus, Martin; Boxerman, Jerrold; Barboriak, Daniel; Erickson, Bradley J.; Smits, Marion; Nelson, Sarah J.; Gerstner, Elizabeth; Alexander, Brian; Goldmacher, Gregory; Wick, Wolfgang; Vogelbaum, Michael; Weller, Michael; Galanis, Evanthia; Kalpathy-Cramer, Jayashree; Shankar, Lalitha; Jacobs, Paula; Pope, Whitney B.; Yang, Dewen; Chung, Caroline; Knopp, Michael V.; Cha, Soonme; van den Bent, Martin J.; Chang, Susan; Al Yung, W.K.; Cloughesy, Timothy F.; Wen, Patrick Y.; Gilbert, Mark R.

    2015-01-01

    A recent joint meeting was held on January 30, 2014, with the US Food and Drug Administration (FDA), National Cancer Institute (NCI), clinical scientists, imaging experts, pharmaceutical and biotech companies, clinical trials cooperative groups, and patient advocate groups to discuss imaging endpoints for clinical trials in glioblastoma. This workshop developed a set of priorities and action items including the creation of a standardized MRI protocol for multicenter studies. The current document outlines consensus recommendations for a standardized Brain Tumor Imaging Protocol (BTIP), along with the scientific and practical justifications for these recommendations, resulting from a series of discussions between various experts involved in aspects of neuro-oncology neuroimaging for clinical trials. The minimum recommended sequences include: (i) parameter-matched precontrast and postcontrast inversion recovery-prepared, isotropic 3D T1-weighted gradient-recalled echo; (ii) axial 2D T2-weighted turbo spin-echo acquired after contrast injection and before postcontrast 3D T1-weighted images to control timing of images after contrast administration; (iii) precontrast, axial 2D T2-weighted fluid-attenuated inversion recovery; and (iv) precontrast, axial 2D, 3-directional diffusion-weighted images. Recommended ranges of sequence parameters are provided for both 1.5 T and 3 T MR systems. PMID:26250565

  6. Full-sun synchronic EUV and coronal hole mapping using multi-instrument images: Data and software made available

    NASA Astrophysics Data System (ADS)

    Caplan, R. M.; Downs, C.; Linker, J.

    2015-12-01

    A method for the automatic generation of EUV and coronal hole (CH) maps using simultaneous multi-instrument imaging data is described. Synchronized EUV images from STEREO/EUVI A&B 195Å and SDO/AIA 193Å undergo preprocessing steps that include PSF-deconvolution and the application of nonlinear data-derived intensity corrections that account for center-to-limb variations (limb-brightening) and inter-instrument intensity normalization. The latter two corrections are derived using a robust, systematic approach that takes advantage of unbiased long-term averages of data and serve to flatten the images by converting all pixel intensities to a unified disk center equivalent. While the number of applications are broad, we demonstrate how this technique is very useful for CH detection as it enables the use of a fast and simplified image segmentation algorithm to obtain consistent detection results. The multi-instrument nature of the technique also allows one to track evolving features consistently for longer periods than is possible with a single instrument, and preliminary results quantifying CH area and shape evolution are shown.Most importantly, several data and software products are made available to the community for use. For the ~4 year period of 6/10/2010 to 8/18/2014, we provide synchronic EUV and coronal hole maps at 6-hour cadence as well as the data-derived limb brightening and inter-instrument correction factors that we applied. We also make available a ready-to-use MATLAB script EUV2CHM used to generate the maps, which loads EUV images, applies our preprocessing steps, and then uses our GPU-accelerated/CPU-multithreaded segmentation algorithm EZSEG to detect coronal holes.

  7. Software component quality evaluation

    NASA Technical Reports Server (NTRS)

    Clough, A. J.

    1991-01-01

    The paper describes a software inspection process that can be used to evaluate the quality of software components. Quality criteria, process application, independent testing of the process and proposed associated tool support are covered. Early results indicate that this technique is well suited for assessing software component quality in a standardized fashion. With automated machine assistance to facilitate both the evaluation and selection of software components, such a technique should promote effective reuse of software components.

  8. Development of fast patient position verification software using 2D-3D image registration and its clinical experience

    PubMed Central

    Mori, Shinichiro; Kumagai, Motoki; Miki, Kentaro; Fukuhara, Riki; Haneishi, Hideaki

    2015-01-01

    To improve treatment workflow, we developed a graphic processing unit (GPU)-based patient positional verification software application and integrated it into carbon-ion scanning beam treatment. Here, we evaluated the basic performance of the software. The algorithm provides 2D/3D registration matching using CT and orthogonal X-ray flat panel detector (FPD) images. The participants were 53 patients with tumors of the head and neck, prostate or lung receiving carbon-ion beam treatment. 2D/3D-ITchi-Gime (ITG) calculation accuracy was evaluated in terms of computation time and registration accuracy. Registration calculation was determined using the similarity measurement metrics gradient difference (GD), normalized mutual information (NMI), zero-mean normalized cross-correlation (ZNCC), and their combination. Registration accuracy was dependent on the particular metric used. Representative examples were determined to have target registration error (TRE) = 0.45 ± 0.23 mm and angular error (AE) = 0.35 ± 0.18° with ZNCC + GD for a head and neck tumor; TRE = 0.12 ± 0.07 mm and AE = 0.16 ± 0.07° with ZNCC for a pelvic tumor; and TRE = 1.19 ± 0.78 mm and AE = 0.83 ± 0.61° with ZNCC for lung tumor. Calculation time was less than 7.26 s.The new registration software has been successfully installed and implemented in our treatment process. We expect that it will improve both treatment workflow and treatment accuracy. PMID:26081313

  9. Development of fast patient position verification software using 2D-3D image registration and its clinical experience.

    PubMed

    Mori, Shinichiro; Kumagai, Motoki; Miki, Kentaro; Fukuhara, Riki; Haneishi, Hideaki

    2015-09-01

    To improve treatment workflow, we developed a graphic processing unit (GPU)-based patient positional verification software application and integrated it into carbon-ion scanning beam treatment. Here, we evaluated the basic performance of the software. The algorithm provides 2D/3D registration matching using CT and orthogonal X-ray flat panel detector (FPD) images. The participants were 53 patients with tumors of the head and neck, prostate or lung receiving carbon-ion beam treatment. 2D/3D-ITchi-Gime (ITG) calculation accuracy was evaluated in terms of computation time and registration accuracy. Registration calculation was determined using the similarity measurement metrics gradient difference (GD), normalized mutual information (NMI), zero-mean normalized cross-correlation (ZNCC), and their combination. Registration accuracy was dependent on the particular metric used. Representative examples were determined to have target registration error (TRE) = 0.45 ± 0.23 mm and angular error (AE) = 0.35 ± 0.18° with ZNCC + GD for a head and neck tumor; TRE = 0.12 ± 0.07 mm and AE = 0.16 ± 0.07° with ZNCC for a pelvic tumor; and TRE = 1.19 ± 0.78 mm and AE = 0.83 ± 0.61° with ZNCC for lung tumor. Calculation time was less than 7.26 s.The new registration software has been successfully installed and implemented in our treatment process. We expect that it will improve both treatment workflow and treatment accuracy.

  10. Photon counting imaging and centroiding with an electron-bombarded CCD using single molecule localisation software

    NASA Astrophysics Data System (ADS)

    Hirvonen, Liisa M.; Barber, Matthew J.; Suhling, Klaus

    2016-06-01

    Photon event centroiding in photon counting imaging and single-molecule localisation in super-resolution fluorescence microscopy share many traits. Although photon event centroiding has traditionally been performed with simple single-iteration algorithms, we recently reported that iterative fitting algorithms originally developed for single-molecule localisation fluorescence microscopy work very well when applied to centroiding photon events imaged with an MCP-intensified CMOS camera. Here, we have applied these algorithms for centroiding of photon events from an electron-bombarded CCD (EBCCD). We find that centroiding algorithms based on iterative fitting of the photon events yield excellent results and allow fitting of overlapping photon events, a feature not reported before and an important aspect to facilitate an increased count rate and shorter acquisition times.

  11. Photon counting imaging and centroiding with an electron-bombarded CCD using single molecule localisation software

    PubMed Central

    Hirvonen, Liisa M.; Barber, Matthew J.; Suhling, Klaus

    2016-01-01

    Photon event centroiding in photon counting imaging and single-molecule localisation in super-resolution fluorescence microscopy share many traits. Although photon event centroiding has traditionally been performed with simple single-iteration algorithms, we recently reported that iterative fitting algorithms originally developed for single-molecule localisation fluorescence microscopy work very well when applied to centroiding photon events imaged with an MCP-intensified CMOS camera. Here, we have applied these algorithms for centroiding of photon events from an electron-bombarded CCD (EBCCD). We find that centroiding algorithms based on iterative fitting of the photon events yield excellent results and allow fitting of overlapping photon events, a feature not reported before and an important aspect to facilitate an increased count rate and shorter acquisition times. PMID:27274604

  12. Color voltage contrast: A new method of implementing fault contrast with color imaging software

    SciTech Connect

    Colvin, J.

    1995-12-31

    Although voltage contrast and fault contrast methods are well established, the current methods of implementation are frequently tedious. A new method of mapping voltage contrast (VC) images in a qualitative (stroboscopic) color mode allows multiple logic states to be simultaneously viewed and updated in color. A shortcoming of image subtraction is that only one direction of logic change is represented unless the frames are exclusive OR`ed together. Although this gives fault information it does not include the VC of neighboring unchanged nodes. When tracking failures such as a saturated transistor resulting from a logic short somewhere else, all logic states; both static and transitional need to be understood and viewed simultaneously if an expedient analysis is desired.

  13. Predicting standard-dose PET image from low-dose PET and multimodal MR images using mapping-based sparse representation

    NASA Astrophysics Data System (ADS)

    Wang, Yan; Zhang, Pei; An, Le; Ma, Guangkai; Kang, Jiayin; Shi, Feng; Wu, Xi; Zhou, Jiliu; Lalush, David S.; Lin, Weili; Shen, Dinggang

    2016-01-01

    Positron emission tomography (PET) has been widely used in clinical diagnosis for diseases and disorders. To obtain high-quality PET images requires a standard-dose radionuclide (tracer) injection into the human body, which inevitably increases risk of radiation exposure. One possible solution to this problem is to predict the standard-dose PET image from its low-dose counterpart and its corresponding multimodal magnetic resonance (MR) images. Inspired by the success of patch-based sparse representation (SR) in super-resolution image reconstruction, we propose a mapping-based SR (m-SR) framework for standard-dose PET image prediction. Compared with the conventional patch-based SR, our method uses a mapping strategy to ensure that the sparse coefficients, estimated from the multimodal MR images and low-dose PET image, can be applied directly to the prediction of standard-dose PET image. As the mapping between multimodal MR images (or low-dose PET image) and standard-dose PET images can be particularly complex, one step of mapping is often insufficient. To this end, an incremental refinement framework is therefore proposed. Specifically, the predicted standard-dose PET image is further mapped to the target standard-dose PET image, and then the SR is performed again to predict a new standard-dose PET image. This procedure can be repeated for prediction refinement of the iterations. Also, a patch selection based dictionary construction method is further used to speed up the prediction process. The proposed method is validated on a human brain dataset. The experimental results show that our method can outperform benchmark methods in both qualitative and quantitative measures.

  14. The Java Image Science Toolkit (JIST) for rapid prototyping and publishing of neuroimaging software.

    PubMed

    Lucas, Blake C; Bogovic, John A; Carass, Aaron; Bazin, Pierre-Louis; Prince, Jerry L; Pham, Dzung L; Landman, Bennett A

    2010-03-01

    Non-invasive neuroimaging techniques enable extraordinarily sensitive and specific in vivo study of the structure, functional response and connectivity of biological mechanisms. With these advanced methods comes a heavy reliance on computer-based processing, analysis and interpretation. While the neuroimaging community has produced many excellent academic and commercial tool packages, new tools are often required to interpret new modalities and paradigms. Developing custom tools and ensuring interoperability with existing tools is a significant hurdle. To address these limitations, we present a new framework for algorithm development that implicitly ensures tool interoperability, generates graphical user interfaces, provides advanced batch processing tools, and, most importantly, requires minimal additional programming or computational overhead. Java-based rapid prototyping with this system is an efficient and practical approach to evaluate new algorithms since the proposed system ensures that rapidly constructed prototypes are actually fully-functional processing modules with support for multiple GUI's, a broad range of file formats, and distributed computation. Herein, we demonstrate MRI image processing with the proposed system for cortical surface extraction in large cross-sectional cohorts, provide a system for fully automated diffusion tensor image analysis, and illustrate how the system can be used as a simulation framework for the development of a new image analysis method. The system is released as open source under the Lesser GNU Public License (LGPL) through the Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC).

  15. ORBS, ORCS, OACS, a Software Suite for Data Reduction and Analysis of the Hyperspectral Imagers SITELLE and SpIOMM

    NASA Astrophysics Data System (ADS)

    Martin, T.; Drissen, L.; Joncas, G.

    2015-09-01

    SITELLE (installed in 2015 at the Canada-France-Hawaii Telescope) and SpIOMM (a prototype attached to the Observatoire du Mont-Mégantic) are the first Imaging Fourier Transform Spectrometers (IFTS) capable of obtaining a hyperspectral data cube which samples a 12 arc minutes field of view into four millions of visible spectra. The result of each observation is made up of two interferometric data cubes which need to be merged, corrected, transformed and calibrated in order to get a spectral cube of the observed region ready to be analysed. ORBS is a fully automatic data reduction software that has been entirely designed for this purpose. The data size (up to 68 Gb for larger science cases) and the computational needs have been challenging and the highly parallelized object-oriented architecture of ORBS reflects the solutions adopted which made possible to process 68 Gb of raw data in less than 11 hours using 8 cores and 22.6 Gb of RAM. It is based on a core framework (ORB) that has been designed to support the whole software suite for data analysis (ORCS and OACS), data simulation (ORUS) and data acquisition (IRIS). They all aim to provide a strong basis for the creation and development of specialized analysis modules that could benefit the scientific community working with SITELLE and SpIOMM.

  16. Positioning Standardized Acupuncture Points on the Whole Body Based on X-Ray Computed Tomography Images.

    PubMed

    Kim, Jungdae; Kang, Dae-In

    2014-02-01

    Objective: The goal of this research was to position all the standardized 361 acupuncture points on the entire human body based on a 3-dimensional (3D) virtual body. Materials and Methods: Digital data from a healthy Korean male with a normal body shape were obtained in the form of cross-sectional images generated by X-ray computed tomography (CT), and the 3D models for the bones and the skin's surface were created through the image-processing steps. Results: The reference points or the landmarks were positioned based on the standard descriptions of the acupoints, and the formulae for the proportionalities between the acupoints and the reference points were presented. About 37% of the 361 standardized acupoints were automatically linked with the reference points, the reference points accounted for 11% of the 361 acupoints, and the remaining acupoints (52%) were positioned point-by-point by using the OpenGL 3D graphics libraries. Based on the projective 2D descriptions of the standard acupuncture points, the volumetric 3D acupoint model was developed; it was extracted from the X-ray CT images. Conclusions: This modality for positioning acupoints may modernize acupuncture research and enable acupuncture treatments to be more personalized.

  17. Positioning Standardized Acupuncture Points on the Whole Body Based on X-Ray Computed Tomography Images

    PubMed Central

    Kim, Jungdae

    2014-01-01

    Abstract Objective: The goal of this research was to position all the standardized 361 acupuncture points on the entire human body based on a 3-dimensional (3D) virtual body. Materials and Methods: Digital data from a healthy Korean male with a normal body shape were obtained in the form of cross-sectional images generated by X-ray computed tomography (CT), and the 3D models for the bones and the skin's surface were created through the image-processing steps. Results: The reference points or the landmarks were positioned based on the standard descriptions of the acupoints, and the formulae for the proportionalities between the acupoints and the reference points were presented. About 37% of the 361 standardized acupoints were automatically linked with the reference points, the reference points accounted for 11% of the 361 acupoints, and the remaining acupoints (52%) were positioned point-by-point by using the OpenGL 3D graphics libraries. Based on the projective 2D descriptions of the standard acupuncture points, the volumetric 3D acupoint model was developed; it was extracted from the X-ray CT images. Conclusions: This modality for positioning acupoints may modernize acupuncture research and enable acupuncture treatments to be more personalized. PMID:24761187

  18. Control Software

    NASA Technical Reports Server (NTRS)

    1997-01-01

    Real-Time Innovations, Inc. (RTI) collaborated with Ames Research Center, the Jet Propulsion Laboratory and Stanford University to leverage NASA research to produce ControlShell software. RTI is the first "graduate" of Ames Research Center's Technology Commercialization Center. The ControlShell system was used extensively on a cooperative project to enhance the capabilities of a Russian-built Marsokhod rover being evaluated for eventual flight to Mars. RTI's ControlShell is complex, real-time command and control software, capable of processing information and controlling mechanical devices. One ControlShell tool is StethoScope. As a real-time data collection and display tool, StethoScope allows a user to see how a program is running without changing its execution. RTI has successfully applied its software savvy in other arenas, such as telecommunications, networking, video editing, semiconductor manufacturing, automobile systems, and medical imaging.

  19. 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.

  20. MO-G-9A-01: Imaging Refresher for Standard of Care Radiation Therapy

    SciTech Connect

    Labby, Z; Sensakovic, W; Hipp, E; Altman, M

    2014-06-15

    Imaging techniques and technology which were previously the domain of diagnostic medicine are becoming increasingly integrated and utilized in radiation therapy (RT) clinical practice. As such, there are a number of specific imaging topics that are highly applicable to modern radiation therapy physics. As imaging becomes more widely integrated into standard clinical radiation oncology practice, the impetus is on RT physicists to be informed and up-to-date on those imaging modalities relevant to the design and delivery of therapeutic radiation treatments. For example, knowing that, for a given situation, a fluid attenuated inversion recovery (FLAIR) image set is most likely what the physician would like to import and contour is helpful, but may not be sufficient to providing the best quality of care. Understanding the physics of how that pulse sequence works and why it is used could help assess its utility and determine if it is the optimal sequence for aiding in that specific clinical situation. It is thus important that clinical medical physicists be able to understand and explain the physics behind the imaging techniques used in all aspects of clinical radiation oncology practice. This session will provide the basic physics for a variety of imaging modalities for applications that are highly relevant to radiation oncology practice: computed tomography (CT) (including kV, MV, cone beam CT [CBCT], and 4DCT), positron emission tomography (PET)/CT, magnetic resonance imaging (MRI), and imaging specific to brachytherapy (including ultrasound and some brachytherapy specific topics in MR). For each unique modality, the image formation process will be reviewed, trade-offs between image quality and other factors (e.g. imaging time or radiation dose) will be clarified, and typically used cases for each modality will be introduced. The current and near-future uses of these modalities and techniques in radiation oncology clinical practice will also be discussed. Learning

  1. A comparative performance study characterizing breast tissue microarrays using standard RGB and multispectral imaging

    NASA Astrophysics Data System (ADS)

    Qi, Xin; Cukierski, William; Foran, David J.

    2010-02-01

    The lack of clear consensus over the utility of multispectral imaging (MSI) for bright-field imaging prompted our team to investigate the benefit of using MSI on breast tissue microarrays (TMA). We have conducted performance studies to compare MSI with standard bright-field imaging in hematoxylin stained breast tissue. The methodology has three components. The first extracts a region of interest using adaptive thresholding and morphological processing. The second performs texture feature extraction from a local binary pattern within each spectral channel and compared to features of co-occurrence matrix and texture feature coding in third component. The third component performs feature selection and classification. For each spectrum, exhaustive feature selection was used to search for the combination of features that yields the best classification accuracy. AdaBoost with a linear perceptron least-square classifier was applied. The spectra carrying the greatest discriminatory power were automatically chosen and a majority vote was used to make the final classification. 92 breast TMA discs were included in the study. Sensitivity of 0.96 and specificity of 0.89 were achieved on the multispectral data, compared with sensitivity of 0.83 and specificity of 0.85 on RGB data. MSI consistently achieved better classification results than those obtained using standard RGB images. While the benefits of MSI for unmixing multi-stained specimens are well documented, this study demonstrated statistically significant improvements in the automated analysis of single stained bright-field images.

  2. SU-E-I-63: Quantitative Evaluation of the Effects of Orthopedic Metal Artifact Reduction (OMAR) Software On CT Images for Radiotherapy Simulation

    SciTech Connect

    Jani, S

    2014-06-01

    Purpose: CT simulation for patients with metal implants can often be challenging due to artifacts that obscure tumor/target delineation and normal organ definition. Our objective was to evaluate the effectiveness of Orthopedic Metal Artifact Reduction (OMAR), a commercially available software, in reducing metal-induced artifacts and its effect on computed dose during treatment planning. Methods: CT images of water surrounding metallic cylindrical rods made of aluminum, copper and iron were studied in terms of Hounsfield Units (HU) spread. Metal-induced artifacts were characterized in terms of HU/Volume Histogram (HVH) using the Pinnacle treatment planning system. Effects of OMAR on enhancing our ability to delineate organs on CT and subsequent dose computation were examined in nine (9) patients with hip implants and two (2) patients with breast tissue expanders. Results: Our study characterized water at 1000 HU with a standard deviation (SD) of about 20 HU. The HVHs allowed us to evaluate how the presence of metal changed the HU spread. For example, introducing a 2.54 cm diameter copper rod in water increased the SD in HU of the surrounding water from 20 to 209, representing an increase in artifacts. Subsequent use of OMAR brought the SD down to 78. Aluminum produced least artifacts whereas Iron showed largest amount of artifacts. In general, an increase in kVp and mA during CT scanning showed better effectiveness of OMAR in reducing artifacts. Our dose analysis showed that some isodose contours shifted by several mm with OMAR but infrequently and were nonsignificant in planning process. Computed volumes of various dose levels showed <2% change. Conclusions: In our experience, OMAR software greatly reduced the metal-induced CT artifacts for the majority of patients with implants, thereby improving our ability to delineate tumor and surrounding organs. OMAR had a clinically negligible effect on computed dose within tissues. Partially funded by unrestricted

  3. High-throughput image analysis of tumor spheroids: a user-friendly software application to measure the size of spheroids automatically and accurately.

    PubMed

    Chen, Wenjin; Wong, Chung; Vosburgh, Evan; Levine, Arnold J; Foran, David J; Xu, Eugenia Y

    2014-07-08

    The increasing number of applications of three-dimensional (3D) tumor spheroids as an in vitro model for drug discovery requires their adaptation to large-scale screening formats in every step of a drug screen, including large-scale image analysis. Currently there is no ready-to-use and free image analysis software to meet this large-scale format. Most existing methods involve manually drawing the length and width of the imaged 3D spheroids, which is a tedious and time-consuming process. This study presents a high-throughput image analysis software application - SpheroidSizer, which measures the major and minor axial length of the imaged 3D tumor spheroids automatically and accurately; calculates the volume of each individual 3D tumor spheroid; then outputs the results in two different forms in spreadsheets for easy manipulations in the subsequent data analysis. The main advantage of this software is its powerful image analysis application that is adapted for large numbers of images. It provides high-throughput computation and quality-control workflow. The estimated time to process 1,000 images is about 15 min on a minimally configured laptop, or around 1 min on a multi-core performance workstation. The graphical user interface (GUI) is also designed for easy quality control, and users can manually override the computer results. The key method used in this software is adapted from the active contour algorithm, also known as Snakes, which is especially suitable for images with uneven illumination and noisy background that often plagues automated imaging processing in high-throughput screens. The complimentary "Manual Initialize" and "Hand Draw" tools provide the flexibility to SpheroidSizer in dealing with various types of spheroids and diverse quality images. This high-throughput image analysis software remarkably reduces labor and speeds up the analysis process. Implementing this software is beneficial for 3D tumor spheroids to become a routine in vitro model

  4. C++ software integration for a high-throughput phase imaging platform

    NASA Astrophysics Data System (ADS)

    Kandel, Mikhail E.; Luo, Zelun; Han, Kevin; Popescu, Gabriel

    2015-03-01

    The multi-shot approach in SLIM requires reliable, synchronous, and parallel operation of three independent hardware devices - not meeting these challenges results in degraded phase and slow acquisition speeds, narrowing applications to holistic statements about complex phenomena. The relative youth of quantitative imaging and the lack of ready-made commercial hardware and tools further compounds the problem as Higher level programming languages result in inflexible, experiment specific instruments limited by ill-fitting computational modules, resulting in a palpable chasm between promised and realized hardware performance. Furthermore, general unfamiliarity with intricacies such as background calibration, objective lens attenuation, along with spatial light modular alignment, makes successful measurements difficult for the inattentive or uninitiated. This poses an immediate challenge for moving our techniques beyond the lab to biologically oriented collaborators and clinical practitioners. To meet these challenges, we present our new Quantitative Phase Imaging pipeline, with improved instrument performance, friendly user interface and robust data processing features, enabling us to acquire and catalog clinical datasets hundreds of gigapixels in size.

  5. Fire service and first responder thermal imaging camera (TIC) advances and standards

    NASA Astrophysics Data System (ADS)

    Konsin, Lawrence S.; Nixdorff, Stuart

    2007-04-01

    Fire Service and First Responder Thermal Imaging Camera (TIC) applications are growing, saving lives and preventing injury and property damage. Firefighters face a wide range of serious hazards. TICs help mitigate the risks by protecting Firefighters and preventing injury, while reducing time spent fighting the fire and resources needed to do so. Most fire safety equipment is covered by performance standards. Fire TICs, however, are not covered by such standards and are also subject to inadequate operational performance and insufficient user training. Meanwhile, advancements in Fire TICs and lower costs are driving product demand. The need for a Fire TIC Standard was spurred in late 2004 through a Government sponsored Workshop where experts from the First Responder community, component manufacturers, firefighter training, and those doing research on TICs discussed strategies, technologies, procedures, best practices and R&D that could improve Fire TICs. The workshop identified pressing image quality, performance metrics, and standards issues. Durability and ruggedness metrics and standard testing methods were also seen as important, as was TIC training and certification of end-users. A progress report on several efforts in these areas and their impact on the IR sensor industry will be given. This paper is a follow up to the SPIE Orlando 2004 paper on Fire TIC usage (entitled Emergency Responders' Critical Infrared) which explored the technological development of this IR industry segment from the viewpoint of the end user, in light of the studies and reports that had established TICs as a mission critical tool for firefighters.

  6. Imaging of the optic disk in caring for patients with glaucoma: ophthalmoscopy and photography remain the gold standard.

    PubMed

    Spaeth, George L; Reddy, Swathi C

    2014-01-01

    Optic disk imaging is integral to the diagnosis and treatment of patients with glaucoma. We discuss the various forms of imaging the optic nerve, including ophthalmoscopy, photography, and newer imaging modalities, including optical coherence tomography (OCT), confocal scanning laser ophthalmoscopy (HRT), and scanning laser polarimetry (GDx), specifically highlighting their benefits and disadvantages. We argue that ophthalmoscopy and photography remain the gold standard of imaging due to portability, ease of interpretation, and the presence of a large database of images for comparison.

  7. On Software Compatibility.

    ERIC Educational Resources Information Center

    Ershov, Andrei P.

    The problem of compatibility of software hampers the development of computer application. One solution lies in standardization of languages, terms, peripherais, operating systems and computer characteristics. (AB)

  8. Accuracy of software designed for automated localization of the inferior alveolar nerve canal on cone beam CT images

    PubMed Central

    Zamani, Ali; Kashkouli, Sadegh; Soltanimehr, Elham; Ghofrani Jahromi, Mohsen; Sanaeian Pourshirazi, Zahra

    2016-01-01

    Objectives: The aim of this study was to design and evaluate a new method for automated localization of the inferior alveolar nerve canal on CBCT images. Methods: The proposed method is based on traversing both panoramic and cross-sectional slices. For the panoramic slices, morphological skeletonization is imposed, and a modified Hough transform is used while traversing the cross-sectional slices. A total of 40 CBCT images were randomly selected. Two experts twice located the inferior alveolar nerve canal during two examinations set 6 weeks apart. Agreement between experts was achieved, and the result of this manual technique was considered the gold standard for our study. The distances for the automated method and those determined using the gold standard method were calculated and recorded. The mean time required for the automated detection was also recorded. Results: The average mean distance error from the baseline was 0.75 ± 0.34 mm. In all, 86% of the detected points had a mean error of <1 mm compared with those determined by the manual gold standard method. Conclusions: The proposed method is far more accurate and faster than previous methods. It also provides more accuracy than human annotation within a shorter time. PMID:26652929

  9. 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.

  10. Using Image Pro Plus Software to Develop Particle Mapping on Genesis Solar Wind Collector Surfaces

    NASA Technical Reports Server (NTRS)

    Rodriquez, Melissa C.; Allton, J. H.; Burkett, P. J.

    2012-01-01

    The continued success of the Genesis mission science team in analyzing solar wind collector array samples is partially based on close collaboration of the JSC curation team with science team members who develop cleaning techniques and those who assess elemental cleanliness at the levels of detection. The goal of this collaboration is to develop a reservoir of solar wind collectors of known cleanliness to be available to investigators. The heart and driving force behind this effort is Genesis mission PI Don Burnett. While JSC contributes characterization, safe clean storage, and benign collector cleaning with ultrapure water (UPW) and UV ozone, Burnett has coordinated more exotic and rigorous cleaning which is contributed by science team members. He also coordinates cleanliness assessment requiring expertise and instruments not available in curation, such as XPS, TRXRF [1,2] and synchrotron TRXRF. JSC participates by optically documenting the particle distributions as cleaning steps progress. Thus, optical document supplements SEM imaging and analysis, and elemental assessment by TRXRF.

  11. Cytopathology whole slide images and virtual microscopy adaptive tutorials: A software pilot

    PubMed Central

    Van Es, Simone L.; Pryor, Wendy M.; Belinson, Zack; Salisbury, Elizabeth L.; Velan, Gary M.

    2015-01-01

    Background: The constant growth in the body of knowledge in medicine requires pathologists and pathology trainees to engage in continuing education. Providing them with equitable access to efficient and effective forms of education in pathology (especially in remote and rural settings) is important, but challenging. Methods: We developed three pilot cytopathology virtual microscopy adaptive tutorials (VMATs) to explore a novel adaptive E-learning platform (AeLP) which can incorporate whole slide images for pathology education. We collected user feedback to further develop this educational material and to subsequently deploy randomized trials in both pathology specialist trainee and also medical student cohorts. Cytopathology whole slide images were first acquired then novel VMATs teaching cytopathology were created using the AeLP, an intelligent tutoring system developed by Smart Sparrow. The pilot was run for Australian pathologists and trainees through the education section of Royal College of Pathologists of Australasia website over a period of 9 months. Feedback on the usability, impact on learning and any technical issues was obtained using 5-point Likert scale items and open-ended feedback in online questionnaires. Results: A total of 181 pathologists and pathology trainees anonymously attempted the three adaptive tutorials, a smaller proportion of whom went on to provide feedback at the end of each tutorial. VMATs were perceived as effective and efficient E-learning tools for pathology education. User feedback was positive. There were no significant technical issues. Conclusion: During this pilot, the user feedback on the educational content and interface and the lack of technical issues were helpful. Large scale trials of similar online cytopathology adaptive tutorials were planned for the future. PMID:26605119

  12. An Upgrade of the Imaging for Hypersonic Experimental Aeroheating Testing (IHEAT) Software

    NASA Technical Reports Server (NTRS)

    Mason, Michelle L.; Rufer, Shann J.

    2015-01-01

    The Imaging for Hypersonic Experimental Aeroheating Testing (IHEAT) code is used at NASA Langley Research Center to analyze global aeroheating data on wind tunnel models tested in the Langley Aerothermodynamics Laboratory. One-dimensional, semi-infinite heating data derived from IHEAT are used to design thermal protection systems to mitigate the risks due to the aeroheating loads on hypersonic vehicles, such as re-entry vehicles during descent and landing procedures. This code was originally written in the PV-WAVE programming language to analyze phosphor thermography data from the two-color, relativeintensity system developed at Langley. To increase the efficiency, functionality, and reliability of IHEAT, the code was migrated to MATLAB syntax and compiled as a stand-alone executable file labeled version 4.0. New features of IHEAT 4.0 include the options to batch process all of the data from a wind tunnel run, to map the two-dimensional heating distribution to a three-dimensional computer-aided design model of the vehicle to be viewed in Tecplot, and to extract data from a segmented line that follows an interesting feature in the data. Results from IHEAT 4.0 were compared on a pixel level to the output images from the legacy code to validate the program. The differences between the two codes were on the order of 10-5 to 10-7. IHEAT 4.0 replaces the PV-WAVE version as the production code for aeroheating experiments conducted in the hypersonic facilities at NASA Langley.

  13. Software reengineering

    NASA Technical Reports Server (NTRS)

    Fridge, Ernest M., III

    1991-01-01

    Today's software systems generally use obsolete technology, are not integrated properly with other software systems, and are difficult and costly to maintain. The discipline of reverse engineering is becoming prominent as organizations try to move their systems up to more modern and maintainable technology in a cost effective manner. JSC created a significant set of tools to develop and maintain FORTRAN and C code during development of the Space Shuttle. This tool set forms the basis for an integrated environment to re-engineer existing code into modern software engineering structures which are then easier and less costly to maintain and which allow a fairly straightforward translation into other target languages. The environment will support these structures and practices even in areas where the language definition and compilers do not enforce good software engineering. The knowledge and data captured using the reverse engineering tools is passed to standard forward engineering tools to redesign or perform major upgrades to software systems in a much more cost effective manner than using older technologies. A beta vision of the environment was released in Mar. 1991. The commercial potential for such re-engineering tools is very great. CASE TRENDS magazine reported it to be the primary concern of over four hundred of the top MIS executives.

  14. Software engineering

    NASA Technical Reports Server (NTRS)

    Fridge, Ernest M., III; Hiott, Jim; Golej, Jim; Plumb, Allan

    1993-01-01

    Today's software systems generally use obsolete technology, are not integrated properly with other software systems, and are difficult and costly to maintain. The discipline of reverse engineering is becoming prominent as organizations try to move their systems up to more modern and maintainable technology in a cost effective manner. The Johnson Space Center (JSC) created a significant set of tools to develop and maintain FORTRAN and C code during development of the space shuttle. This tool set forms the basis for an integrated environment to reengineer existing code into modern software engineering structures which are then easier and less costly to maintain and which allow a fairly straightforward translation into other target languages. The environment will support these structures and practices even in areas where the language definition and compilers do not enforce good software engineering. The knowledge and data captured using the reverse engineering tools is passed to standard forward engineering tools to redesign or perform major upgrades to software systems in a much more cost effective manner than using older technologies. The latest release of the environment was in Feb. 1992.

  15. Development and Evaluation of Reference Standards for Image-based Telemedicine Diagnosis and Clinical Research Studies in Ophthalmology

    PubMed Central

    Ryan, Michael C.; Ostmo, Susan; Jonas, Karyn; Berrocal, Audina; Drenser, Kimberly; Horowitz, Jason; Lee, Thomas C.; Simmons, Charles; Martinez-Castellanos, Maria-Ana; Chan, R.V. Paul; Chiang, Michael F.

    2014-01-01

    Information systems managing image-based data for telemedicine or clinical research applications require a reference standard representing the correct diagnosis. Accurate reference standards are difficult to establish because of imperfect agreement among physicians, and discrepancies between clinical vs. image-based diagnosis. This study is designed to describe the development and evaluation of reference standards for image-based diagnosis, which combine diagnostic impressions of multiple image readers with the actual clinical diagnoses. We show that agreement between image reading and clinical examinations was imperfect (689 [32%] discrepancies in 2148 image readings), as was inter-reader agreement (kappa 0.490-0.652). This was improved by establishing an image-based reference standard defined as the majority diagnosis given by three readers (13% discrepancies with image readers). It was further improved by establishing an overall reference standard that incorporated the clinical diagnosis (10% discrepancies with image readers). These principles of establishing reference standards may be applied to improve robustness of real-world systems supporting image-based diagnosis. PMID:25954463

  16. Development and Evaluation of Reference Standards for Image-based Telemedicine Diagnosis and Clinical Research Studies in Ophthalmology.

    PubMed

    Ryan, Michael C; Ostmo, Susan; Jonas, Karyn; Berrocal, Audina; Drenser, Kimberly; Horowitz, Jason; Lee, Thomas C; Simmons, Charles; Martinez-Castellanos, Maria-Ana; Chan, R V Paul; Chiang, Michael F

    2014-01-01

    Information systems managing image-based data for telemedicine or clinical research applications require a reference standard representing the correct diagnosis. Accurate reference standards are difficult to establish because of imperfect agreement among physicians, and discrepancies between clinical vs. image-based diagnosis. This study is designed to describe the development and evaluation of reference standards for image-based diagnosis, which combine diagnostic impressions of multiple image readers with the actual clinical diagnoses. We show that agreement between image reading and clinical examinations was imperfect (689 [32%] discrepancies in 2148 image readings), as was inter-reader agreement (kappa 0.490-0.652). This was improved by establishing an image-based reference standard defined as the majority diagnosis given by three readers (13% discrepancies with image readers). It was further improved by establishing an overall reference standard that incorporated the clinical diagnosis (10% discrepancies with image readers). These principles of establishing reference standards may be applied to improve robustness of real-world systems supporting image-based diagnosis.

  17. WASI-2D: A software tool for regionally optimized analysis of imaging spectrometer data from deep and shallow waters

    NASA Astrophysics Data System (ADS)

    Gege, Peter

    2014-01-01

    An image processing software has been developed which allows quantitative analysis of multi- and hyperspectral data from oceanic, coastal and inland waters. It has been implemented into the Water Colour Simulator WASI, which is a tool for the simulation and analysis of optical properties and light field parameters of deep and shallow waters. The new module WASI-2D can import atmospherically corrected images from airborne sensors and satellite instruments in various data formats and units like remote sensing reflectance or radiance. It can be easily adapted by the user to different sensors and to optical properties of the studied area. Data analysis is done by inverse modelling using established analytical models. The bio-optical model of the water column accounts for gelbstoff (coloured dissolved organic matter, CDOM), detritus, and mixtures of up to 6 phytoplankton classes and 2 spectrally different types of suspended matter. The reflectance of the sea floor is treated as sum of up to 6 substrate types. An analytic model of downwelling irradiance allows wavelength dependent modelling of sun glint and sky glint at the water surface. The provided database covers the spectral range from 350 to 1000 nm in 1 nm intervals. It can be exchanged easily to represent the optical properties of water constituents, bottom types and the atmosphere of the studied area.

  18. Leap Motion Gesture Control With Carestream Software in the Operating Room to Control Imaging: Installation Guide and Discussion.

    PubMed

    Pauchot, Julien; Di Tommaso, Laetitia; Lounis, Ahmed; Benassarou, Mourad; Mathieu, Pierre; Bernot, Dominique; Aubry, Sébastien

    2015-12-01

    Nowadays, routine cross-sectional imaging viewing during a surgical procedure requires physical contact with an interface (mouse or touch-sensitive screen). Such contact risks exposure to aseptic conditions and causes loss of time. Devices such as the recently introduced Leap Motion (Leap Motion Society, San Francisco, CA), which enables interaction with the computer without any physical contact, are of wide interest in the field of surgery, but configuration and ergonomics are key challenges for the practitioner, imaging software, and surgical environment. This article aims to suggest an easy configuration of Leap Motion on a PC for optimized use with Carestream Vue PACS v11.3.4 (Carestream Health, Inc, Rochester, NY) using a plug-in (to download at https://drive.google.com/open?id=0B_F4eBeBQc3yNENvTXlnY09qS00&authuser=0) and a video tutorial (https://www.youtube.com/watch?v=yVPTgxg-SIk). Videos of surgical procedure and discussion about innovative gesture control technology and its various configurations are provided in this article.

  19. Collecting field data from Mars Exploration Rover Spirit and Opportunity Images: Development of 3-D Visualization and Data-Mining Software

    NASA Astrophysics Data System (ADS)

    Eppes, M. C.; Willis, A.; Zhou, B.

    2010-12-01

    NASA’s two Mars rover spacecraft, Spirit and Opportunity, have collected more than 4 years worth of data from nine imaging instruments producing greater than 200k images. To date, however, the potential ‘field’ data that these images represent has remained relatively untapped because of a lack of software with which to readily analyze the images quantitatively. We have developed prototype software that allows scientists to locate and explore 2D and 3D imagery captured by the NASA's Mars Exploratory Rover (MER) mission robots Spirit and Opportunity. For example, using our software, a person could measure the dimensions of a rock or the strike and dip of a bedding plane. The developed software has three aspects that make it distinct from existing approaches for indexing large sets of imagery: (1) a computationally efficient image search engine capable of locating MER images containing features of interest, rocks in particular, (2) an interface for making measurements (distances and orientations) from stereographic image pairs and (3) remote browsing and storage capabilities that removes the burden of storing and managing these very large image sets. Two methods of search are supported (i) a rock detection algorithm for finding images that contain rock-like structures having a specified size and (ii) a generic query-by-image search which uses exemplar image(s) of a desired object to locate other images within the MER data repository that contain similar structures (i.e. one could search for all images of sand dunes). Query by image capabilities are made possible via a bag-of-features (e.g. Labeznik et. al. 2003; Schmid et. al. 2002) representation of the image data which compresses the image into a small set of features which are robust to changes in illumination and perspective. Searches are then reduced to looking for feature sets which have similar values; a task that is computationally tractable providing quick search results for complex image-based queries

  20. Amplitude remapping as a step towards standardizing the analysis of MR-images

    NASA Astrophysics Data System (ADS)

    Frommert, M.; Sidorenko, I.; Bauer, J.; Müller, D.; Rummeny, E.; Eckstein, F.; Monetti, R.; Räth, C.

    2011-03-01

    We investigate the utility of amplitude remapping of magnetic resonance (MR)-images for making the analysis of such images more independent of the MR-device, the selected sequence, and its parameters. To this end, we analyze the morphological structure of trabecular bones using weighted scaling indices and Minkowski functionals in the context of osteoporosis. After remapping the amplitude distribution of MR-images onto a normal distribution with zero mean and unit variance, we study how the diagnostic performance of the structure measures is affected by this remapping. The diagnostic performance of the scaling index method is stable under the remapping for both spin echo (SE) and gradient echo (GE) sequences: The area under curve (AUC) value from the ROC analysis changes only slightly from 0.76 (original image) to 0.74 (remapped image) for the SE sequence and from 0.78 to 0.77 for the GE sequence. For the Minkowski functionals, the diagnostic performance suffers significantly for the SE sequence, whereas it is much more robust for the GE sequence. Therefore, the scaling index method should be the method of choice when analyzing MR-images after amplitude remapping. We also find that in the scaling index analysis, the remapping makes the results much more consistent between the SE and the GE sequence by bringing the histograms of the scaling indices closer together. Thus, the amplitude remapping can be used as a first step to standardize the scaling index analysis between different sequences of an MRI device.

  1. Image-guided tumor ablation: standardization of terminology and reporting criteria--a 10-year update.

    PubMed

    Ahmed, Muneeb; Solbiati, Luigi; Brace, Christopher L; Breen, David J; Callstrom, Matthew R; Charboneau, J William; Chen, Min-Hua; Choi, Byung Ihn; de Baère, Thierry; Dodd, Gerald D; Dupuy, Damian E; Gervais, Debra A; Gianfelice, David; Gillams, Alice R; Lee, Fred T; Leen, Edward; Lencioni, Riccardo; Littrup, Peter J; Livraghi, Tito; Lu, David S; McGahan, John P; Meloni, Maria Franca; Nikolic, Boris; Pereira, Philippe L; Liang, Ping; Rhim, Hyunchul; Rose, Steven C; Salem, Riad; Sofocleous, Constantinos T; Solomon, Stephen B; Soulen, Michael C; Tanaka, Masatoshi; Vogl, Thomas J; Wood, Bradford J; Goldberg, S Nahum

    2014-10-01

    Image-guided tumor ablation has become a well-established hallmark of local cancer therapy. The breadth of options available in this growing field increases the need for standardization of terminology and reporting criteria to facilitate effective communication of ideas and appropriate comparison among treatments that use different technologies, such as chemical (eg, ethanol or acetic acid) ablation, thermal therapies (eg, radiofrequency, laser, microwave, focused ultrasound, and cryoablation) and newer ablative modalities such as irreversible electroporation. This updated consensus document provides a framework that will facilitate the clearest communication among investigators regarding ablative technologies. An appropriate vehicle is proposed for reporting the various aspects of image-guided ablation therapy including classification of therapies, procedure terms, descriptors of imaging guidance, and terminology for imaging and pathologic findings. Methods are addressed for standardizing reporting of technique, follow-up, complications, and clinical results. As noted in the original document from 2003, adherence to the recommendations will improve the precision of communications in this field, leading to more accurate comparison of technologies and results, and ultimately to improved patient outcomes. Online supplemental material is available for this article .

  2. Image-guided tumor ablation: standardization of terminology and reporting criteria--a 10-year update.

    PubMed

    Ahmed, Muneeb; Solbiati, Luigi; Brace, Christopher L; Breen, David J; Callstrom, Matthew R; Charboneau, J William; Chen, Min-Hua; Choi, Byung Ihn; de Baère, Thierry; Dodd, Gerald D; Dupuy, Damian E; Gervais, Debra A; Gianfelice, David; Gillams, Alice R; Lee, Fred T; Leen, Edward; Lencioni, Riccardo; Littrup, Peter J; Livraghi, Tito; Lu, David S; McGahan, John P; Meloni, Maria Franca; Nikolic, Boris; Pereira, Philippe L; Liang, Ping; Rhim, Hyunchul; Rose, Steven C; Salem, Riad; Sofocleous, Constantinos T; Solomon, Stephen B; Soulen, Michael C; Tanaka, Masatoshi; Vogl, Thomas J; Wood, Bradford J; Goldberg, S Nahum

    2014-11-01

    Image-guided tumor ablation has become a well-established hallmark of local cancer therapy. The breadth of options available in this growing field increases the need for standardization of terminology and reporting criteria to facilitate effective communication of ideas and appropriate comparison among treatments that use different technologies, such as chemical (eg, ethanol or acetic acid) ablation, thermal therapies (eg, radiofrequency, laser, microwave, focused ultrasound, and cryoablation) and newer ablative modalities such as irreversible electroporation. This updated consensus document provides a framework that will facilitate the clearest communication among investigators regarding ablative technologies. An appropriate vehicle is proposed for reporting the various aspects of image-guided ablation therapy including classification of therapies, procedure terms, descriptors of imaging guidance, and terminology for imaging and pathologic findings. Methods are addressed for standardizing reporting of technique, follow-up, complications, and clinical results. As noted in the original document from 2003, adherence to the recommendations will improve the precision of communications in this field, leading to more accurate comparison of technologies and results, and ultimately to improved patient outcomes.

  3. Image-guided Tumor Ablation: Standardization of Terminology and Reporting Criteria—A 10-Year Update

    PubMed Central

    Solbiati, Luigi; Brace, Christopher L.; Breen, David J.; Callstrom, Matthew R.; Charboneau, J. William; Chen, Min-Hua; Choi, Byung Ihn; de Baère, Thierry; Dodd, Gerald D.; Dupuy, Damian E.; Gervais, Debra A.; Gianfelice, David; Gillams, Alice R.; Lee, Fred T.; Leen, Edward; Lencioni, Riccardo; Littrup, Peter J.; Livraghi, Tito; Lu, David S.; McGahan, John P.; Meloni, Maria Franca; Nikolic, Boris; Pereira, Philippe L.; Liang, Ping; Rhim, Hyunchul; Rose, Steven C.; Salem, Riad; Sofocleous, Constantinos T.; Solomon, Stephen B.; Soulen, Michael C.; Tanaka, Masatoshi; Vogl, Thomas J.; Wood, Bradford J.; Goldberg, S. Nahum

    2014-01-01

    Image-guided tumor ablation has become a well-established hallmark of local cancer therapy. The breadth of options available in this growing field increases the need for standardization of terminology and reporting criteria to facilitate effective communication of ideas and appropriate comparison among treatments that use different technologies, such as chemical (eg, ethanol or acetic acid) ablation, thermal therapies (eg, radiofrequency, laser, microwave, focused ultrasound, and cryoablation) and newer ablative modalities such as irreversible electroporation. This updated consensus document provides a framework that will facilitate the clearest communication among investigators regarding ablative technologies. An appropriate vehicle is proposed for reporting the various aspects of image-guided ablation therapy including classification of therapies, procedure terms, descriptors of imaging guidance, and terminology for imaging and pathologic findings. Methods are addressed for standardizing reporting of technique, follow-up, complications, and clinical results. As noted in the original document from 2003, adherence to the recommendations will improve the precision of communications in this field, leading to more accurate comparison of technologies and results, and ultimately to improved patient outcomes. © RSNA, 2014 Online supplemental material is available for this article. PMID:24927329

  4. The Decoding Toolbox (TDT): a versatile software package for multivariate analyses of functional imaging data

    PubMed Central

    Hebart, Martin N.; Görgen, Kai; Haynes, John-Dylan

    2015-01-01

    The multivariate analysis of brain signals has recently sparked a great amount of interest, yet accessible and versatile tools to carry out decoding analyses are scarce. Here we introduce The Decoding Toolbox (TDT) which represents a user-friendly, powerful and flexible package for multivariate analysis of functional brain imaging data. TDT is written in Matlab and equipped with an interface to the widely used brain data analysis package SPM. The toolbox allows running fast whole-brain analyses, region-of-interest analyses and searchlight analyses, using machine learning classifiers, pattern correlation analysis, or representational similarity analysis. It offers automatic creation and visualization of diverse cross-validation schemes, feature scaling, nested parameter selection, a variety of feature selection methods, multiclass capabilities, and pattern reconstruction from classifier weights. While basic users can implement a generic analysis in one line of code, advanced users can extend the toolbox to their needs or exploit the structure to combine it with external high-performance classification toolboxes. The toolbox comes with an example data set which can be used to try out the various analysis methods. Taken together, TDT offers a promising option for researchers who want to employ multivariate analyses of brain activity patterns. PMID:25610393

  5. User's guide for mapIMG 3--Map image re-projection software package

    USGS Publications Warehouse

    Finn, Michael P.; Mattli, David M.

    2012-01-01

    Version 0.0 (1995), Dan Steinwand, U.S. Geological Survey (USGS)/Earth Resources Observation Systems (EROS) Data Center (EDC)--Version 0.0 was a command line version for UNIX that required four arguments: the input metadata, the output metadata, the input data file, and the output destination path. Version 1.0 (2003), Stephen Posch and Michael P. Finn, USGS/Mid-Continent Mapping Center (MCMC--Version 1.0 added a GUI interface that was built using the Qt library for cross platform development. Version 1.01 (2004), Jason Trent and Michael P. Finn, USGS/MCMC--Version 1.01 suggested bounds for the parameters of each projection. Support was added for larger input files, storage of the last used input and output folders, and for TIFF/ GeoTIFF input images. Version 2.0 (2005), Robert Buehler, Jason Trent, and Michael P. Finn, USGS/National Geospatial Technical Operations Center (NGTOC)--Version 2.0 added Resampling Methods (Mean, Mode, Min, Max, and Sum), updated the GUI design, and added the viewer/pre-viewer. The metadata style was changed to XML and was switched to a new naming convention. Version 3.0 (2009), David Mattli and Michael P. Finn, USGS/Center of Excellence for Geospatial Information Science (CEGIS)--Version 3.0 brings optimized resampling methods, an updated GUI, support for less than global datasets, UTM support and the whole codebase was ported to Qt4.

  6. On-line access to weather satellite imagery and image manipulation software

    NASA Technical Reports Server (NTRS)

    Emery, W.; Kelley, T.; Dozier, J.; Rotar, P.

    1995-01-01

    Advanced Very High Resolution Radiometer and Geostationary Operational Environmental Satellite imagery, received by antennas located at the University of Colorado, are made available to the Internet users through an on-line data access system. Created as a 'test bed' system for the National Aeronautics and Space Administration's future Earth Observing System Data and Information System, this test bed provides an opportunity to test both the technical requirements of an on-line data system and the different ways in which the general user community would employ such a system. Initiated in December 1991, the basic data system experiment four major evolutionary changes in response to user requests and requirements. Features added with these changes were the addition of on-line browse, user subsetting, and dynamic image processing/navigation. Over its lifetime the system has grown to a maximum of over 2500 registered users, and after losing many of these users due to hardware changes, the system is once again growing with its own independent mass storage system.

  7. On-Line Access to Weather Satellite Imagery and Image Manipulation Software

    NASA Technical Reports Server (NTRS)

    Emery, William J.; Kelley, T.; Dozier, J.; Rotar, P.

    1995-01-01

    Advanced Very High Resolution Radiometer and Geostationary Operational Environmental Satellite Imagery, received by antennas located at the University of Colorado, are made available to the Internet users through an on-line data access system. Created as a 'test bed' data system for the National Aeronautics and Space Administration's future Earth Observing System Data and Information System, this test bed provides an opportunity to test both the technical requirements of an on-line data system and the different ways in which the general user community would employ such a system. Initiated in December 1991, the basic data system experienced four major evolutionary changes in response to user requests and requirements. Features added with these changes were the addition of on-line browse, user subsetting, and dynamic image processing/navigation. Over its lifetime the system has grown to a maximum of over 2500 registered users, and after losing many of these users due to hardware changes, the system is once again growing with its own independent mass storage system.

  8. Microcomputer Software Collections.

    ERIC Educational Resources Information Center

    Demas, Samuel

    1985-01-01

    Presents overview of special considerations in developing microcomputer software collections, review of standardized cataloging practices, and discussion of problems of selection and acquisition of software. Policies governing loan procedures for microcomputer software which involve four types of copy protection (patent, trade secret, contract,…

  9. The analysis and rationale behind the upgrading of existing standard definition thermal imagers to high definition

    NASA Astrophysics Data System (ADS)

    Goss, Tristan M.

    2016-05-01

    With 640x512 pixel format IR detector arrays having been on the market for the past decade, Standard Definition (SD) thermal imaging sensors have been developed and deployed across the world. Now with 1280x1024 pixel format IR detector arrays becoming readily available designers of thermal imager systems face new challenges as pixel sizes reduce and the demand and applications for High Definition (HD) thermal imaging sensors increases. In many instances the upgrading of existing under-sampled SD thermal imaging sensors into more optimally sampled or oversampled HD thermal imaging sensors provides a more cost effective and reduced time to market option than to design and develop a completely new sensor. This paper presents the analysis and rationale behind the selection of the best suited HD pixel format MWIR detector for the upgrade of an existing SD thermal imaging sensor to a higher performing HD thermal imaging sensor. Several commercially available and "soon to be" commercially available HD small pixel IR detector options are included as part of the analysis and are considered for this upgrade. The impact the proposed detectors have on the sensor's overall sensitivity, noise and resolution is analyzed, and the improved range performance is predicted. Furthermore with reduced dark currents due to the smaller pixel sizes, the candidate HD MWIR detectors are operated at higher temperatures when compared to their SD predecessors. Therefore, as an additional constraint and as a design goal, the feasibility of achieving upgraded performance without any increase in the size, weight and power consumption of the thermal imager is discussed herein.

  10. Comparison of retinal thickness by Fourier-domain optical coherence tomography and OCT retinal image analysis software segmentation analysis derived from Stratus optical coherence tomography images

    NASA Astrophysics Data System (ADS)

    Tátrai, Erika; Ranganathan, Sudarshan; Ferencz, Mária; Debuc, Delia Cabrera; Somfai, Gábor Márk

    2011-05-01

    Purpose: To compare thickness measurements between Fourier-domain optical coherence tomography (FD-OCT) and time-domain OCT images analyzed with a custom-built OCT retinal image analysis software (OCTRIMA). Methods: Macular mapping (MM) by StratusOCT and MM5 and MM6 scanning protocols by an RTVue-100 FD-OCT device are performed on 11 subjects with no retinal pathology. Retinal thickness (RT) and the thickness of the ganglion cell complex (GCC) obtained with the MM6 protocol are compared for each early treatment diabetic retinopathy study (ETDRS)-like region with corresponding results obtained with OCTRIMA. RT results are compared by analysis of variance with Dunnett post hoc test, while GCC results are compared by paired t-test. Results: A high correlation is obtained for the RT between OCTRIMA and MM5 and MM6 protocols. In all regions, the StratusOCT provide the lowest RT values (mean difference 43 +/- 8 μm compared to OCTRIMA, and 42 +/- 14 μm compared to RTVue MM6). All RTVue GCC measurements were significantly thicker (mean difference between 6 and 12 μm) than the GCC measurements of OCTRIMA. Conclusion: High correspondence of RT measurements is obtained not only for RT but also for the segmentation of intraretinal layers between FD-OCT and StratusOCT-derived OCTRIMA analysis. However, a correction factor is required to compensate for OCT-specific differences to make measurements more comparable to any available OCT device.

  11. Towards a repository for standardized medical image and signal case data annotated with ground truth.

    PubMed

    Deserno, Thomas M; Welter, Petra; Horsch, Alexander

    2012-04-01

    Validation of medical signal and image processing systems requires quality-assured, representative and generally acknowledged databases accompanied by appropriate reference (ground truth) and clinical metadata, which are composed laboriously for each project and are not shared with the scientific community. In our vision, such data will be stored centrally in an open repository. We propose an architecture for a standardized case data and ground truth information repository supporting the evaluation and analysis of computer-aided diagnosis based on (a) the Reference Model for an Open Archival Information System (OAIS) provided by the NASA Consultative Committee for Space Data Systems (ISO 14721:2003), (b) the Dublin Core Metadata Initiative (DCMI) Element Set (ISO 15836:2009), (c) the Open Archive Initiative (OAI) Protocol for Metadata Harvesting, and (d) the Image Retrieval in Medical Applications (IRMA) framework. In our implementation, a portal bunches all of the functionalities that are needed for data submission and retrieval. The complete life cycle of the data (define, create, store, sustain, share, use, and improve) is managed. Sophisticated search tools make it easier to use the datasets, which may be merged from different providers. An integrated history record guarantees reproducibility. A standardized creation report is generated with a permanent digital object identifier. This creation report must be referenced by all of the data users. Peer-reviewed e-publishing of these reports will create a reputation for the data contributors and will form de-facto standards regarding image and signal datasets. Good practice guidelines for validation methodology complement the concept of the case repository. This procedure will increase the comparability of evaluation studies for medical signal and image processing methods and applications.

  12. TU-AB-303-08: GPU-Based Software Platform for Efficient Image-Guided Adaptive Radiation Therapy

    SciTech Connect

    Park, S; Robinson, A; McNutt, T; Wong, J; Lee, J; Plishker, W; Zaki, G; Shekhar, R

    2015-06-15

    Purpose: In this study, we develop an integrated software platform for adaptive radiation therapy (ART) that combines fast and accurate image registration, segmentation, and dose computation/accumulation methods. Methods: The proposed system consists of three key components; 1) deformable image registration (DIR), 2) automatic segmentation, and 3) dose computation/accumulation. The computationally intensive modules including DIR and dose computation have been implemented on a graphics processing unit (GPU). All required patient-specific data including the planning CT (pCT) with contours, daily cone-beam CTs, and treatment plan are automatically queried and retrieved from their own databases. To improve the accuracy of DIR between pCT and CBCTs, we use the double force demons DIR algorithm in combination with iterative CBCT intensity correction by local intensity histogram matching. Segmentation of daily CBCT is then obtained by propagating contours from the pCT. Daily dose delivered to the patient is computed on the registered pCT by a GPU-accelerated superposition/convolution algorithm. Finally, computed daily doses are accumulated to show the total delivered dose to date. Results: Since the accuracy of DIR critically affects the quality of the other processes, we first evaluated our DIR method on eight head-and-neck cancer cases and compared its performance. Normalized mutual-information (NMI) and normalized cross-correlation (NCC) computed as similarity measures, and our method produced overall NMI of 0.663 and NCC of 0.987, outperforming conventional methods by 3.8% and 1.9%, respectively. Experimental results show that our registration method is more consistent and roust than existing algorithms, and also computationally efficient. Computation time at each fraction took around one minute (30–50 seconds for registration and 15–25 seconds for dose computation). Conclusion: We developed an integrated GPU-accelerated software platform that enables accurate and

  13. Stereo Imaging Velocimetry Technique Using Standard Off-the-Shelf CCD Cameras

    NASA Technical Reports Server (NTRS)

    McDowell, Mark; Gray, Elizabeth

    2004-01-01

    Stereo imaging velocimetry is a fluid physics technique for measuring three-dimensional (3D) velocities at a plurality of points. This technique provides full-field 3D analysis of any optically clear fluid or gas experiment seeded with tracer particles. Unlike current 3D particle imaging velocimetry systems that rely primarily on laser-based systems, stereo imaging velocimetry uses standard off-the-shelf charge-coupled device (CCD) cameras to provide accurate and reproducible 3D velocity profiles for experiments that require 3D analysis. Using two cameras aligned orthogonally, we present a closed mathematical solution resulting in an accurate 3D approximation of the observation volume. The stereo imaging velocimetry technique is divided into four phases: 3D camera calibration, particle overlap decomposition, particle tracking, and stereo matching. Each phase is explained in detail. In addition to being utilized for space shuttle experiments, stereo imaging velocimetry has been applied to the fields of fluid physics, bioscience, and colloidal microscopy.

  14. In vivo validation of cardiac output assessment in non-standard 3D echocardiographic images

    NASA Astrophysics Data System (ADS)

    Nillesen, M. M.; Lopata, R. G. P.; de Boode, W. P.; Gerrits, I. H.; Huisman, H. J.; Thijssen, J. M.; Kapusta, L.; de Korte, C. L.

    2009-04-01

    Automatic segmentation of the endocardial surface in three-dimensional (3D) echocardiographic images is an important tool to assess left ventricular (LV) geometry and cardiac output (CO). The presence of speckle noise as well as the nonisotropic characteristics of the myocardium impose strong demands on the segmentation algorithm. In the analysis of normal heart geometries of standardized (apical) views, it is advantageous to incorporate a priori knowledge about the shape and appearance of the heart. In contrast, when analyzing abnormal heart geometries, for example in children with congenital malformations, this a priori knowledge about the shape and anatomy of the LV might induce erroneous segmentation results. This study describes a fully automated segmentation method for the analysis of non-standard echocardiographic images, without making strong assumptions on the shape and appearance of the heart. The method was validated in vivo in a piglet model. Real-time 3D echocardiographic image sequences of five piglets were acquired in radiofrequency (rf) format. These ECG-gated full volume images were acquired intra-operatively in a non-standard view. Cardiac blood flow was measured simultaneously by an ultrasound transit time flow probe positioned around the common pulmonary artery. Three-dimensional adaptive filtering using the characteristics of speckle was performed on the demodulated rf data to reduce the influence of speckle noise and to optimize the distinction between blood and myocardium. A gradient-based 3D deformable simplex mesh was then used to segment the endocardial surface. A gradient and a speed force were included as external forces of the model. To balance data fitting and mesh regularity, one fixed set of weighting parameters of internal, gradient and speed forces was used for all data sets. End-diastolic and end-systolic volumes were computed from the segmented endocardial surface. The cardiac output derived from this automatic segmentation was

  15. Light sources and cameras for standard in vitro membrane potential and high-speed ion imaging.

    PubMed

    Davies, R; Graham, J; Canepari, M

    2013-07-01

    Membrane potential and fast ion imaging are now standard optical techniques routinely used to record dynamic physiological signals in several preparations in vitro. Although detailed resolution of optical signals can be improved by confocal or two-photon microscopy, high spatial and temporal resolution can be obtained using conventional microscopy and affordable light sources and cameras. Thus, standard wide-field imaging methods are still the most common in research laboratories and can often produce measurements with a signal-to-noise ratio that is superior to other optical approaches. This paper seeks to review the most important instrumentation used in these experiments, with particular reference to recent technological advances. We analyse in detail the optical constraints dictating the type of signals that are obtained with voltage and ion imaging and we discuss how to use this information to choose the optimal apparatus. Then, we discuss the available light sources with specific attention to light emitting diodes and solid state lasers. We then address the current state-of-the-art of available charge coupled device, electron multiplying charge coupled device and complementary metal oxide semiconductor cameras and we analyse the characteristics that need to be taken into account for the choice of optimal detector. Finally, we conclude by discussing prospective future developments that are likely to further improve the quality of the signals expanding the capability of the techniques and opening the gate to novel applications.

  16. Proposal for future diagnosis and management of vascular tumors by using automatic software for image processing and statistic prediction

    PubMed Central

    Popescu, MD; Draghici, L; Secheli, I; Secheli, M; Codrescu, M; Draghici, I

    2015-01-01

    Rationale. Infantile Hemangiomas (IH) are the most frequent tumors of vascular origin, and the differential diagnosis from vascular malformations is difficult to establish. Specific types of IH due to the location, dimensions and fast evolution, can determine important functional and esthetic sequels. To avoid these unfortunate consequences it is necessary to establish the exact appropriate moment to begin the treatment and decide which the most adequate therapeutic procedure is. Objective. Based on clinical data collected by a serial clinical observations correlated with imaging data, and processed by a computer-aided diagnosis system (CAD), the study intended to develop a treatment algorithm to accurately predict the best final results, from the esthetical and functional point of view, for a certain type of lesion. Methods and Results. The preliminary database was composed of 75 patients divided into 4 groups according to the treatment management they received: medical therapy, sclerotherapy, surgical excision and no treatment. The serial clinical observation was performed each month and all the data was processed by using CAD. Discussions. The project goal was to create a software that incorporated advanced methods to accurately measure the specific IH lesions, integrated medical information, statistical methods and computational methods to correlate this information with that obtained from the processing of images. Based on these correlations, a prediction mechanism of the evolution of hemangioma, which helped determine the best method of therapeutic intervention to minimize further complications, was established. Abbreviations: Infantile Hemangiomas = IH, Computer Aided Diagnosis = CAD, Society for the Study of Vascular Anomalies = ISSVA, Color-coded duplex sonography = CCDS PMID:25914738

  17. Latest developments in the iLids performance standard: from multiple standard camera views to new imaging modalities

    NASA Astrophysics Data System (ADS)

    Sage, K. H.; Nilski, A. J.; Sillett, I. M.

    2009-09-01

    The Imagery Library for Intelligent Detection Systems (iLids) is the UK Government's standard for Video Based Detection Systems (VBDS). The first four iLids scenarios were released in November 2006 and annual evaluations for these four scenarios began in 2007. The Home Office Scientific Development Branch (HOSDB), in partnership with the Centre for the Protection of National Infrastructure (CPNI), has also developed a fifth iLids Scenario; Multiple Camera Tracking (MCT). The fifth scenario data sets were made available in November 2008 to industry, academic and commercial research organizations The imagery contains various staged events of people walking through the camera views. Multiple Camera Tracking Systems (MCTS) are expected to initialise on a specific target and be able to track the target over some or all of the camera views. HOSDB and CPNI are now working on a sixth iLids dataset series. These datasets will cover several technology areas: • Thermal imaging systems • Systems that rely on active IR illumination The aim is to develop libraries that promote the development of systems that are able to demonstrate effective performance in the key application area of people and vehicular detection at a distance. This paper will: • Describe the evaluation process, infrastructure and tools that HOSDB will use to evaluate MCT systems. Building on the success of our previous automated tools for evaluation, HOSDB has developed the MCT evaluation tool CLAYMORE. CLAYMORE is a tool for the real-time evaluation of MCT systems. • Provide an overview of the new sixth scenario aims and objectives, library specifications and timescales for release.

  18. Repeatability and Reproducibility of Quantitative Corneal Shape Analysis after Orthokeratology Treatment Using Image-Pro Plus Software

    PubMed Central

    Mei, Ying; Tang, Zhiping

    2016-01-01

    Purpose. To evaluate the repeatability and reproducibility of quantitative analysis of the morphological corneal changes after orthokeratology treatment using “Image-Pro Plus 6.0” software (IPP). Methods. Three sets of measurements were obtained: two sets by examiner 1 with 5 days apart and one set by examiner 2 on the same day. Parameters of the eccentric distance, eccentric angle, area, and roundness of the corneal treatment zone were measured using IPP. The intraclass correlation coefficient (ICC) and repetitive coefficient (COR) were used to calculate the repeatability and reproducibility of these three sets of measurements. Results. ICC analysis suggested “excellent” reliability of more than 0.885 for all variables, and COR values were less than 10% for all variables within the same examiner. ICC analysis suggested “excellent” reliability for all variables of more than 0.90, and COR values were less than 10% for all variables between different examiners. All extreme values of the eccentric distance and area of the treatment zone pointed to the same material number in three sets of measurements. Conclusions. IPP could be used to acquire the exact data of the characteristic morphological corneal changes after orthokeratology treatment with good repeatability and reproducibility. This trial is registered with trial registration number: ChiCTR-IPR-14005505. PMID:27774312

  19. Radiotherapy of high-grade gliomas: current standards and new concepts, innovations in imaging and radiotherapy, and new therapeutic approaches

    PubMed Central

    Dhermain, Frederic

    2014-01-01

    The current standards in radiotherapy of high-grade gliomas (HGG) are based on anatomic imaging techniques, usually computed tomography (CT) scanning and magnetic resonance imaging (MRI). The guidelines vary depending on whether the HGG is a histological grade 3 anaplastic glioma (AG) or a grade 4 glioblastoma multiforme (GBM). For AG, T2-weighted MRI sequences plus the region of contrast enhancement in T1 are considered for the delineation of the gross tumor volume (GTV), and an isotropic expansion of 15 to 20 mm is recommended for the clinical target volume (CTV). For GBM, the Radiation Therapy Oncology Group favors a two-step technique, with an initial phase (CTV1) including any T2 hyperintensity area (edema) plus a 20 mm margin treated with up to 46 Gy in 23 fractions, followed by a reduction in CTV2 to the contrast enhancement region in T1 with an additional 25 mm margin. The European Organisation of Research and Treatment of Cancer recommends a single-phase technique with a unique GTV, which comprises the T1 contrast enhancement region plus a margin of 20 to 30 mm. A total dose of 60 Gy in 30 fractions is usually delivered for GBM, and a dose of 59.4 Gy in 33 fractions is typically given for AG. As more than 85% of HGGs recur in field, dose-escalation studies have shown that 70 to 75 Gy can be delivered in 6 weeks with relevant toxicities developing in < 10% of the patients. However, the only randomized dose-escalation trial, in which the boost dose was guided by conventional MRI, did not show any survival advantage of this treatment over the reference arm. HGGs are amongst the most infiltrative and heterogeneous tumors, and it was hypothesized that the most highly aggressive areas were missed; thus, better visualization of these high-risk regions for radiation boost could decrease the recurrence rate. Innovations in imaging and linear accelerators (LINAC) could help deliver the right doses of radiation to the right subvolumes according to the dose

  20. Dental application of novel finite element analysis software for three-dimensional finite element modeling of a dentulous mandible from its computed tomography images.

    PubMed

    Nakamura, Keiko; Tajima, Kiyoshi; Chen, Ker-Kong; Nagamatsu, Yuki; Kakigawa, Hiroshi; Masumi, Shin-ich

    2013-12-01

    This study focused on the application of novel finite-element analysis software for constructing a finite-element model from the computed tomography data of a human dentulous mandible. The finite-element model is necessary for evaluating the mechanical response of the alveolar part of the mandible, resulting from occlusal force applied to the teeth during biting. Commercially available patient-specific general computed tomography-based finite-element analysis software was solely applied to the finite-element analysis for the extraction of computed tomography data. The mandibular bone with teeth was extracted from the original images. Both the enamel and the dentin were extracted after image processing, and the periodontal ligament was created from the segmented dentin. The constructed finite-element model was reasonably accurate using a total of 234,644 nodes and 1,268,784 tetrahedral and 40,665 shell elements. The elastic moduli of the heterogeneous mandibular bone were determined from the bone density data of the computed tomography images. The results suggested that the software applied in this study is both useful and powerful for creating a more accurate three-dimensional finite-element model of a dentulous mandible from the computed tomography data without the need for any other software.

  1. Vehicle occupancy detection camera position optimization using design of experiments and standard image references

    NASA Astrophysics Data System (ADS)

    Paul, Peter; Hoover, Martin; Rabbani, Mojgan

    2013-03-01

    Camera positioning and orientation is important to applications in domains such as transportation since the objects to be imaged vary greatly in shape and size. In a typical transportation application that requires capturing still images, inductive loops buried in the ground or laser trigger sensors are used when a vehicle reaches the image capture zone to trigger the image capture system. The camera in such a system is in a fixed position pointed at the roadway and at a fixed orientation. Thus the problem is to determine the optimal location and orientation of the camera when capturing images from a wide variety of vehicles. Methods from Design for Six Sigma, including identifying important parameters and noise sources and performing systematically designed experiments (DOE) can be used to determine an effective set of parameter settings for the camera position and orientation under these conditions. In the transportation application of high occupancy vehicle lane enforcement, the number of passengers in the vehicle is to be counted. Past work has described front seat vehicle occupant counting using a camera mounted on an overhead gantry looking through the front windshield in order to capture images of vehicle occupants. However, viewing rear seat passengers is more problematic due to obstructions including the vehicle body frame structures and seats. One approach is to view the rear seats through the side window. In this situation the problem of optimally positioning and orienting the camera to adequately capture the rear seats through the side window can be addressed through a designed experiment. In any automated traffic enforcement system it is necessary for humans to be able to review any automatically captured digital imagery in order to verify detected infractions. Thus for defining an output to be optimized for the designed experiment, a human defined standard image reference (SIR) was used to quantify the quality of the line-of-sight to the rear seats of

  2. Comparisons of neural networks to standard techniques for image classification and correlation

    NASA Technical Reports Server (NTRS)

    Paola, Justin D.; Schowengerdt, Robert A.

    1994-01-01

    Neural network techniques for multispectral image classification and spatial pattern detection are compared to the standard techniques of maximum-likelihood classification and spatial correlation. The neural network produced a more accurate classification than maximum-likelihood of a Landsat scene of Tucson, Arizona. Some of the errors in the maximum-likelihood classification are illustrated using decision region and class probability density plots. As expected, the main drawback to the neural network method is the long time required for the training stage. The network was trained using several different hidden layer sizes to optimize both the classification accuracy and training speed, and it was found that one node per class was optimal. The performance improved when 3x3 local windows of image data were entered into the net. This modification introduces texture into the classification without explicit calculation of a texture measure. Larger windows were successfully used for the detection of spatial features in Landsat and Magellan synthetic aperture radar imagery.

  3. A passive autofocus system by using standard deviation of the image on a liquid lens

    NASA Astrophysics Data System (ADS)

    Rasti, Pejman; Kesküla, Arko; Haus, Henry; Schlaak, Helmut F.; Anbarjafari, Gholamreza; Aabloo, Alvo; Kiefer, Rudolf

    2015-04-01

    Today most of applications have a small camera such as cell phones, tablets and medical devices. A micro lens is required in order to reduce the size of the devices. In this paper an auto focus system is used in order to find the best position of a liquid lens without any active components such as ultrasonic or infrared. In fact a passive auto focus system by using standard deviation of the images on a liquid lens which consist of a Dielectric Elastomer Actuator (DEA) membrane between oil and water is proposed.

  4. A no-gold-standard technique for objective assessment of quantitative nuclear-medicine imaging methods.

    PubMed

    Jha, Abhinav K; Caffo, Brian; Frey, Eric C

    2016-04-07

    The objective optimization and evaluation of nuclear-medicine quantitative imaging methods using patient data is highly desirable but often hindered by the lack of a gold standard. Previously, a regression-without-truth (RWT) approach has been proposed for evaluating quantitative imaging methods in the absence of a gold standard, but this approach implicitly assumes that bounds on the distribution of true values are known. Several quantitative imaging methods in nuclear-medicine imaging measure parameters where these bounds are not known, such as the activity concentration in an organ or the volume of a tumor. We extended upon the RWT approach to develop a no-gold-standard (NGS) technique for objectively evaluating such quantitative nuclear-medicine imaging methods with patient data in the absence of any ground truth. Using the parameters estimated with the NGS technique, a figure of merit, the noise-to-slope ratio (NSR), can be computed, which can rank the methods on the basis of precision. An issue with NGS evaluation techniques is the requirement of a large number of patient studies. To reduce this requirement, the proposed method explored the use of multiple quantitative measurements from the same patient, such as the activity concentration values from different organs in the same patient. The proposed technique was evaluated using rigorous numerical experiments and using data from realistic simulation studies. The numerical experiments demonstrated that the NSR was estimated accurately using the proposed NGS technique when the bounds on the distribution of true values were not precisely known, thus serving as a very reliable metric for ranking the methods on the basis of precision. In the realistic simulation study, the NGS technique was used to rank reconstruction methods for quantitative single-photon emission computed tomography (SPECT) based on their performance on the task of estimating the mean activity concentration within a known volume of interest

  5. A no-gold-standard technique for objective assessment of quantitative nuclear-medicine imaging methods

    NASA Astrophysics Data System (ADS)

    Jha, Abhinav K.; Caffo, Brian; Frey, Eric C.

    2016-04-01

    The objective optimization and evaluation of nuclear-medicine quantitative imaging methods using patient data is highly desirable but often hindered by the lack of a gold standard. Previously, a regression-without-truth (RWT) approach has been proposed for evaluating quantitative imaging methods in the absence of a gold standard, but this approach implicitly assumes that bounds on the distribution of true values are known. Several quantitative imaging methods in nuclear-medicine imaging measure parameters where these bounds are not known, such as the activity concentration in an organ or the volume of a tumor. We extended upon the RWT approach to develop a no-gold-standard (NGS) technique for objectively evaluating such quantitative nuclear-medicine imaging methods with patient data in the absence of any ground truth. Using the parameters estimated with the NGS technique, a figure of merit, the noise-to-slope ratio (NSR), can be computed, which can rank the methods on the basis of precision. An issue with NGS evaluation techniques is the requirement of a large number of patient studies. To reduce this requirement, the proposed method explored the use of multiple quantitative measurements from the same patient, such as the activity concentration values from different organs in the same patient. The proposed technique was evaluated using rigorous numerical experiments and using data from realistic simulation studies. The numerical experiments demonstrated that the NSR was estimated accurately using the proposed NGS technique when the bounds on the distribution of true values were not precisely known, thus serving as a very reliable metric for ranking the methods on the basis of precision. In the realistic simulation study, the NGS technique was used to rank reconstruction methods for quantitative single-photon emission computed tomography (SPECT) based on their performance on the task of estimating the mean activity concentration within a known volume of interest

  6. Validation of spectral radiance assignments to integrating sphere radiance standards for the Advanced Baseline Imager

    NASA Astrophysics Data System (ADS)

    Johnson, B. C.; Maxwell, Stephen; Shirley, Eric; Slack, Kim; Graham, Gary D.

    2014-09-01

    The Advanced Baseline Imager (ABI) is the next-generation imaging sensor for the National Oceanic and Atmospheric Administration's (NOAA's) operational meteorological satellites in geostationary orbit. One pathway for traceability to reference standards of the visible and near-infrared radiometric response for ABI is to a 1.65 m diameter integrating sphere source standard of spectral radiance. This source illuminates the full entrance pupil via the ABI Earth-view port, thus determining the absolute spectral radiance responsivity in the visible and shortwave infrared. The spectral radiance values of the large sphere are assigned by Exelis using a double monochromator and a 15.24 cm diameter integrating sphere source standard that is calibrated by NIST. As part of the ABI program, Exelis was required by NASA to have the spectral radiance values assigned by Exelis to the large sphere be validated by NIST. Here we report the results of that activity, which took place in April, 2013. During the week of April 8, Exelis calibrated the 1.65 m diameter sphere at all 24 levels that correspond to the ABI calibration protocol. During the week of April 15, the NIST validation exercise for five selected levels took place. NIST deployed a portable spectral radiance source, a filter radiometer restricted to the visible and near-infrared, and two spectroradiometers that covered from 350 nm to 2500 nm. The NIST sphere source served as the validation standard. The comparison results, which are reported at the ABI bands, agreed to within the combined uncertainties. We describe the methodology, results, and uncertainty estimates related to this effort.

  7. Software Quality Assurance Metrics

    NASA Technical Reports Server (NTRS)

    McRae, Kalindra A.

    2004-01-01

    Software Quality Assurance (SQA) is a planned and systematic set of activities that ensures conformance of software life cycle processes and products conform to requirements, standards and procedures. In software development, software quality means meeting requirements and a degree of excellence and refinement of a project or product. Software Quality is a set of attributes of a software product by which its quality is described and evaluated. The set of attributes includes functionality, reliability, usability, efficiency, maintainability, and portability. Software Metrics help us understand the technical process that is used to develop a product. The process is measured to improve it and the product is measured to increase quality throughout the life cycle of software. Software Metrics are measurements of the quality of software. Software is measured to indicate the quality of the product, to assess the productivity of the people who produce the product, to assess the benefits derived from new software engineering methods and tools, to form a baseline for estimation, and to help justify requests for new tools or additional training. Any part of the software development can be measured. If Software Metrics are implemented in software development, it can save time, money, and allow the organization to identify the caused of defects which have the greatest effect on software development. The summer of 2004, I worked with Cynthia Calhoun and Frank Robinson in the Software Assurance/Risk Management department. My task was to research and collect, compile, and analyze SQA Metrics that have been used in other projects that are not currently being used by the SA team and report them to the Software Assurance team to see if any metrics can be implemented in their software assurance life cycle process.

  8. 123I-Meta-iodobenzylguanidine Sympathetic Imaging: Standardization and Application to Neurological Diseases

    PubMed Central

    Yamada, Masahito

    2016-01-01

    123I-meta-iodobenzylguanidine (MIBG) has become widely applied in Japan since its introduction to clinical cardiology and neurology practice in the 1990s. Neurological studies found decreased cardiac uptake of 123I-MIBG in Lewy-body diseases including Parkinson's disease and dementia with Lewy bodies. Thus, cardiac MIBG uptake is now considered a biomarker of Lewy body diseases. Although scintigraphic images of 123I-MIBG can be visually interpreted, an average count ratio of heart-to-mediastinum (H/M) has commonly served as a semi-quantitative marker of sympathetic activity. Since H/M ratios significantly vary according to acquisition and processing conditions, quality control should be appropriate, and quantitation should be standardized. The threshold H/M ratio for differentiating Lewy-body disease is 2.0-2.1, and was based on standardized H/M ratios to comparable values of medium-energy collimators. Parkinson's disease can be separated from various types of parkinsonian syndromes using cardiac 123I-MIBG, whereas activity is decreased on images of Lewy-body diseases using both 123I-ioflupane for the striatum and 123I-MIBG. Despite being a simple index, the H/M ratio of 123I-MIBG uptake is reproducible and can serve as an effective tool to support a diagnosis of Lewy-body diseases in neurological practice. PMID:27689024

  9. Computer-aided 2D and 3D quantification of human stem cell fate from in vitro samples using Volocity high performance image analysis software.

    PubMed

    Piltti, Katja M; Haus, Daniel L; Do, Eileen; Perez, Harvey; Anderson, A J; Cummings, B J

    2011-11-01

    Accurate automated cell fate analysis of immunostained human stem cells from 2- and 3-dimensional (2D-3D) images would improve efficiency in the field of stem cell research. Development of an accurate and precise tool that reduces variability and the time needed for human stem cell fate analysis will improve productivity and interpretability of the data across research groups. In this study, we have created protocols for high performance image analysis software Volocity® to classify and quantify cytoplasmic and nuclear cell fate markers from 2D-3D images of human neural stem cells after in vitro differentiation. To enhance 3D image capture efficiency, we optimized the image acquisition settings of an Olympus FV10i® confocal laser scanning microscope to match our quantification protocols and improve cell fate classification. The methods developed in this study will allow for a more time efficient and accurate software based, operator validated, stem cell fate classification and quantification from 2D and 3D images, and yield the highest ≥94.4% correspondence with human recognized objects.

  10. Piezoresistive AFM cantilevers surpassing standard optical beam deflection in low noise topography imaging

    PubMed Central

    Dukic, Maja; Adams, Jonathan D.; Fantner, Georg E.

    2015-01-01

    Optical beam deflection (OBD) is the most prevalent method for measuring cantilever deflections in atomic force microscopy (AFM), mainly due to its excellent noise performance. In contrast, piezoresistive strain-sensing techniques provide benefits over OBD in readout size and the ability to image in light-sensitive or opaque environments, but traditionally have worse noise performance. Miniaturisation of cantilevers, however, brings much greater benefit to the noise performance of piezoresistive sensing than to OBD. In this paper, we show both theoretically and experimentally that by using small-sized piezoresistive cantilevers, the AFM imaging noise equal or lower than the OBD readout noise is feasible, at standard scanning speeds and power dissipation. We demonstrate that with both readouts we achieve a system noise of ≈0.3 Å at 20 kHz measurement bandwidth. Finally, we show that small-sized piezoresistive cantilevers are well suited for piezoresistive nanoscale imaging of biological and solid state samples in air. PMID:26574164

  11. Piezoresistive AFM cantilevers surpassing standard optical beam deflection in low noise topography imaging

    NASA Astrophysics Data System (ADS)

    Dukic, Maja; Adams, Jonathan D.; Fantner, Georg E.

    2015-11-01

    Optical beam deflection (OBD) is the most prevalent method for measuring cantilever deflections in atomic force microscopy (AFM), mainly due to its excellent noise performance. In contrast, piezoresistive strain-sensing techniques provide benefits over OBD in readout size and the ability to image in light-sensitive or opaque environments, but traditionally have worse noise performance. Miniaturisation of cantilevers, however, brings much greater benefit to the noise performance of piezoresistive sensing than to OBD. In this paper, we show both theoretically and experimentally that by using small-sized piezoresistive cantilevers, the AFM imaging noise equal or lower than the OBD readout noise is feasible, at standard scanning speeds and power dissipation. We demonstrate that with both readouts we achieve a system noise of ≈0.3 Å at 20 kHz measurement bandwidth. Finally, we show that small-sized piezoresistive cantilevers are well suited for piezoresistive nanoscale imaging of biological and solid state samples in air.

  12. Piezoresistive AFM cantilevers surpassing standard optical beam deflection in low noise topography imaging.

    PubMed

    Dukic, Maja; Adams, Jonathan D; Fantner, Georg E

    2015-11-17

    Optical beam deflection (OBD) is the most prevalent method for measuring cantilever deflections in atomic force microscopy (AFM), mainly due to its excellent noise performance. In contrast, piezoresistive strain-sensing techniques provide benefits over OBD in readout size and the ability to image in light-sensitive or opaque environments, but traditionally have worse noise performance. Miniaturisation of cantilevers, however, brings much greater benefit to the noise performance of piezoresistive sensing than to OBD. In this paper, we show both theoretically and experimentally that by using small-sized piezoresistive cantilevers, the AFM imaging noise equal or lower than the OBD readout noise is feasible, at standard scanning speeds and power dissipation. We demonstrate that with both readouts we achieve a system noise of ≈0.3 Å at 20 kHz measurement bandwidth. Finally, we show that small-sized piezoresistive cantilevers are well suited for piezoresistive nanoscale imaging of biological and solid state samples in air.

  13. Semi-automatic construction of reference standards for evaluation of image registration.

    PubMed

    Murphy, K; van Ginneken, B; Klein, S; Staring, M; de Hoop, B J; Viergever, M A; Pluim, J P W

    2011-02-01

    Quantitative evaluation of image registration algorithms is a difficult and under-addressed issue due to the lack of a reference standard in most registration problems. In this work a method is presented whereby detailed reference standard data may be constructed in an efficient semi-automatic fashion. A well-distributed set of n landmarks is detected fully automatically in one scan of a pair to be registered. Using a custom-designed interface, observers define corresponding anatomic locations in the second scan for a specified subset of s of these landmarks. The remaining n-s landmarks are matched fully automatically by a thin-plate-spline based system using the s manual landmark correspondences to model the relationship between the scans. The method is applied to 47 pairs of temporal thoracic CT scans, three pairs of brain MR scans and five thoracic CT datasets with synthetic deformations. Interobserver differences are used to demonstrate the accuracy of the matched points. The utility of the reference standard data as a tool in evaluating registration is shown by the comparison of six sets of registration results on the 47 pairs of thoracic CT data.

  14. Automated digital image analysis of islet cell mass using Nikon's inverted eclipse Ti microscope and software to improve engraftment may help to advance the therapeutic efficacy and accessibility of islet transplantation across centers.

    PubMed

    Gmyr, Valery; Bonner, Caroline; Lukowiak, Bruno; Pawlowski, Valerie; Dellaleau, Nathalie; Belaich, Sandrine; Aluka, Isanga; Moermann, Ericka; Thevenet, Julien; Ezzouaoui, Rimed; Queniat, Gurvan; Pattou, Francois; Kerr-Conte, Julie

    2015-01-01

    Reliable assessment of islet viability, mass, and purity must be met prior to transplanting an islet preparation into patients with type 1 diabetes. The standard method for quantifying human islet preparations is by direct microscopic analysis of dithizone-stained islet samples, but this technique may be susceptible to inter-/intraobserver variability, which may induce false positive/negative islet counts. Here we describe a simple, reliable, automated digital image analysis (ADIA) technique for accurately quantifying islets into total islet number, islet equivalent number (IEQ), and islet purity before islet transplantation. Islets were isolated and purified from n = 42 human pancreata according to the automated method of Ricordi et al. For each preparation, three islet samples were stained with dithizone and expressed as IEQ number. Islets were analyzed manually by microscopy or automatically quantified using Nikon's inverted Eclipse Ti microscope with built-in NIS-Elements Advanced Research (AR) software. The AIDA method significantly enhanced the number of islet preparations eligible for engraftment compared to the standard manual method (p < 0.001). Comparisons of individual methods showed good correlations between mean values of IEQ number (r(2) = 0.91) and total islet number (r(2) = 0.88) and thus increased to r(2) = 0.93 when islet surface area was estimated comparatively with IEQ number. The ADIA method showed very high intraobserver reproducibility compared to the standard manual method (p < 0.001). However, islet purity was routinely estimated as significantly higher with the manual method versus the ADIA method (p < 0.001). The ADIA method also detected small islets between 10 and 50 µm in size. Automated digital image analysis utilizing the Nikon Instruments software is an unbiased, simple, and reliable teaching tool to comprehensively assess the individual size of each islet cell preparation prior to transplantation. Implementation of this

  15. GOATS Image Projection Component

    NASA Technical Reports Server (NTRS)

    Haber, Benjamin M.; Green, Joseph J.

    2011-01-01

    When doing mission analysis and design of an imaging system in orbit around the Earth, answering the fundamental question of imaging performance requires an understanding of the image products that will be produced by the imaging system. GOATS software represents a series of MATLAB functions to provide for geometric image projections. Unique features of the software include function modularity, a standard MATLAB interface, easy-to-understand first-principles-based analysis, and the ability to perform geometric image projections of framing type imaging systems. The software modules are created for maximum analysis utility, and can all be used independently for many varied analysis tasks, or used in conjunction with other orbit analysis tools.

  16. Calibration standard of body tissue with magnetic nanocomposites for MRI and X-ray imaging

    NASA Astrophysics Data System (ADS)

    Rahn, Helene; Woodward, Robert; House, Michael; Engineer, Diana; Feindel, Kirk; Dutz, Silvio; Odenbach, Stefan; StPierre, Tim

    2016-05-01

    We present a first study of a long-term phantom for Magnetic Resonance Imaging (MRI) and X-ray imaging of biological tissues with magnetic nanocomposites (MNC) suitable for 3-dimensional and quantitative imaging of tissues after, e.g. magnetically assisted cancer treatments. We performed a cross-calibration of X-ray microcomputed tomography (XμCT) and MRI with a joint calibration standard for both imaging techniques. For this, we have designed a phantom for MRI and X-ray computed tomography which represents biological tissue enriched with MNC. The developed phantoms consist of an elastomer with different concentrations of multi-core MNC. The matrix material is a synthetic thermoplastic gel, PermaGel (PG). The developed phantoms have been analyzed with Nuclear Magnetic Resonance (NMR) Relaxometry (Bruker minispec mq 60) at 1.4 T to obtain R2 transverse relaxation rates, with SQUID (Superconducting QUantum Interference Device) magnetometry and Inductively Coupled Plasma Mass Spectrometry (ICP-MS) to verify the magnetite concentration, and with XμCT and 9.4 T MRI to visualize the phantoms 3-dimensionally and also to obtain T2 relaxation times. A specification of a sensitivity range is determined for standard imaging techniques X-ray computed tomography (XCT) and MRI as well as with NMR. These novel phantoms show a long-term stability over several months up to years. It was possible to suspend a particular MNC within the PG reaching a concentration range from 0 mg/ml to 6.914 mg/ml. The R2 relaxation rates from 1.4 T NMR-relaxometry show a clear connection (R2=0.994) with MNC concentrations between 0 mg/ml and 4.5 mg/ml. The MRI experiments have shown a linear correlation of R2 relaxation and MNC concentrations as well but in a range between MNC concentrations of 0 mg/ml and 1.435 mg/ml. It could be shown that XμCT displays best moderate and high MNC concentrations. The sensitivity range for this particular XμCT apparatus yields from 0.569 mg/ml to 6.914 mg/ml. The

  17. Comparison of Standard Versus Wide-Field Composite Images of the Corneal Subbasal Layer by In Vivo Confocal Microscopy

    PubMed Central

    Kheirkhah, Ahmad; Muller, Rodrigo; Mikolajczak, Janine; Ren, Ai; Kadas, Ella Maria; Zimmermann, Hanna; Pruess, Harald; Paul, Friedemann; Brandt, Alexander U.; Hamrah, Pedram

    2015-01-01

    Purpose To evaluate whether the densities of corneal subbasal nerves and epithelial immune dendritiform cells (DCs) are comparable between a set of three representative standard images of in vivo confocal microscopy (IVCM) and the wide-field mapped composite IVCM images. Methods This prospective, cross-sectional, and masked study included 110 eyes of 58 patients seen in a neurology clinic who underwent laser-scanning IVCM (Heidelberg Retina Tomograph 3) of the central cornea. Densities of subbasal corneal nerves and DCs were compared between the average of three representative standard images and the wide-field mapped composite images, which were reconstructed by automated mapping. Results There were no statistically significant differences between the average of three representative standard images (0.16 mm2 each) and the wide-field composite images (1.29 ± 0.64 mm2) in terms of mean subbasal nerve density (17.10 ± 6.10 vs. 17.17 ± 5.60 mm/mm2, respectively, P = 0.87) and mean subbasal DC density (53.2 ± 67.8 vs. 49.0 ± 54.3 cells/mm2, respectively, P = 0.43). However, there were notable differences in subbasal nerve and DC densities between these two methods in eyes with very low nerve density or very high DC density. Conclusions There are no significant differences in the mean subbasal nerve and DC densities between the average values of three representative standard IVCM images and wide-field mapped composite images. Therefore, these standard images can be used in clinical studies to accurately measure cellular structures in the subbasal layer. PMID:26325419

  18. Characterizing the energy output generated by a standard electric detonator using shadowgraph imaging

    NASA Astrophysics Data System (ADS)

    Petr, V.; Lozano, E.

    2017-03-01

    This paper overviews a complete method for the characterization of the explosive energy output from a standard detonator. Measurements of the output of explosives are commonly based upon the detonation parameters of the chemical energy content of the explosive. These quantities provide a correct understanding of the energy stored in an explosive, but they do not provide a direct measure of the different modes in which the energy is released. This optically based technique combines high-speed and ultra-high-speed imaging to characterize the casing fragmentation and the detonator-driven shock load. The procedure presented here could be used as an alternative to current indirect methods—such as the Trauzl lead block test—because of its simplicity, high data accuracy, and minimum demand for test repetition. This technique was applied to experimentally measure air shock expansion versus time and calculating the blast wave energy from the detonation of the high explosive charge inside the detonator. Direct measurements of the shock front geometry provide insight into the physics of the initiation buildup. Because of their geometry, standard detonators show an initial ellipsoidal shock expansion that degenerates into a final spherical wave. This non-uniform shape creates variable blast parameters along the primary blast wave. Additionally, optical measurements are validated using piezoelectric pressure transducers. The energy fraction spent in the acceleration of the metal shell is experimentally measured and correlated with the Gurney model, as well as to several empirical formulations for blasts from fragmenting munitions. The fragment area distribution is also studied using digital particle imaging analysis and correlated with the Mott distribution. Understanding the fragmentation distribution plays a critical role when performing hazard evaluation from these types of devices. In general, this technique allows for characterization of the detonator within 6-8% error

  19. An intelligent pre-processing framework for standardizing medical images for CAD and other post-processing applications

    NASA Astrophysics Data System (ADS)

    Raghupathi, Lakshminarasimhan; Devarakota, Pandu R.; Wolf, Matthias

    2012-03-01

    There is an increasing need to provide end-users with seamless and secure access to healthcare information acquired from a diverse range of sources. This might include local and remote hospital sites equipped with different vendors and practicing varied acquisition protocols and also heterogeneous external sources such as the Internet cloud. In such scenarios, image post-processing tools such as CAD (computer-aided diagnosis) which were hitherto developed using a smaller set of images may not always work optimally on newer set of images having entirely different characteristics. In this paper, we propose a framework that assesses the quality of a given input image and automatically applies an appropriate pre-processing method in such a manner that the image characteristics are normalized regardless of its source. We focus mainly on medical images, and the objective of the said preprocessing method is to standardize the performance of various image processing and workflow applications like CAD to perform in a consistent manner. First, our system consists of an assessment step wherein an image is evaluated based on criteria such as noise, image sharpness, etc. Depending on the measured characteristic, we then apply an appropriate normalization technique thus giving way to our overall pre-processing framework. A systematic evaluation of the proposed scheme is carried out on large set of CT images acquired from various vendors including images reconstructed with next generation iterative methods. Results demonstrate that the images are normalized and thus suitable for an existing LungCAD prototype1.

  20. Healthcare Software Assurance

    PubMed Central

    Cooper, Jason G.; Pauley, Keith A.

    2006-01-01

    Software assurance is a rigorous, lifecycle phase-independent set of activities which ensure completeness, safety, and reliability of software processes and products. This is accomplished by guaranteeing conformance to all requirements, standards, procedures, and regulations. These assurance processes are even more important when coupled with healthcare software systems, embedded software in medical instrumentation, and other healthcare-oriented life-critical systems. The current Food and Drug Administration (FDA) regulatory requirements and guidance documentation do not address certain aspects of complete software assurance activities. In addition, the FDA’s software oversight processes require enhancement to include increasingly complex healthcare systems such as Hospital Information Systems (HIS). The importance of complete software assurance is introduced, current regulatory requirements and guidance discussed, and the necessity for enhancements to the current processes shall be highlighted. PMID:17238324

  1. The DTI Challenge: Towards Standardized Evaluation of Diffusion Tensor Imaging Tractography for Neurosurgery

    PubMed Central

    Pujol, Sonia; Wells, William; Pierpaoli, Carlo; Brun, Caroline; Gee, James; Cheng, Guang; Vemuri, Baba; Commowick, Olivier; Prima, Sylvain; Stamm, Aymeric; Goubran, Maged; Khan, Ali; Peters, Terry; Neher, Peter; Maier-Hein, Klaus H.; Shi, Yundi; Tristan-Vega, Antonio; Veni, Gopalkrishna; Whitaker, Ross; Styner, Martin; Westin, Carl-Fredrik; Gouttard, Sylvain; Norton, Isaiah; Chauvin, Laurent; Mamata, Hatsuho; Gerig, Guido; Nabavi, Arya; Golby, Alexandra; Kikinis, Ron

    2015-01-01

    Background and Purpose Diffusion tensor imaging tractography reconstruction of white matter pathways can help guide brain tumor resection. However, DTI tracts are complex mathematical objects and the validity of tractography-derived information in clinical settings has yet to be fully established. To address this issue, we initiated the DTI Challenge, an international working group of clinicians and scientists whose goal was to provide standardized evaluation of tractography methods for neurosurgery. The purpose of this empirical study was to evaluate different tractography techniques in the first DTI Challenge workshop. Methods Eight international teams from leading institutions reconstructed the pyramidal tract in four neurosurgical cases presenting with a glioma near the motor cortex. Tractography methods included deterministic, probabilistic, filtered, and global approaches. Standardized evaluation of the tracts consisted in the qualitative review of the pyramidal pathways by a panel of neurosurgeons and DTI experts and the quantitative evaluation of the degree of agreement among methods. Results The evaluation of tractography reconstructions showed a great inter-algorithm variability. Although most methods found projections of the pyramidal tract from the medial portion of the motor strip, only a few algorithms could trace the lateral projections from the hand, face, and tongue area. In addition, the structure of disagreement among methods was similar across hemispheres despite the anatomical distortions caused by pathological tissues. Conclusions The DTI Challenge provides a benchmark for the standardized evaluation of tractography methods on neurosurgical data. This study suggests that there are still limitations to the clinical use of tractography for neurosurgical decision-making. PMID:26259925

  2. Documentation Driven Software Development

    DTIC Science & Technology

    2010-06-01

    reliability standards, ease of reconfigurability, and interoperability with other systems. The key challenges encountered during design of complex...software life cycles. The challenge here is to ensure proper transformation of project requirements, which may be specified informally, into the formal...software is becoming a more challenging task— often resulting in unexpected safety risks, schedule delays, and cost overruns. This research is

  3. Software Quality Metrics

    DTIC Science & Technology

    1991-07-01

    March 1979, pp. 121-128. Gorla, Narasimhaiah, Alan C. Benander, and Barbara A. Benander, "Debugging Effort Estimation Using Software Metrics", IEEE...Society, IEEE Guide for the Use of IEEE Standard Dictionary of Measures to Produce Reliable Software, IEEE Std 982.2-1988, June 1989. Jones, Capers

  4. Split-screen display system and standardized methods for ultrasound image acquisition and multi-frame data processing

    NASA Technical Reports Server (NTRS)

    Selzer, Robert H. (Inventor); Hodis, Howard N. (Inventor)

    2011-01-01

    A standardized acquisition methodology assists operators to accurately replicate high resolution B-mode ultrasound images obtained over several spaced-apart examinations utilizing a split-screen display in which the arterial ultrasound image from an earlier examination is displayed on one side of the screen while a real-time "live" ultrasound image from a current examination is displayed next to the earlier image on the opposite side of the screen. By viewing both images, whether simultaneously or alternately, while manually adjusting the ultrasound transducer, an operator is able to bring into view the real-time image that best matches a selected image from the earlier ultrasound examination. Utilizing this methodology, dynamic material properties of arterial structures, such as IMT and diameter, are measured in a standard region over successive image frames. Each frame of the sequence has its echo edge boundaries automatically determined by using the immediately prior frame's true echo edge coordinates as initial boundary conditions. Computerized echo edge recognition and tracking over multiple successive image frames enhances measurement of arterial diameter and IMT and allows for improved vascular dimension measurements, including vascular stiffness and IMT determinations.

  5. JPL Robotics Laboratory computer vision software library

    NASA Technical Reports Server (NTRS)

    Cunningham, R.

    1984-01-01

    The past ten years of research on computer vision have matured into a powerful real time system comprised of standardized commercial hardware, computers, and pipeline processing laboratory prototypes, supported by anextensive set of image processing algorithms. The software system was constructed to be transportable via the choice of a popular high level language (PASCAL) and a widely used computer (VAX-11/750), it comprises a whole realm of low level and high level processing software that has proven to be versatile for applications ranging from factory automation to space satellite tracking and grappling.

  6. [The Development of a Normal Database of Elderly People for Use with the Statistical Analysis Software Easy Z-score Imaging System with 99mTc-ECD SPECT].

    PubMed

    Nemoto, Hirobumi; Iwasaka, Akemi; Hashimoto, Shingo; Hara, Tadashi; Nemoto, Kiyotaka; Asada, Takashi

    2015-11-01

    We created a new normal database of elderly individuals (Tsukuba-NDB) for easy Z-score Imaging System (eZIS), a statistical imaging analysis software, comprised of 44 healthy individuals aged 75 to 89 years. The Tsukuba-NDB was compared with a conventional NDB (Musashi-NDB) using Statistical Parametric Mapping (SPM8), eZIS analysis, mean images, standard deviation (SD) images, SD values, specific volume of interest analysis (SVA). Furthermore, the association of the mean cerebral blood flow (mCBF) with various clinical indicators was statistically analyzed. A group comparison using SPM8 indicated that the t-value of the Tsukuba-NDB was lower in the frontoparietal region but tended to be higher in the bilateral temporal lobes and the base of the brain than that of the Musashi-NDB. The results of eZIS analysis by Musashi-NDB in 48 subjects indicated the presence of mild decreases in cerebral blood flow in the bilateral frontoparietal lobes of 9 subjects, precuneus and posterior cingulate gyrus of 5 subjects, lingual gyrus of 4 subjects, and near the left frontal gyrus, temporal lobe, superior temporal gyrus, and lenticular nucleus of 12 subjects. The mean images showed that there were no visual differences between both NDBs. The SD images intensities and SD values were lower in Tsukuba-NDB. Clinical case comparison and visual evaluation demonstrated that the sites of decrease in blood flow were more clearly indicated by the Tsukuba-NDB. Furthermore, mCBF was 40.87 ± 0.52 ml/100 g/min (mean ± SE), and tended to decrease with age. The tendency was stronger in male subjects than female subjects. Among various clinical indicators, the platelet count was statistically significantly correlated with CBF. In conclusion, our results suggest that Tsukuba-NDB, which is incorporated into a statistical imaging analysis software, eZIS, is sensitive to changes in cerebral blood flow caused by Cranial nerve disease, dementia and cerebrovascular accidents, and can provide precise

  7. Modified approach to the characterization of adrenal nodules using a standard abdominal magnetic resonance imaging protocol

    PubMed Central

    Matos, António P.; Semelka, Richard C.; Herédia, Vasco; AlObaidiy, Mamdoh; Gomes, Filipe Veloso; Ramalho, Miguel

    2017-01-01

    Objective To describe a modified approach to the evaluation of adrenal nodules using a standard abdominal magnetic resonance imaging protocol. Materials and Methods Our sample comprised 149 subjects (collectively presenting with 132 adenomas and 40 nonadenomas). The adrenal signal intensity index was calculated. Lesions were grouped by pattern of enhancement (PE), according to the phase during which the wash-in peaked: arterial phase (type 1 PE); portal venous phase (type 2 PE); and interstitial phase (type 3 PE). The relative and absolute wash-out values were calculated. To test for mean differences between adenomas and nonadenomas, Student's t-tests were used. Receiver operating characteristic curve analysis was also performed. Results The mean adrenal signal intensity index was significantly higher for the adenomas than for the nonadenomas (p < 0.0001). Chemical shift imaging showed a sensitivity and specificity of 94.4% and 100%, respectively, for differentiating adenomas from nonadenomas. Of the adenomas, 47.6%, 48.5%, and 3.9%, respectively, exhibited type 1, 2, and 3 PEs. For the mean wash-in proportions, significant differences were found among the enhancement patterns. The wash-out calculations revealed a trend toward better lesion differentiation for lesions exhibiting a type 1 PE, showing a sensitivity and specificity of 71.4% and 80.0%, respectively, when the absolute values were referenced, as well as for lesions exhibiting a type 2 PE, showing a sensitivity and specificity of 68.0% and 100%, respectively, when the relative values were referenced. The calculated probability of a lipid-poor lesion that exhibited a type 3 PE being a nonadenoma was > 99%. Conclusion Subgrouping dynamic enhancement patterns yields high diagnostic accuracy in differentiating adenomas from nonadenomas. PMID:28298728

  8. A multisite validation of whole slide imaging for primary diagnosis using standardized data collection and analysis

    PubMed Central

    Wack, Katy; Drogowski, Laura; Treloar, Murray; Evans, Andrew; Ho, Jonhan; Parwani, Anil; Montalto, Michael C.

    2016-01-01

    Context: Text-based reporting and manual arbitration for whole slide imaging (WSI) validation studies are labor intensive and do not allow for consistent, scalable, and repeatable data collection or analysis. Objective: The objective of this study was to establish a method of data capture and analysis using standardized codified checklists and predetermined synoptic discordance tables and to use these methods in a pilot multisite validation study. Methods and Study Design: Fifteen case report form checklists were generated from the College of American Pathology cancer protocols. Prior to data collection, all hypothetical pairwise comparisons were generated, and a level of harm was determined for each possible discordance. Four sites with four pathologists each generated 264 independent reads of 33 cases. Preestablished discordance tables were applied to determine site by site and pooled accuracy, intrareader/intramodality, and interreader intramodality error rates. Results: Over 10,000 hypothetical pairwise comparisons were evaluated and assigned harm in discordance tables. The average difference in error rates between WSI and glass, as compared to ground truth, was 0.75% with a lower bound of 3.23% (95% confidence interval). Major discordances occurred on challenging cases, regardless of modality. The average inter-reader agreement across sites for glass was 76.5% (weighted kappa of 0.68) and for digital it was 79.1% (weighted kappa of 0.72). Conclusion: These results demonstrate the feasibility and utility of employing standardized synoptic checklists and predetermined discordance tables to gather consistent, comprehensive diagnostic data for WSI validation studies. This method of data capture and analysis can be applied in large-scale multisite WSI validations. PMID:27994941

  9. Adapting astronomical source detection software to help detect animals in thermal images obtained by unmanned aerial systems

    NASA Astrophysics Data System (ADS)

    Longmore, S. N.; Collins, R. P.; Pfeifer, S.; Fox, S. E.; Mulero-Pazmany, M.; Bezombes, F.; Goodwind, A.; de Juan Ovelar, M.; Knapen, J. H.; Wich, S. A.

    2017-02-01

    In this paper we describe an unmanned aerial system equipped with a thermal-infrared camera and software pipeline that we have developed to monitor animal populations for conservation purposes. Taking a multi-disciplinary approach to tackle this problem, we use freely available astronomical source detection software and the associated expertise of astronomers, to efficiently and reliably detect humans and animals in aerial thermal-infrared footage. Combining this astronomical detection software with existing machine learning algorithms into a single, automated, end-to-end pipeline, we test the software using aerial video footage taken in a controlled, field-like environment. We demonstrate that the pipeline works reliably and describe how it can be used to estimate the completeness of different observational datasets to objects of a given type as a function of height, observing conditions etc. - a crucial step in converting video footage to scientifically useful information such as the spatial distribution and density of different animal species. Finally, having demonstrated the potential utility of the system, we describe the steps we are taking to adapt the system for work in the field, in particular systematic monitoring of endangered species at National Parks around the world.

  10. Onboard utilization of ground control points for image correction. Volume 3: Ground control point simulation software design

    NASA Technical Reports Server (NTRS)

    1981-01-01

    The software developed to simulate the ground control point navigation system is described. The Ground Control Point Simulation Program (GCPSIM) is designed as an analysis tool to predict the performance of the navigation system. The system consists of two star trackers, a global positioning system receiver, a gyro package, and a landmark tracker.

  11. Software Formal Inspections Guidebook

    NASA Technical Reports Server (NTRS)

    1993-01-01

    The Software Formal Inspections Guidebook is designed to support the inspection process of software developed by and for NASA. This document provides information on how to implement a recommended and proven method for conducting formal inspections of NASA software. This Guidebook is a companion document to NASA Standard 2202-93, Software Formal Inspections Standard, approved April 1993, which provides the rules, procedures, and specific requirements for conducting software formal inspections. Application of the Formal Inspections Standard is optional to NASA program or project management. In cases where program or project management decide to use the formal inspections method, this Guidebook provides additional information on how to establish and implement the process. The goal of the formal inspections process as documented in the above-mentioned Standard and this Guidebook is to provide a framework and model for an inspection process that will enable the detection and elimination of defects as early as possible in the software life cycle. An ancillary aspect of the formal inspection process incorporates the collection and analysis of inspection data to effect continual improvement in the inspection process and the quality of the software subjected to the process.

  12. Risk Assessment Methodology for Software Supportability (RAMSS): guidelines for Adapting Software Supportability Evaluations

    DTIC Science & Technology

    1986-04-14

    implemented various software OT&E method - ologies. Two of these methods , Software Product maintainability evaluation and Software Support Resources evaluation... methods have matured and have become the Air Force standard for evaluating, software supportablllty. Each of these developed methods evaluates...assessment method which provides software testers with areas which require testing emphasis, and decision makers with an assessment of the software sup

  13. Automatic standard plane adjustment on mobile C-Arm CT images of the calcaneus using atlas-based feature registration

    NASA Astrophysics Data System (ADS)

    Brehler, Michael; Görres, Joseph; Wolf, Ivo; Franke, Jochen; von Recum, Jan; Grützner, Paul A.; Meinzer, Hans-Peter; Nabers, Diana

    2014-03-01

    Intraarticular fractures of the calcaneus are routinely treated by open reduction and internal fixation followed by intraoperative imaging to validate the repositioning of bone fragments. C-Arm CT offers surgeons the possibility to directly verify the alignment of the fracture parts in 3D. Although the device provides more mobility, there is no sufficient information about the device-to-patient orientation for standard plane reconstruction. Hence, physicians have to manually align the image planes in a position that intersects with the articular surfaces. This can be a time-consuming step and imprecise adjustments lead to diagnostic errors. We address this issue by introducing novel semi-/automatic methods for adjustment of the standard planes on mobile C-Arm CT images. With the semi-automatic method, physicians can quickly adjust the planes by setting six points based on anatomical landmarks. The automatic method reconstructs the standard planes in two steps, first SURF keypoints (2D and newly introduced pseudo-3D) are generated for each image slice; secondly, these features are registered to an atlas point set and the parameters of the image planes are transformed accordingly. The accuracy of our method was evaluated on 51 mobile C-Arm CT images from clinical routine with manually adjusted standard planes by three physicians of different expertise. The average time of the experts (46s) deviated from the intermediate user (55s) by 9 seconds. By applying 2D SURF key points 88% of the articular surfaces were intersected correctly by the transformed standard planes with a calculation time of 10 seconds. The pseudo-3D features performed even better with 91% and 8 seconds.

  14. Analysis of He I 1083 nm Imaging Spectroscopy Using a Spectral Standard

    NASA Technical Reports Server (NTRS)

    Malanushenko, Elena V.; Jones, Harrison P.

    2004-01-01

    We develop a technique. for the analysis of He I 1083 nanometer spectra which addresses several difficulties through determination of a continuum background by comparison with a well calibrated standard and through removal of nearby solar and telluric blends by differential comparison to an average spectrum. The method is compared with earlier analysis of imaging spectroscopy obtained at the National Solar Observatory/Kitt Peak Vacuum Telescope (NSO/KPVT) with the NASA/NSO Spectromagnetograph (SPM). We examine distributions of Doppler velocity and line width as a function of central intensity for an active region, filament, quiet Sun, and coronal hole. For our example, we find that line widths and central intensity are oppositely correlated in a coronal hole and quiet Sun. Line widths are comparable to the quiet sun in the active region, are systematically lower in the filament, and extend to higher values in the coronal hole. Outward velocities of approximately equal to 2 to 4 kilometers per second are typically observed in the coronal hole. The sensitivity of these results to analysis technique is discussed.

  15. Computerized assessment of body image in anorexia nervosa and bulimia nervosa: comparison with standardized body image assessment tool.

    PubMed

    Caspi, Asaf; Amiaz, Revital; Davidson, Noa; Czerniak, Efrat; Gur, Eitan; Kiryati, Nahum; Harari, Daniel; Furst, Miriam; Stein, Daniel

    2017-02-01

    Body image disturbances are a prominent feature of eating disorders (EDs). Our aim was to test and evaluate a computerized assessment of body image (CABI), to compare the body image disturbances in different ED types, and to assess the factors affecting body image. The body image of 22 individuals undergoing inpatient treatment with restricting anorexia nervosa (AN-R), 22 with binge/purge AN (AN-B/P), 20 with bulimia nervosa (BN), and 41 healthy controls was assessed using the Contour Drawing Rating Scale (CDRS), the CABI, which simulated the participants' self-image in different levels of weight changes, and the Eating Disorder Inventory-2-Body Dissatisfaction (EDI-2-BD) scale. Severity of depression and anxiety was also assessed. Significant differences were found among the three scales assessing body image, although most of their dimensions differentiated between patients with EDs and controls. Our findings support the use of the CABI in the comparison of body image disturbances in patients with EDs vs.

  16. 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.

  17. TIA Software User's Manual

    NASA Technical Reports Server (NTRS)

    Cramer, K. Elliott; Syed, Hazari I.

    1995-01-01

    This user's manual describes the installation and operation of TIA, the Thermal-Imaging acquisition and processing Application, developed by the Nondestructive Evaluation Sciences Branch at NASA Langley Research Center, Hampton, Virginia. TIA is a user friendly graphical interface application for the Macintosh 2 and higher series computers. The software has been developed to interface with the Perceptics/Westinghouse Pixelpipe(TM) and PixelStore(TM) NuBus cards and the GW Instruments MacADIOS(TM) input-output (I/O) card for the Macintosh for imaging thermal data. The software is also capable of performing generic image-processing functions.

  18. Magnetic resonance image segmentation using semi-automated software for quantification of knee articular cartilage—initial evaluation of a technique for paired scans

    PubMed Central

    Brem, M. H.; Lang, P. K.; Neumann, G.; Schlechtweg, P. M.; Schneider, E.; Jackson, R.; Yu, J.; Eaton, C. B.; Hennig, F. F.; Yoshioka, H.; Pappas, G.; Duryea, J.

    2010-01-01

    Purpose Software-based image analysis is important for studies of cartilage changes in knee osteoarthritis (OA). This study describes an evaluation of a semi-automated cartilage segmentation software tool capable of quantifying paired images for potential use in longitudinal studies of knee OA. We describe the methodology behind the analysis and demonstrate its use by determination of test–retest analysis precision of duplicate knee magnetic resonance imaging (MRI) data sets. Methods Test–retest knee MR images of 12 subjects with a ra