Science.gov

Sample records for imaging workspace software

  1. Combining speech recognition software with Digital Imaging and Communications in Medicine (DICOM) workstation software on a Microsoft Windows platform.

    PubMed

    Ernst, R; Carpenter, W; Torres, W; Wheeler, S

    2001-06-01

    This presentation describes our experience in combining speech recognition software, clinical review software, and other software products on a single computer. Different processor speeds, random access memory (RAM), and computer costs were evaluated. We found that combining continuous speech recognition software with Digital Imaging and Communications in Medicine (DICOM) workstation software on the same platform is feasible and can lead to substantial savings of hardware cost. This combination optimizes use of limited workspace and can improve radiology workflow.

  2. 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

  3. Teacher Workspaces

    ERIC Educational Resources Information Center

    Gordon, Douglas

    2010-01-01

    Well-designed and -equipped teacher workspaces provide the opportunity to improve student achievement at every step of their K-12 education. Shared workspace enhances communication among teachers as they evaluate student performance individually and collectively, and share insights with one another. This paper addresses the key elements found in…

  4. Image Processing Software

    NASA Technical Reports Server (NTRS)

    1990-01-01

    The Ames digital image velocimetry technology has been incorporated in a commercially available image processing software package that allows motion measurement of images on a PC alone. The software, manufactured by Werner Frei Associates, is IMAGELAB FFT. IMAGELAB FFT is a general purpose image processing system with a variety of other applications, among them image enhancement of fingerprints and use by banks and law enforcement agencies for analysis of videos run during robberies.

  5. SAPHIRE 8 Volume 5 - Workspaces

    SciTech Connect

    C. L. Smith; J. K. Knudsen; D. O'Neal

    2011-03-01

    The Systems Analysis Programs for Hands-on Integrated Reliability Evaluations (SAPHIRE) Version 8 is a software application developed for performing a complete probabilistic risk assessment using a personal computer running the Microsoft Windows™ operating system. SAPHIRE 8 is funded by the U.S. Nuclear Regulatory Commission (NRC). The role of the Idaho National Laboratory (INL) in this project is that of software developer and tester. In older versions of SAPHIRE, the model creation and analysis functions were intermingled. However, in SAPHIRE 8, the act of creating a model has been separated from the analysis of that model in order to improve the quality of both the model (e.g., by avoiding inadvertent changes) and the analysis. Consequently, in SAPHIRE 8, the analysis of models is performed by using what are called Workspaces. Currently, there are Workspaces for three types of analyses: (1) the NRC’s Accident Sequence Precursor program, where the workspace is called “Events and Condition Assessment (ECA);” (2) the NRC’s Significance Determination Process (SDP); and (3) the General Analysis (GA) workspace. Workspaces for each type are created and saved separately from the base model which keeps the original database intact. Workspaces are independent of each other and modifications or calculations made within one workspace will not affect another. In addition, each workspace has a user interface and reports tailored for their intended uses.

  6. 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.

  7. 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

  8. 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.

  9. Quantitative Redox Imaging Software.

    PubMed

    Fricker, Mark D

    2016-05-01

    A wealth of fluorescent reporters and imaging systems are now available to characterize dynamic physiological processes in living cells with high spatiotemporal resolution. The most reliable probes for quantitative measurements show shifts in their excitation or emission spectrum, rather than just a change in intensity, as spectral shifts are independent of optical path length, illumination intensity, probe concentration, and photobleaching, and they can be easily determined by ratiometric measurements at two wavelengths. A number of ratiometric fluorescent reporters, such as reduction-oxidation-sensitive green fluorescent protein (roGFP), have been developed that respond to the glutathione redox potential and allow redox imaging in vivo. roGFP and its derivatives can be expressed in the cytoplasm or targeted to different organelles, giving fine control of measurements from sub-cellular compartments. Furthermore, roGFP can be imaged with probes for other physiological parameters, such as reactive oxygen species or mitochondrial membrane potential, to give multi-channel, multi-dimensional 4D (x,y,z,t) images. Live cell imaging approaches are needed to capture transient or highly spatially localized physiological behavior from intact, living specimens, which are often not accessible by other biochemical or genetic means. The next challenge is to be able to extract useful data rapidly from such large (GByte) images with due care given to the assumptions used during image processing. This article describes a suite of software programs, available for download, that provide intuitive user interfaces to conduct multi-channel ratio imaging, or alternative analysis methods such as pixel-population statistics or image segmentation and object-based ratio analysis. Antioxid. Redox Signal. 24, 752-762.

  10. 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.

  11. Flyover Animation of Phoenix Workspace

    NASA Technical Reports Server (NTRS)

    2008-01-01

    [figure removed for brevity, see original site] Click on image for animation

    This animated 'flyover' of the workspace of NASA's Phoenix Mars Lander's was created from images taken by the Surface Stereo Imager on Sol 14 (June 8, 2008), or the 14th Martian day after landing.

    The visualization uses both of the camera's 'eyes' to provide depth perception and ranging. The camera is looking north over the workspace.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  12. Flyover Animation of Phoenix Workspace

    NASA Technical Reports Server (NTRS)

    2008-01-01

    [figure removed for brevity, see original site] Click on image for animation

    This animated 'flyover' of the workspace of NASA's Phoenix Mars Lander's was created from images taken by the Surface Stereo Imager on Sol 14 (June 8, 2008), or the 14th Martian day after landing.

    The visualization uses both of the camera's 'eyes' to provide depth perception and ranging. The camera is looking north over the workspace.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. False Color Terrain Model of Phoenix Workspace

    NASA Image and Video Library

    2008-05-28

    This is a terrain model of Phoenix Robotic Arm workspace. It has been color coded by depth with a lander model for context. The model has been derived using images from the depth perception feature from Phoenix Surface Stereo Imager SSI.

  19. Phoenix Robotic Arm's Workspace After 90 Sols

    NASA Technical Reports Server (NTRS)

    2008-01-01

    During the first 90 Martian days, or sols, after its May 25, 2008, landing on an arctic plain of Mars, NASA's Phoenix Mars Lander dug several trenches in the workspace reachable with the lander's robotic arm.

    The lander's Surface Stereo Imager camera recorded this view of the workspace on Sol 90, early afternoon local Mars time (overnight Aug. 25 to Aug. 26, 2008). The shadow of the the camera itself, atop its mast, is just left of the center of the image and roughly a third of a meter (one foot) wide.

    The workspace is on the north side of the lander. The trench just to the right of center is called 'Neverland.'

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  20. Phoenix Robotic Arm's Workspace After 90 Sols

    NASA Technical Reports Server (NTRS)

    2008-01-01

    During the first 90 Martian days, or sols, after its May 25, 2008, landing on an arctic plain of Mars, NASA's Phoenix Mars Lander dug several trenches in the workspace reachable with the lander's robotic arm.

    The lander's Surface Stereo Imager camera recorded this view of the workspace on Sol 90, early afternoon local Mars time (overnight Aug. 25 to Aug. 26, 2008). The shadow of the the camera itself, atop its mast, is just left of the center of the image and roughly a third of a meter (one foot) wide.

    The workspace is on the north side of the lander. The trench just to the right of center is called 'Neverland.'

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  1. 3-D Visualization on Workspace of Parallel Manipulators

    NASA Astrophysics Data System (ADS)

    Tanaka, Yoshito; Yokomichi, Isao; Ishii, Junko; Makino, Toshiaki

    In parallel mechanisms, the form and volume of workspace also change variously with the attitude of a platform. This paper presents a method to search for the workspace of parallel mechanisms with 6-DOF and 3D visualization of the workspace. Workspace is a search for the movable range of the central point of a platform when it moves with a given orientation. In order to search workspace, geometric analysis based on inverse kinematics is considered. Plots of 2D of calculations are compared with those measured by position sensors. The test results are shown to have good agreement with simulation results. The workspace variations are demonstrated in terms of 3D and 2D plots for prototype mechanisms. The workspace plots are created with OpenGL and Visual C++ by implementation of the algorithm. An application module is developed, which displays workspace of the mechanism in 3D images. The effectiveness and practicability of 3D visualization on workspace are successfully demonstrated by 6-DOF parallel mechanisms.

  2. 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.

  3. 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.

  4. 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.

  5. 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/

  6. Collaborative Workspaces to Accelerate Discovery

    NASA Astrophysics Data System (ADS)

    Meade, Bernard; Fluke, Christopher; Cooke, Jeff; Andreoni, Igor; Pritchard, Tyler; Curtin, Christopher; Bernard, Stephanie R.; Asher, Albany; Mack, Katherine J.; Murphy, Michael T.; Vohl, Dany; Codoreanu, Alex; Kotuš, Srđan M.; Rumokoy, Fanuel; Horst, Chuck; Reynolds, Tristan

    2017-05-01

    By applying a display ecology to the Deeper, Wider, Faster proactive, simultaneous telescope observing campaign, we have shown a dramatic reduction in the time taken to inspect DECam CCD images for potential transient candidates and to produce time-critical triggers to standby telescopes. We also show how facilitating rapid corroboration of potential candidates and the exclusion of non-candidates improves the accuracy of detection; and establish that a practical and enjoyable workspace can improve the experience of an otherwise taxing task for astronomers. We provide a critical road test of two advanced displays in a research context-a rare opportunity to demonstrate how they can be used rather than simply discuss how they might be used to accelerate discovery.

  7. 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.

  8. 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

  9. Software for Simulation of Hyperspectral Images

    NASA Technical Reports Server (NTRS)

    Richtsmeier, Steven C.; Singer-Berk, Alexander; Bernstein, Lawrence S.

    2002-01-01

    A package of software generates simulated hyperspectral images for use in validating algorithms that generate estimates of Earth-surface spectral reflectance from hyperspectral images acquired by airborne and spaceborne instruments. This software is based on a direct simulation Monte Carlo approach for modeling three-dimensional atmospheric radiative transport as well as surfaces characterized by spatially inhomogeneous bidirectional reflectance distribution functions. In this approach, 'ground truth' is accurately known through input specification of surface and atmospheric properties, and it is practical to consider wide variations of these properties. The software can treat both land and ocean surfaces and the effects of finite clouds with surface shadowing. The spectral/spatial data cubes computed by use of this software can serve both as a substitute for and a supplement to field validation data.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. Workspaces that move people.

    PubMed

    Waber, Ben; Magnolfi, Jennifer; Lindsay, Greg

    2014-10-01

    Few companies measure whether the design of their workspaces helps or hurts performance, but they should. The authors have collected data that capture individuals' interactions, communications, and location information. They've learned that face-to-face interactions are by far the most important activity in an office; creating chance encounters between knowledge workers, both inside and outside the organization, improves performance. The Norwegian telecom company Telenor was ahead of its time in 2003, when it incorporated "hot desking" (no assigned seats) and spaces that could easily be reconfigured for different tasks and evolving teams. The CEO credits the design of the offices with helping Telenor shift from a state-run monopoly to a competitive multinational carrier with 150 million subscribers. In another example, data collected at one pharmaceuticals company showed that when a salesperson increased interactions with coworkers on other teams by 10%, his or her sales increased by 10%. To get the sales staff running into colleagues from other departments, management shifted from one coffee machine for every six employees to one for every 120 and created a new large cafeteria for everyone. Sales rose by 20%, or $200 million, afterjust one quarter, quickly justifying the capital investment in the redesign.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. False Color Terrain Model of Phoenix Workspace

    NASA Technical Reports Server (NTRS)

    2008-01-01

    This is a terrain model of Phoenix's Robotic Arm workspace. It has been color coded by depth with a lander model for context. The model has been derived using images from the depth perception feature from Phoenix's Surface Stereo Imager (SSI). Red indicates low-lying areas that appear to be troughs. Blue indicates higher areas that appear to be polygons.

    The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  1. Telescope image modelling software in STSDAS

    NASA Technical Reports Server (NTRS)

    Hodge, P. E.; Eisenhamer, J. D.; Shaw, R. A.; Williamson, R. L., II

    1992-01-01

    The Telescope Image Modelling (TIM) system creates model point spread functions for optical systems based on ray-trace information. The original TIM runs only on VAX/VMS systems, but we are modifying the software to run under IRAF in the STSDAS package in order to make TIM more widely available. The current status of this project will be discussed. Initially the changes will be restricted to the user interface and replacing VAX-specific code. Soon thereafter the IMSL and NAG subroutines will be replaced by public-domain software, and some of the algorithms may be improved.

  2. 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.

  3. Image analysis software and sample preparation demands

    NASA Astrophysics Data System (ADS)

    Roth, Karl n.; Wenzelides, Knut; Wolf, Guenter; Hufnagl, Peter

    1990-11-01

    Image analysis offers the opportunity to analyse many processes in medicine, biology and engeneering in a quantitative manner. Experience shows that it is only by awareness of preparation methods and attention to software design that full benefit can be reaped from a picture processing system in the fields of cytology and histology. Some examples of special stains for automated analysis are given here and the effectiveness of commercially available software packages is investigated. The application of picture processing and development of related special hardware and software has been increasing within the last years. As PC-based picture processing systems can be purchased at reasonable costs more and more users are confronted with these problems. Experience shows that the quality of commercially available software packages differ and the requirements on the sample preparation needed for successful problem solutions are often underestimated. But as always, sample preparation is still the key to success in automated image analysis for cells and tissues. Hence, a problem solution requires the permanent interaction between sample preparation methods and algorithm development.

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. Medical image database for software and algorithm evaluation

    NASA Astrophysics Data System (ADS)

    dos Santos, Marcelo; Furuie, Sergio S.

    2005-04-01

    This work presents the development of a framework to make available a free, online, multipurpose and multimodality medical image database for software and algorithm evaluation. We have implemented a distributed architecture for medical image database, including authoring, storage, and repository for documents and image processing software. The system aims to offer a complete test bed and a set of resources including software, link to scientific papers, gold standards, reference images and post-processed images, enabling medical image processing community (scientists, physicians, students and industrials) to be more aware of evaluation issues. Our focus of development was on convenience and easy of use of a generic system adaptable to different contexts.

  12. User questionnaire to evaluate the radiological workspace.

    PubMed

    van Ooijen, Peter M A; Koesoema, Allya P; Oudkerk, Matthijs

    2006-01-01

    Over the past few years, an increase in digitalization of radiology departments can be seen, which has a large impact on the work of the radiologists. This impact is not only demonstrated by the increased use of digital images but also by changing demands on the whole reading environment. In this study, we evaluated the satisfaction of our radiologists with our digital Picture Archival and Communication System environment and their workspace. This evaluation was performed by distribution of a questionnaire consisting of a score sheet and some open questions to all radiologists and residents. Out of 25 questionnaires, 12 were adequately answered and returned. Results clearly showed that most problems were present in the area of reading room design and layout and comfort and ergonomics. Based on the results from this study, adaptations were made and the results were also used in the planning of the redesign of the entire department of radiology.

  13. Workspaces in the Semantic Web

    NASA Technical Reports Server (NTRS)

    Wolfe, Shawn R.; Keller, RIchard M.

    2005-01-01

    Due to the recency and relatively limited adoption of Semantic Web technologies. practical issues related to technology scaling have received less attention than foundational issues. Nonetheless, these issues must be addressed if the Semantic Web is to realize its full potential. In particular, we concentrate on the lack of scoping methods that reduce the size of semantic information spaces so they are more efficient to work with and more relevant to an agent's needs. We provide some intuition to motivate the need for such reduced information spaces, called workspaces, give a formal definition, and suggest possible methods of deriving them.

  14. Deploying HEP applications using Xen and Globus Virtual Workspaces

    NASA Astrophysics Data System (ADS)

    Agarwal, A.; Desmarais, R.; Gable, I.; Grundy, D.; P-Brown, D.; Seuster, R.; Vanderster, D. C.; Charbonneau, A.; Enge, R.; Sobie, R.

    2008-07-01

    The deployment of HEP applications in heterogeneous grid environments can be challenging because many of the applications are dependent on specific OS versions and have a large number of complex software dependencies. Virtual machine monitors such as Xen could be used to package HEP applications, complete with their execution environments, to run on resources that do not meet their operating system requirements. Our previous work has shown HEP applications running within Xen suffer little or no performance penalty as a result of virtualization. However, a practical strategy is required for remotely deploying, booting, and controlling virtual machines on a remote cluster. One tool that promises to overcome the deployment hurdles using standard grid technology is the Globus Virtual Workspaces project. We describe strategies for the deployment of Xen virtual machines using Globus Virtual Workspace middleware that simplify the deployment of HEP applications.

  15. 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.

  16. Retina Image Screening and Analysis Software Version 2.0

    SciTech Connect

    Tobin, Jr., Kenneth W.; Karnowski, Thomas P.; Aykac, Deniz

    2009-04-01

    The software allows physicians or researchers to ground-truth images of retinas, identifying key physiological features and lesions that are indicative of disease. The software features methods to automatically detect the physiological features and lesions. The software contains code to measure the quality of images received from a telemedicine network; create and populate a database for a telemedicine network; review and report the diagnosis of a set of images; and also contains components to transmit images from a Zeiss camera to the network through SFTP.

  17. 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.

  18. 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.

  19. Workspace Program for Complex-Number Arithmetic

    NASA Technical Reports Server (NTRS)

    Patrick, M. C.; Howell, Leonard W., Jr.

    1986-01-01

    COMPLEX is workspace program designed to empower APL with complexnumber capabilities. Complex-variable methods provide analytical tools invaluable for applications in mathematics, science, and engineering. COMPLEX written in APL.

  20. Workspace Program for Complex-Number Arithmetic

    NASA Technical Reports Server (NTRS)

    Patrick, M. C.; Howell, Leonard W., Jr.

    1986-01-01

    COMPLEX is workspace program designed to empower APL with complexnumber capabilities. Complex-variable methods provide analytical tools invaluable for applications in mathematics, science, and engineering. COMPLEX written in APL.

  1. A Workspace-oriented Needle Guiding Robot for 3T MRI-guided Transperineal Prostate Intervention: Evaluation of In-bore Workspace and MRI Compatibility

    PubMed Central

    Song, Sang-Eun; Hata, Nobuhiko; Iordachita, Iulian; Fichtinger, Gabor; Tempany, Clare; Tokuda, Junichi

    2013-01-01

    Background Magnetic Resonance Imaging (MRI) guided prostate interventions have been introduced to enhance the cancer detection. For accurate needle positioning, in-bore operated robotic systems have been developed and optimal use of the confined in-bore space become a critical engineering challenge. Methods As preliminary evaluation of our prostate intervention robot, we conducted a workspace design analysis using a new evaluation method that we developed for in-bore operated robots for transperineal prostate interventions, and an MRI compatibility study. Results The workspace analysis resulted in the effective workspace (VW) of 0.32, which is greater than that of our early prototype despite that the current robot is approximately 50% larger than the early prototype in sectional space. The MRI compatibility study resulted in less than 15% signal-to-noise ratio (SNR) reduction. Conclusions The new workspace evaluation method quantifies the workspace utilization of the in-bore operated robots for MRI-guided transperineal prostate interventions, providing a useful tool for evaluation and new robot design. The robot creates insignificant electromagnetic noise during typical prostate imaging sequences. PMID:22492680

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. A Global Workspace perspective on mental disorders

    PubMed Central

    Wallace, Rodrick

    2005-01-01

    Background Recent developments in Global Workspace theory suggest that human consciousness can suffer interpenetrating dysfunctions of mutual and reciprocal interaction with embedding environments which will have early onset and often insidious staged developmental progression, possibly according to a cancer model, in which a set of long-evolved control strategies progressively fails. Methods and results A rate distortion argument implies that, if an external information source carries a damaging 'message', then sufficient exposure to it, particularly during critical developmental periods, is sure to write a sufficiently accurate image of it on mind and body in a punctuated manner so as to initiate or promote similarly progressively punctuated developmental disorder, in essence either a staged failure affecting large-scale brain connectivity, which is the sine qua non of human consciousness, or else damaging the ability of embedding goal contexts to contain conscious dynamics. Conclusion The key intervention, at the population level, is clearly to limit exposure to factors triggering developmental disorders, a question of proper environmental sanitation, in a large sense, primarily a matter of social justice which has long been known to be determined almost entirely by the interactions of cultural trajectory, group power relations, and economic structure, with public policy. Intervention at the individual level appears limited to triggering or extending periods of remission, representing reestablishment of an extensive, but largely unexplored, spectrum of evolved control strategies, in contrast with the far better-understood case of cancer. PMID:16371149

  10. A Global Workspace perspective on mental disorders.

    PubMed

    Wallace, Rodrick

    2005-12-21

    Recent developments in Global Workspace theory suggest that human consciousness can suffer interpenetrating dysfunctions of mutual and reciprocal interaction with embedding environments which will have early onset and often insidious staged developmental progression, possibly according to a cancer model, in which a set of long-evolved control strategies progressively fails. A rate distortion argument implies that, if an external information source carries a damaging 'message', then sufficient exposure to it, particularly during critical developmental periods, is sure to write a sufficiently accurate image of it on mind and body in a punctuated manner so as to initiate or promote similarly progressively punctuated developmental disorder, in essence either a staged failure affecting large-scale brain connectivity, which is the sine qua non of human consciousness, or else damaging the ability of embedding goal contexts to contain conscious dynamics. The key intervention, at the population level, is clearly to limit exposure to factors triggering developmental disorders, a question of proper environmental sanitation, in a large sense, primarily a matter of social justice which has long been known to be determined almost entirely by the interactions of cultural trajectory, group power relations, and economic structure, with public policy. Intervention at the individual level appears limited to triggering or extending periods of remission, representing reestablishment of an extensive, but largely unexplored, spectrum of evolved control strategies, in contrast with the far better-understood case of cancer.

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. MOPEX: a software package for astronomical image processing and visualization

    NASA Astrophysics Data System (ADS)

    Makovoz, David; Roby, Trey; Khan, Iffat; Booth, Hartley

    2006-06-01

    We present MOPEX - a software package for astronomical image processing and display. The package is a combination of command-line driven image processing software written in C/C++ with a Java-based GUI. The main image processing capabilities include creating mosaic images, image registration, background matching, point source extraction, as well as a number of minor image processing tasks. The combination of the image processing and display capabilities allows for much more intuitive and efficient way of performing image processing. The GUI allows for the control over the image processing and display to be closely intertwined. Parameter setting, validation, and specific processing options are entered by the user through a set of intuitive dialog boxes. Visualization feeds back into further processing by providing a prompt feedback of the processing results. The GUI also allows for further analysis by accessing and displaying data from existing image and catalog servers using a virtual observatory approach. Even though originally designed for the Spitzer Space Telescope mission, a lot of functionalities are of general usefulness and can be used for working with existing astronomical data and for new missions. The software used in the package has undergone intensive testing and benefited greatly from effective software reuse. The visualization part has been used for observation planning for both the Spitzer and Herschel Space Telescopes as part the tool Spot. The visualization capabilities of Spot have been enhanced and integrated with the image processing functionality of the command-line driven MOPEX. The image processing software is used in the Spitzer automated pipeline processing, which has been in operation for nearly 3 years. The image processing capabilities have also been tested in off-line processing by numerous astronomers at various institutions around the world. The package is multi-platform and includes automatic update capabilities. The software

  17. 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.

  18. 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.

  19. 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.

  20. Metamodels for Planar 3R Workspace Optimization.

    SciTech Connect

    Turner, C. J.

    2002-01-01

    Robotic workspace optimization is a central element of robot system design. To formulate the optimization problem, the complex relationships between design variables, tuning parameters, and performance indices need to be accurately and efficiently represented. The nature of the relationships suggests that metamodels, or models of the models, should be used to derive suitable objective functions. A comparison of two metamodeling techniques for robotic workspace optimization problems for several trial cases suggests that non-uniform rational B-spline models, derived from computer graphics and computer-aided design techniques, are as suitable as response surface models to solve planar 3R workspace optimization problems. Promising nonlinear modeling results with B-spline models suggest future work is justified and performance gains can be realized.

  1. 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.

  2. Analyzing huge pathology images with open source software

    PubMed Central

    2013-01-01

    Background Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer’s memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. Results We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Conclusions Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. Virtual slides The virtual slide(s) for this article can be found here: http

  3. Analyzing huge pathology images with open source software.

    PubMed

    Deroulers, Christophe; Ameisen, David; Badoual, Mathilde; Gerin, Chloé; Granier, Alexandre; Lartaud, Marc

    2013-06-06

    Digital pathology images are increasingly used both for diagnosis and research, because slide scanners are nowadays broadly available and because the quantitative study of these images yields new insights in systems biology. However, such virtual slides build up a technical challenge since the images occupy often several gigabytes and cannot be fully opened in a computer's memory. Moreover, there is no standard format. Therefore, most common open source tools such as ImageJ fail at treating them, and the others require expensive hardware while still being prohibitively slow. We have developed several cross-platform open source software tools to overcome these limitations. The NDPITools provide a way to transform microscopy images initially in the loosely supported NDPI format into one or several standard TIFF files, and to create mosaics (division of huge images into small ones, with or without overlap) in various TIFF and JPEG formats. They can be driven through ImageJ plugins. The LargeTIFFTools achieve similar functionality for huge TIFF images which do not fit into RAM. We test the performance of these tools on several digital slides and compare them, when applicable, to standard software. A statistical study of the cells in a tissue sample from an oligodendroglioma was performed on an average laptop computer to demonstrate the efficiency of the tools. Our open source software enables dealing with huge images with standard software on average computers. They are cross-platform, independent of proprietary libraries and very modular, allowing them to be used in other open source projects. They have excellent performance in terms of execution speed and RAM requirements. They open promising perspectives both to the clinician who wants to study a single slide and to the research team or data centre who do image analysis of many slides on a computer cluster. The virtual slide(s) for this article can be found here

  4. Software development for a Ring Imaging Detector

    NASA Astrophysics Data System (ADS)

    Torisky, Benjamin; Benmokhtar, Fatiha

    2015-04-01

    Jefferson Lab (Jlab) is performing a large-scale upgrade to their Continuous Electron Beam Accelerator Facility (CEBAF) up to 12 GeV 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 my work on the implementation of Java based reconstruction programs for the RICH in the CLAS12 main analysis package.

  5. 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.

  6. 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

  7. QA, QC and validation of imaging hardware and software

    SciTech Connect

    Weber, D.A.; Ivanovic, M.

    1988-01-01

    This paper addresses the development, testing, quality assurance (QA) and validation (V) of imaging hardware and software in nuclear medicine. QA, QC and V are discussed from the perspective of the nuclear medicine specialist, the regulator and the legal specialist. Complete testing programs and specific methods of QA, QC and V of nuclear medicine hardware and software are presented. NEMA standards for performance measurements of planar scintillation cameras and camera SPECT systems are reviewed; FDA policy on regulation of software used in medicine is discussed; legal aspects underlying the development of clinical software, and the practical value of copyright and patents are presented; and new, promising directions in hardware and software development are given. Since the primary focus of the meeting is QA, QC and V of gamma camera, single photon emission computed tomography (SPECT) and positron emission tomography (PET) systems and related imaging software, we introduce the presentations and proceedings with discussion of a few questions that are key to the use and understanding of these tests and measurements. 22 refs., 10 figs., 1 tab.

  8. 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.

  9. 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.

  10. SIMA: Python software for analysis of dynamic fluorescence imaging data.

    PubMed

    Kaifosh, Patrick; Zaremba, Jeffrey D; Danielson, Nathan B; Losonczy, Attila

    2014-01-01

    Fluorescence imaging is a powerful method for monitoring dynamic signals in the nervous system. However, analysis of dynamic fluorescence imaging data remains burdensome, in part due to the shortage of available software tools. To address this need, we have developed SIMA, an open source Python package that facilitates common analysis tasks related to fluorescence imaging. Functionality of this package includes correction of motion artifacts occurring during in vivo imaging with laser-scanning microscopy, segmentation of imaged fields into regions of interest (ROIs), and extraction of signals from the segmented ROIs. We have also developed a graphical user interface (GUI) for manual editing of the automatically segmented ROIs and automated registration of ROIs across multiple imaging datasets. This software has been designed with flexibility in mind to allow for future extension with different analysis methods and potential integration with other packages. Software, documentation, and source code for the SIMA package and ROI Buddy GUI are freely available at http://www.losonczylab.org/sima/.

  11. Predicting the image nonuniformities on IR devices: a dedicated software

    NASA Astrophysics Data System (ADS)

    Rollin, Joel

    1993-04-01

    This paper deals with illumination assessment for IR devices: a skill software has been developed to predict image non-uniformities, including Narcissus effect. Built upon real raytraces, special algorithms have been carried out to reduce the computation time and to increase the accuracy. Some tutorial examples are provided.

  12. The Role and Design of Screen Images in Software Documentation.

    ERIC Educational Resources Information Center

    van der Meij, Hans

    2000-01-01

    Discussion of learning a new computer software program focuses on how to support the joint handling of a manual, input devices, and screen display. Describes a study that examined three design styles for manuals that included screen images to reduce split-attention problems and discusses theory versus practice and cognitive load theory.…

  13. 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.

  14. Image analysis software versus direct anthropometry for breast measurements.

    PubMed

    Quieregatto, Paulo Rogério; Hochman, Bernardo; Furtado, Fabianne; Machado, Aline Fernanda Perez; Sabino Neto, Miguel; Ferreira, Lydia Masako

    2014-10-01

    To compare breast measurements performed using the software packages ImageTool(r), AutoCAD(r) and Adobe Photoshop(r) with direct anthropometric measurements. Points were marked on the breasts and arms of 40 volunteer women aged between 18 and 60 years. When connecting the points, seven linear segments and one angular measurement on each half of the body, and one medial segment common to both body halves were defined. The volunteers were photographed in a standardized manner. Photogrammetric measurements were performed by three independent observers using the three software packages and compared to direct anthropometric measurements made with calipers and a protractor. Measurements obtained with AutoCAD(r) were the most reproducible and those made with ImageTool(r) were the most similar to direct anthropometry, while measurements with Adobe Photoshop(r) showed the largest differences. Except for angular measurements, significant differences were found between measurements of line segments made using the three software packages and those obtained by direct anthropometry. AutoCAD(r) provided the highest precision and intermediate accuracy; ImageTool(r) had the highest accuracy and lowest precision; and Adobe Photoshop(r) showed intermediate precision and the worst accuracy among the three software packages.

  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. 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.

  17. 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.

  18. 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

  19. 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

  20. 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.

  1. NASA's MERBoard: An Interactive Collaborative Workspace Platform. Chapter 4

    NASA Technical Reports Server (NTRS)

    Trimble, Jay; Wales, Roxana; Gossweiler, Rich

    2003-01-01

    This chapter describes the ongoing process by which a multidisciplinary group at NASA's Ames Research Center is designing and implementing a large interactive work surface called the MERBoard Collaborative Workspace. A MERBoard system involves several distributed, large, touch-enabled, plasma display systems with custom MERBoard software. A centralized server and database back the system. We are continually tuning MERBoard to support over two hundred scientists and engineers during the surface operations of the Mars Exploration Rover Missions. These scientists and engineers come from various disciplines and are working both in small and large groups over a span of space and time. We describe the multidisciplinary, human-centered process by which this h4ERBoard system is being designed, the usage patterns and social interactions that we have observed, and issues we are currently facing.

  2. 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

  3. 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.

  4. 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.).

  5. 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.

  6. 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.

  7. Performance of Personal Workspace Controls Final Report

    SciTech Connect

    Rubinstein, Francis; Kiliccote, Sila; Loffeld, John; Pettler,Pete; Snook, Joel

    2004-12-01

    One of the key deliverables for the DOE-funded controls research at LBNL for FY04 was the development of a prototype Personal Workspace Control system. The successful development of this system is a critical milestone for the LBNL Lighting Controls Research effort because this system demonstrates how IBECS can add value to today's Task Ambient lighting systems. LBNL has argued that by providing both the occupant and the facilities manager with the ability to precisely control the operation of overhead lighting and all task lighting in a coordinated manner, that task ambient lighting can optimize energy performance and occupant comfort simultaneously [Reference Task Ambient Foundation Document]. The Personal Workspace Control system is the application of IBECS to this important lighting problem. This report discusses the development of the Personal Workspace Control to date including descriptions of the different fixture types that have been converted to IBECS operation and a detailed description of the operation of PWC Scene Controller, which provides the end user with precise control of his task ambient lighting system. The objective, from the Annual Plan, is to demonstrate improvements in efficiency, lighting quality and occupant comfort realized using Personal Workspace Controls (PWC) designed to optimize the delivery of lighting to the individual's workstation regardless of which task-ambient lighting solution is chosen. The PWC will be capable of controlling floor-mounted, desk lamps, furniture-mounted and overhead lighting fixtures from a personal computer and handheld remote. The PWC will use an environmental sensor to automatically monitor illuminance, temperature and occupancy and to appropriately modulate ambient lighting according to daylight availability and to switch off task lighting according to local occupancy. [Adding occupancy control to the system would blunt the historical criticism of occupant-controlled lighting - the tendency of the occupant

  8. 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

  9. 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.

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. Desing and Implementation of the Image Format Batch-Conversion Software Based on ImageJ

    NASA Astrophysics Data System (ADS)

    Xu, Jun; Chen, Dong

    2008-09-01

    The authors introduce ImageJ which is the open source and pure Java language image processing procedure and how to use ImageJ package for secondary development. Using the package, they have realized the format conversion from TIFF and SPE that acquised from WinView software to FITS. And based on this, put forward on the method how to use the package to achieve other format conversion as a separate or batch.

  15. 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.

  16. Comparison of quality control software tools for diffusion tensor imaging.

    PubMed

    Liu, Bilan; Zhu, Tong; Zhong, Jianhui

    2015-04-01

    Image quality of diffusion tensor imaging (DTI) is critical for image interpretation, diagnostic accuracy and efficiency. However, DTI is susceptible to numerous detrimental artifacts that may impair the reliability and validity of the obtained data. Although many quality control (QC) software tools are being developed and are widely used and each has its different tradeoffs, there is still no general agreement on an image quality control routine for DTIs, and the practical impact of these tradeoffs is not well studied. An objective comparison that identifies the pros and cons of each of the QC tools will be helpful for the users to make the best choice among tools for specific DTI applications. This study aims to quantitatively compare the effectiveness of three popular QC tools including DTI studio (Johns Hopkins University), DTIprep (University of North Carolina at Chapel Hill, University of Iowa and University of Utah) and TORTOISE (National Institute of Health). Both synthetic and in vivo human brain data were used to quantify adverse effects of major DTI artifacts to tensor calculation as well as the effectiveness of different QC tools in identifying and correcting these artifacts. The technical basis of each tool was discussed, and the ways in which particular techniques affect the output of each of the tools were analyzed. The different functions and I/O formats that three QC tools provide for building a general DTI processing pipeline and integration with other popular image processing tools were also discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

  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. 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.

  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. Automatic Image Registration Using Free and Open Source Software

    NASA Astrophysics Data System (ADS)

    Giri Babu, D.; Raja Shekhar, S. S.; Chandrasekar, K.; Sesha Sai, M. V. R.; Diwakar, P. G.; Dadhwal, V. K.

    2014-11-01

    Image registration is the most critical operation in remote sensing applications to enable location based referencing and analysis of earth features. This is the first step for any process involving identification, time series analysis or change detection using a large set of imagery over a region. Most of the reliable procedures involve time consuming and laborious manual methods of finding the corresponding matching features of the input image with respect to reference. Also the process, as it involves human interaction, does not converge with multiple operations at different times. Automated procedures rely on accurately determining the matching locations or points from both the images under comparison and the procedures are robust and consistent over time. Different algorithms are available to achieve this, based on pattern recognition, feature based detection, similarity techniques etc. In the present study and implementation, Correlation based methods have been used with a improvement over newly developed technique of identifying and pruning the false points of match. Free and Open Source Software (FOSS) have been used to develop the methodology to reach a wider audience, without any dependency on COTS (Commercially off the shelf) software. Standard deviation from foci of the ellipse of correlated points, is a statistical means of ensuring the best match of the points of interest based on both intensity values and location correspondence. The methodology is developed and standardised by enhancements to meet the registration requirements of remote sensing imagery. Results have shown a performance improvement, nearly matching the visual techniques and have been implemented in remote sensing operational projects. The main advantage of the proposed methodology is its viability in production mode environment. This paper also shows that the visualization capabilities of MapWinGIS, GDAL's image handling abilities and OSSIM's correlation facility can be efficiently

  1. Multi-institutional Validation Study of Commercially Available Deformable Image Registration Software for Thoracic Images.

    PubMed

    Kadoya, Noriyuki; Nakajima, Yujiro; Saito, Masahide; Miyabe, Yuki; Kurooka, Masahiko; Kito, Satoshi; Fujita, Yukio; Sasaki, Motoharu; Arai, Kazuhiro; Tani, Kensuke; Yagi, Masashi; Wakita, Akihisa; Tohyama, Naoki; Jingu, Keiichi

    2016-10-01

    To assess the accuracy of the commercially available deformable image registration (DIR) software for thoracic images at multiple institutions. Thoracic 4-dimensional (4D) CT images of 10 patients with esophageal or lung cancer were used. Datasets for these patients were provided by DIR-lab (dir-lab.com) and included a coordinate list of anatomic landmarks (300 bronchial bifurcations) that had been manually identified. Deformable image registration was performed between the peak-inhale and -exhale images. Deformable image registration error was determined by calculating the difference at each landmark point between the displacement calculated by DIR software and that calculated by the landmark. Eleven institutions participated in this study: 4 used RayStation (RaySearch Laboratories, Stockholm, Sweden), 5 used MIM Software (Cleveland, OH), and 3 used Velocity (Varian Medical Systems, Palo Alto, CA). The ranges of the average absolute registration errors over all cases were as follows: 0.48 to 1.51 mm (right-left), 0.53 to 2.86 mm (anterior-posterior), 0.85 to 4.46 mm (superior-inferior), and 1.26 to 6.20 mm (3-dimensional). For each DIR software package, the average 3-dimensional registration error (range) was as follows: RayStation, 3.28 mm (1.26-3.91 mm); MIM Software, 3.29 mm (2.17-3.61 mm); and Velocity, 5.01 mm (4.02-6.20 mm). These results demonstrate that there was moderate variation among institutions, although the DIR software was the same. We evaluated the commercially available DIR software using thoracic 4D-CT images from multiple centers. Our results demonstrated that DIR accuracy differed among institutions because it was dependent on both the DIR software and procedure. Our results could be helpful for establishing prospective clinical trials and for the widespread use of DIR software. In addition, for clinical care, we should try to find the optimal DIR procedure using thoracic 4D-CT data. Copyright © 2016 Elsevier Inc. All rights

  2. Quantification of video-taped images in microcirculation research using inexpensive imaging software (Adobe Photoshop).

    PubMed

    Brunner, J; Krummenauer, F; Lehr, H A

    2000-04-01

    Study end-points in microcirculation research are usually video-taped images rather than numeric computer print-outs. Analysis of these video-taped images for the quantification of microcirculatory parameters usually requires computer-based image analysis systems. Most software programs for image analysis are custom-made, expensive, and limited in their applicability to selected parameters and study end-points. We demonstrate herein that an inexpensive, commercially available computer software (Adobe Photoshop), run on a Macintosh G3 computer with inbuilt graphic capture board provides versatile, easy to use tools for the quantification of digitized video images. Using images obtained by intravital fluorescence microscopy from the pre- and postischemic muscle microcirculation in the skinfold chamber model in hamsters, Photoshop allows simple and rapid quantification (i) of microvessel diameters, (ii) of the functional capillary density and (iii) of postischemic leakage of FITC-labeled high molecular weight dextran from postcapillary venules. We present evidence of the technical accuracy of the software tools and of a high degree of interobserver reliability. Inexpensive commercially available imaging programs (i.e., Adobe Photoshop) provide versatile tools for image analysis with a wide range of potential applications in microcirculation research.

  3. 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

  4. Verification and Validation of a Fingerprint Image Registration Software

    NASA Astrophysics Data System (ADS)

    Desovski, Dejan; Gandikota, Vijai; Liu, Yan; Jiang, Yue; Cukic, Bojan

    2006-12-01

    The need for reliable identification and authentication is driving the increased use of biometric devices and systems. Verification and validation techniques applicable to these systems are rather immature and ad hoc, yet the consequences of the wide deployment of biometric systems could be significant. In this paper we discuss an approach towards validation and reliability estimation of a fingerprint registration software. Our validation approach includes the following three steps: (a) the validation of the source code with respect to the system requirements specification; (b) the validation of the optimization algorithm, which is in the core of the registration system; and (c) the automation of testing. Since the optimization algorithm is heuristic in nature, mathematical analysis and test results are used to estimate the reliability and perform failure analysis of the image registration module.

  5. Development of image-processing software for automatic segmentation of brain tumors in MR images

    PubMed Central

    Vijayakumar, C.; Gharpure, Damayanti Chandrashekhar

    2011-01-01

    Most of the commercially available software for brain tumor segmentation have limited functionality and frequently lack the careful validation that is required for clinical studies. We have developed an image-analysis software package called ‘Prometheus,’ which performs neural system–based segmentation operations on MR images using pre-trained information. The software also has the capability to improve its segmentation performance by using the training module of the neural system. The aim of this article is to present the design and modules of this software. The segmentation module of Prometheus can be used primarily for image analysis in MR images. Prometheus was validated against manual segmentation by a radiologist and its mean sensitivity and specificity was found to be 85.71±4.89% and 93.2±2.87%, respectively. Similarly, the mean segmentation accuracy and mean correspondence ratio was found to be 92.35±3.37% and 0.78±0.046, respectively. PMID:21897560

  6. 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

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

    PubMed

    Mawatari, Yuki; Fukushima, Mikiko

    2016-01-01

    This study aims to evaluate the efficacy of processed images to predict postoperative appearance following levator resection. 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. 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. 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.

  8. Reducing depth uncertainty in large surgical workspaces, with applications to veterinary medicine

    NASA Astrophysics Data System (ADS)

    Audette, Michel A.; Kolahi, Ahmad; Enquobahrie, Andinet; Gatti, Claudio; Cleary, Kevin

    2010-02-01

    This paper presents on-going research that addresses uncertainty along the Z-axis in image-guided surgery, for applications to large surgical workspaces, including those found in veterinary medicine. Veterinary medicine lags human medicine in using image guidance, despite MR and CT data scanning of animals. The positional uncertainty of a surgical tracking device can be modeled as an octahedron with one long axis coinciding with the depth axis of the sensor, where the short axes are determined by pixel resolution and workspace dimensions. The further a 3D point is from this device, the more elongated is this long axis, and the greater the uncertainty along Z of this point's position, in relation to its components along X and Y. Moreover, for a triangulation-based tracker, its position error degrades with the square of distance. Our approach is to use two or more Micron Trackers to communicate with each other, and combine this feature with flexible positioning. Prior knowledge of the type of surgical procedure, and if applicable, the species of animal that determines the scale of the workspace, would allow the surgeon to pre-operatively configure the trackers in the OR for optimal accuracy. Our research also leverages the open-source Image-guided Surgery Toolkit (IGSTK).

  9. Caretta: Integrating Personal and Shared Workspaces to Support Group Activities

    NASA Astrophysics Data System (ADS)

    Hosoi, Kazuhiro; Sugimoto, Masanori; Hashizume, Hiromichi

    In this paper, a system called Caretta that integrates personal and shared workspaces to support face-to-face collaboration is described. We use PDAs for individual users' personal workspaces that enable them to reflect on their own idea. A shared workspace has been implemented by using a multiple-input sensing board, which allows a group of users to simultaneously manipulate physical objects. In order to raise the level of awareness among users, we have used augmented reality technologies and created an immersive environment for the users' shared workspace. Users of Caretta can discuss and negotiate with each other in the shared workspace, while they individually examine their ideas in their own personal workspaces. Therefore, Caretta allows users to participate in group activities interchangeably and seamlessly by using both these workspaces. Caretta can be used for several types of group activities. In this paper, it is used for supporting a group of users in urban planning tasks by allowing the users to actually construct a town on the shared space and evaluate the town through computer simulations. User studies to evaluate Caretta were conducted. Usage logs of Caretta, video analyses, and comments from users proved that each user could utilize personal and shared space interchangeably at their own pace and without being hindered by other users.

  10. 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

  11. 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.

  12. 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)

  13. 50. APPRENTICE WORKSPACE, SECOND FLOOR, SOUTH END OF EAST WING. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    50. APPRENTICE WORKSPACE, SECOND FLOOR, SOUTH END OF EAST WING. NOTE PRODUCTION MOLD STORAGE IN RIGHT BACKGROUND. - Moravian Pottery & Tile Works, Southwest side of State Route 313 (Swamp Road), Northwest of East Court Street, Doylestown, Bucks County, PA

  14. A simple method of image analysis to estimate CAM vascularization by APERIO ImageScope software.

    PubMed

    Marinaccio, Christian; Ribatti, Domenico

    2015-01-01

    The chick chorioallantoic membrane (CAM) assay is a well-established method to test the angiogenic stimulation or inhibition induced by molecules and cells administered onto the CAM. The quantification of blood vessels in the CAM assay relies on a semi-manual image analysis approach which can be time consuming when considering large experimental groups. Therefore we present here a simple and fast volumetric method to inspect differences in vascularization between experimental conditions related to the stimulation and inhibition of CAM angiogenesis based on the Positive Pixel Count algorithm embedded in the APERIO ImageScope software.

  15. 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).

  16. 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

  17. 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

  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. How to Frame Universal Workspace Lighting.

    PubMed

    Mathiasen, Nanet; Frandsen, Anne Kathrine

    2016-01-01

    In 2012 the headquarters for the umbrella organisation 'Disabled people's organisation Denmark' opened, an office building that offers workspace for the administrations of all the member organisations. The ambition for the building was to be the most accessible office building in the world; regardless of disability everybody should be able to move around in the house and work in any of the offices. One, of many ambitions, was to design a functional and effective lighting scheme using as much daylight as possible, and integrating the artificial lighting design and daylight design. The lighting was intended to support all work stations in both one-man offices and open-plan offices with a functional and comfortable visual environment, fit for all users, regardless of disability. Based on a post occupancy evaluation conducted 2 years after the organisations moved in, the present paper evaluates the lighting design in the offices. It reveals that not all the people working in the offices have the same needs and preferences of lighting conditions; these differ even among users with the same disability. Accordingly the findings lead to a discussion on how to understand the concept of Universal Design. Based on the lighting theory of Peter Boyce, the paper discusses the idea of encompassing everyone in the same solution.

  20. Crossing boundaries in a collaborative modeling workspace

    USGS Publications Warehouse

    Morisette, Jeffrey T.; Cravens, Amanda; Miller, Brian; Talbert, Marian; Talbert, Colin; Jarnevich, Catherine S.; Fink, Michelle; Decker, Karin; Odell, Eric

    2017-01-01

    There is substantial literature on the importance of bridging across disciplinary and science–management boundaries. One of the ways commonly suggested to cross boundaries is for participants from both sides of the boundary to jointly produce information (i.e., knowledge co-production). But simply providing tools or bringing people together in the same room is not sufficient. Here we present a case study documenting the mechanisms by which managers and scientists collaborated to incorporate climate change projections into Colorado’s State Wildlife Action Plan. A critical component of the project was the use of a collaborative modeling and visualization workspace: the U.S. Geological Survey’s Resource for Advanced Modeling (RAM). Using video analysis and pre/post surveys from this case study, we examine how the RAM facilitated cognitive and social processes that co-produced a more salient and credible end product. This case provides practical suggestions to scientists and practitioners who want to implement actionable science.

  1. Free and open-source software application for the evaluation of coronary computed tomography angiography images.

    PubMed

    Hadlich, Marcelo Souza; Oliveira, Gláucia Maria Moraes; Feijóo, Raúl A; Azevedo, Clerio F; Tura, Bernardo Rangel; Ziemer, Paulo Gustavo Portela; Blanco, Pablo Javier; Pina, Gustavo; Meira, Márcio; Souza e Silva, Nelson Albuquerque de

    2012-10-01

    The standardization of images used in Medicine in 1993 was performed using the DICOM (Digital Imaging and Communications in Medicine) standard. Several tests use this standard and it is increasingly necessary to design software applications capable of handling this type of image; however, these software applications are not usually free and open-source, and this fact hinders their adjustment to most diverse interests. To develop and validate a free and open-source software application capable of handling DICOM coronary computed tomography angiography images. We developed and tested the ImageLab software in the evaluation of 100 tests randomly selected from a database. We carried out 600 tests divided between two observers using ImageLab and another software sold with Philips Brilliance computed tomography appliances in the evaluation of coronary lesions and plaques around the left main coronary artery (LMCA) and the anterior descending artery (ADA). To evaluate intraobserver, interobserver and intersoftware agreements, we used simple and kappa statistics agreements. The agreements observed between software applications were generally classified as substantial or almost perfect in most comparisons. The ImageLab software agreed with the Philips software in the evaluation of coronary computed tomography angiography tests, especially in patients without lesions, with lesions < 50% in the LMCA and < 70% in the ADA. The agreement for lesions > 70% in the ADA was lower, but this is also observed when the anatomical reference standard is used.

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. Planning maximally smooth hand movements constrained to nonplanar workspaces.

    PubMed

    Liebermann, Dario G; Krasovsky, Tal; Berman, Sigal

    2008-11-01

    The article characterizes hand paths and speed profiles for movements performed in a nonplanar, 2-dimensional workspace (a hemisphere of constant curvature). The authors assessed endpoint kinematics (i.e., paths and speeds) under the minimum-jerk model assumptions and calculated minimal amplitude paths (geodesics) and the corresponding speed profiles. The authors also calculated hand speeds using the 2/3 power law. They then compared modeled results with the empirical observations. In all, 10 participants moved their hands forward and backward from a common starting position toward 3 targets located within a hemispheric workspace of small or large curvature. Comparisons of modeled observed differences using 2-way RM-ANOVAs showed that movement direction had no clear influence on hand kinetics (p < .05). Workspace curvature affected the hand paths, which seldom followed geodesic lines. Constraining the paths to different curvatures did not affect the hand speed profiles. Minimum-jerk speed profiles closely matched the observations and were superior to those predicted by 2/3 power law (p < .001). The authors conclude that speed and path cannot be unambiguously linked under the minimum-jerk assumption when individuals move the hand in a nonplanar 2-dimensional workspace. In such a case, the hands do not follow geodesic paths, but they preserve the speed profile, regardless of the geometric features of the workspace.

  7. An instructional guide for leaf color analysis using digital imaging software

    Treesearch

    Paula F. Murakami; Michelle R. Turner; Abby K. van den Berg; Paul G. Schaberg

    2005-01-01

    Digital color analysis has become an increasingly popular and cost-effective method utilized by resource managers and scientists for evaluating foliar nutrition and health in response to environmental stresses. We developed and tested a new method of digital image analysis that uses Scion Image or NIH image public domain software to quantify leaf color. This...

  8. 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.

  9. [Development of automatic navigation measuring system using template-matching software in image guided neurosurgery].

    PubMed

    Watanabe, Yohei; Hayashi, Yuichiro; Fujii, Masazumi; Kimura, Miyuki; Sugiura, Akihiro; Tsuzaka, Masatoshi; Wakabayashi, Toshihiko

    2010-02-20

    An image-guided neurosurgery and neuronavigation system based on magnetic resonance imaging has been used as an indispensable tool for resection of brain tumors. Therefore, accuracy of the neuronavigation system, provided by periodic quality assurance (QA), is essential for image-guided neurosurgery. Two types of accuracy index, fiducial registration error (FRE) and target registration error (TRE), have been used to evaluate navigation accuracy. FRE shows navigation accuracy on points that have been registered. On the other hand, TRE shows navigation accuracy on points such as tumor, skin, and fiducial markers. This study shows that TRE is more reliable than FRE. However, calculation of TRE is a time-consuming, subjective task. Software for QA was developed to compute TRE. This software calculates TRE automatically by an image processing technique, such as automatic template matching. TRE was calculated by the software and compared with the results obtained by manual calculation. Using the software made it possible to achieve a reliable QA system.

  10. 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.

  11. Intra-operative image update: first experiences with new software in computer-assisted sinus surgery.

    PubMed

    Wurm, Jochen; Bohr, Christopher; Iro, Heinrich; Bumm, Klaus

    2008-09-01

    So far, conventional navigation systems do not provide the opportunity for any modification of acquired image datasets. In particular, the surgical progress in the operating field cannot be visualized unless new imaging scans are performed. In a feasibility study, new software creating intra-operative image updates by virtual means was tested in conjunction with conventional navigation. With this new software, surgically removed tissue volumes can be traced and viewed directly within the diagnostic image data. The new software represents an interesting and helpful amendment to conventional computer-assisted surgery in selected cases. During surgical procedures around bony structures, the surgeon gets an accurate virtual image update of the surgical progress in the operating field and the amount of tissue removed. However, in cases where mobile structures are present or soft tissue shifts are expected, this feature seems to be suitable only to a limited extent.

  12. 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.

  13. Digital radiography: optimization of image quality and dose using multi-frequency software.

    PubMed

    Precht, H; Gerke, O; Rosendahl, K; Tingberg, A; Waaler, D

    2012-09-01

    New developments in processing of digital radiographs (DR), including multi-frequency processing (MFP), allow optimization of image quality and radiation dose. This is particularly promising in children as they are believed to be more sensitive to ionizing radiation than adults. To examine whether the use of MFP software reduces the radiation dose without compromising quality at DR of the femur in 5-year-old-equivalent anthropomorphic and technical phantoms. A total of 110 images of an anthropomorphic phantom were imaged on a DR system (Canon DR with CXDI-50 C detector and MLT[S] software) and analyzed by three pediatric radiologists using Visual Grading Analysis. In addition, 3,500 images taken of a technical contrast-detail phantom (CDRAD 2.0) provide an objective image-quality assessment. Optimal image-quality was maintained at a dose reduction of 61% with MLT(S) optimized images. Even for images of diagnostic quality, MLT(S) provided a dose reduction of 88% as compared to the reference image. Software impact on image quality was found significant for dose (mAs), dynamic range dark region and frequency band. By optimizing image processing parameters, a significant dose reduction is possible without significant loss of image quality.

  14. Detection of patient setup errors with a portal image - DRR registration software application.

    PubMed

    Sutherland, Kenneth; Ishikawa, Masayori; Bengua, Gerard; Ito, Yoichi M; Miyamoto, Yoshiko; Shirato, Hiroki

    2011-02-18

    The purpose of this study was to evaluate a custom portal image - digitally reconstructed radiograph (DRR) registration software application. The software works by transforming the portal image into the coordinate space of the DRR image using three control points placed on each image by the user, and displaying the fused image. In order to test statistically that the software actually improves setup error estimation, an intra- and interobserver phantom study was performed. Portal images of anthropomorphic thoracic and pelvis phantoms with virtually placed irradiation fields at known setup errors were prepared. A group of five doctors was first asked to estimate the setup errors by examining the portal and DRR image side-by-side, not using the software. A second group of four technicians then estimated the same set of images using the registration software. These two groups of human subjects were then compared with an auto-registration feature of the software, which is based on the mutual information between the portal and DRR images. For the thoracic case, the average distance between the actual setup error and the estimated error was 4.3 ± 3.0 mm for doctors using the side-by-side method, 2.1 ± 2.4 mm for technicians using the registration method, and 0.8 ± 0.4mm for the automatic algorithm. For the pelvis case, the average distance between the actual setup error and estimated error was 2.0 ± 0.5 mm for the doctors using the side-by-side method, 2.5 ± 0.4 mm for technicians using the registration method, and 2.0 ± 1.0 mm for the automatic algorithm. The ability of humans to estimate offset values improved statistically using our software for the chest phantom that we tested. Setup error estimation was further improved using our automatic error estimation algorithm. Estimations were not statistically different for the pelvis case. Consistency improved using the software for both the chest and pelvis phantoms. We also tested the automatic algorithm with a

  15. 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.

  16. 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.

  17. Software for Analyzing Sequences of Flow-Related Images

    NASA Technical Reports Server (NTRS)

    Klimek, Robert; Wright, Ted

    2004-01-01

    Spotlight is a computer program for analysis of sequences of images generated in combustion and fluid physics experiments. Spotlight can perform analysis of a single image in an interactive mode or a sequence of images in an automated fashion. The primary type of analysis is tracking of positions of objects over sequences of frames. Features and objects that are typically tracked include flame fronts, particles, droplets, and fluid interfaces. Spotlight automates the analysis of object parameters, such as centroid position, velocity, acceleration, size, shape, intensity, and color. Images can be processed to enhance them before statistical and measurement operations are performed. An unlimited number of objects can be analyzed simultaneously. Spotlight saves results of analyses in a text file that can be exported to other programs for graphing or further analysis. Spotlight is a graphical-user-interface-based program that at present can be executed on Microsoft Windows and Linux operating systems. A version that runs on Macintosh computers is being considered.

  18. Accuracy of 3D Imaging Software in Cephalometric Analysis

    DTIC Science & Technology

    2013-06-21

    of a small region. The two most common types are periapical and bitewing radiographs. Periapical radiographs obtain an image of the entire tooth ...ability to image craniofacial anatomy in three dimensions. For orthodontists, this means improved visualization of tooth position, skeletal features...sufficient to localize the tooth to one side of the alveolus or the other using the “same lingual, opposite buccal” (SLOB) rule (Maverna & Gracco

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-09-01

    Introduction - Beginning of JUPOS in 1989, H.J. Mettig and Grischa Hahn in Dresden - 350.000 positional measures on electronic images of almost 180 observers have been gathered since 1998 - What do we mean by "electronic images": o digitized hi-res chemical photographs o traditional CCD technique o webcam images - 2002 started the implementation of WinJUPOS by Grischa, now finished - Cooperation with the Jupiter Section of the BAA for many years - At present, JUPOS has four active measurers: o Gianluigi Adamoli and Marco Vedovato (Italy) o H.J. Mettig (Germany) o Michel Jacquesson (France) How we work together - Each member of the team measures images of several observers (useful to detect and avoid systematic errors) - When necessary, exchange of problems and ideas by e-mail - During the period of visibility of Jupiter, team leader H.J. Mettig: o collects all recent measurements about once a month o produces drift charts - Once a year or two, the JUPOS team helds an informal meeting Criteria for image selection 1) Validity of time and date: Origins of time errors: 1. local zonal times are wrongly (or, not at all) converted to UT. This is still easy to find out: Either "only" the full hour is erroneous, or/and the date (problem of observers with UTC+10) 2. the computer clock has not been synchronised over a longer period 3. exposure of the final image exceeds the recommended two minutes or observers communicate begin or end of the total period of image recording instead of its middle How to test the validity of the time? - Position of a galilean satellite visible on or near Jupiter - Position of a satellite shadow - Measuring the longitude of permanent or long lived objects whose positions are known from former measurements 2) Avoid measuring the same object on different images taken at about the same time. One image every 1 ½ hours is sufficient 3) Duration of exposure: not more than 2-3 minutes because of the rapid rotation of Jupiter 4) Spectral range: Visual

  5. 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...

  6. 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.

  7. 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.

  8. 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.

  9. A software agent model of consciousness.

    PubMed

    Franklin, S; Graesser, A

    1999-09-01

    Baars (1988, 1997) has proposed a psychological theory of consciousness, called global workspace theory. The present study describes a software agent implementation of that theory, called "Conscious" Mattie (CMattie). CMattie operates in a clerical domain from within a UNIX operating system, sending messages and interpreting messages in natural language that organize seminars at a university. CMattie fleshes out global workspace theory with a detailed computational model that integrates contemporary architectures in cognitive science and artificial intelligence. Baars (1997) lists the psychological "facts that any complete theory of consciousness must explain" in his appendix to In the Theater of Consciousness; global workspace theory was designed to explain these "facts." The present article discusses how the design of CMattie accounts for these facts and thereby the extent to which it implements global workspace theory. Copyright 1999 Academic Press.

  10. PyElph - a software tool for gel images analysis and phylogenetics.

    PubMed

    Pavel, Ana Brânduşa; Vasile, Cristian Ioan

    2012-01-13

    This paper presents PyElph, a software tool which automatically extracts data from gel images, computes the molecular weights of the analyzed molecules or fragments, compares DNA patterns which result from experiments with molecular genetic markers and, also, generates phylogenetic trees computed by five clustering methods, using the information extracted from the analyzed gel image. The software can be successfully used for population genetics, phylogenetics, taxonomic studies and other applications which require gel image analysis. Researchers and students working in molecular biology and genetics would benefit greatly from the proposed software because it is free, open source, easy to use, has a friendly Graphical User Interface and does not depend on specific image acquisition devices like other commercial programs with similar functionalities do. PyElph software tool is entirely implemented in Python which is a very popular programming language among the bioinformatics community. It provides a very friendly Graphical User Interface which was designed in six steps that gradually lead to the results. The user is guided through the following steps: image loading and preparation, lane detection, band detection, molecular weights computation based on a molecular weight marker, band matching and finally, the computation and visualization of phylogenetic trees. A strong point of the software is the visualization component for the processed data. The Graphical User Interface provides operations for image manipulation and highlights lanes, bands and band matching in the analyzed gel image. All the data and images generated in each step can be saved. The software has been tested on several DNA patterns obtained from experiments with different genetic markers. Examples of genetic markers which can be analyzed using PyElph are RFLP (Restriction Fragment Length Polymorphism), AFLP (Amplified Fragment Length Polymorphism), RAPD (Random Amplification of Polymorphic DNA) and

  11. 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.

  12. 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.

  13. Topographic analysis of eyelid position using digital image processing software.

    PubMed

    Chun, Yeoun Sook; Park, Hong Hyun; Park, In Ki; Moon, Nam Ju; Park, Sang Joon; Lee, Jeong Kyu

    2017-04-09

    To propose a novel analysis technique for objective quantification of topographic eyelid position with an algorithmatically calculated scheme and to determine its feasibility. One hundred normal eyelids from 100 patients were segmented using a graph cut algorithm, and 11 shape features of eyelids were semi-automatically quantified using in-house software. To evaluate the intra- and inter-examiner reliability of this software, intra-class correlation coefficients (ICCs) were used. To evaluate the diagnostic value of this scheme, the correlations between semi-automatic and manual measurements of margin reflex distance 1 (MRD1) and margin reflex distance 2 (MRD2) were analysed using a Bland-Altman analysis. To determine the degree of agreement according to manual MRD length, the relationship between the variance of semi-automatic measurements and the manual measurements was evaluated using linear regression. Intra- and inter-examiner reliability were excellent, with ICCs ranging from 0.913 to 0.980 in 11 shape features including MRD1, MRD2, palpebral fissure, lid perimeter, upper and lower lid lengths, roundness, total area, and medial, central, and lateral areas. The correlations between semi-automatic and manual MRDs were also excellent, with better correlation in MRD1 than in MRD2 (R = 0.893 and 0.823, respectively). In addition, significant positive relationships were observed between the variance and the length of MRD1 and 2; the longer the MRD length, the more the variance. The proposed novel optimized integrative scheme, which is shown to have high repeatability and reproducibility, is useful for topographic analysis of eyelid position. © 2017 Acta Ophthalmologica Scandinavica Foundation. Published by John Wiley & Sons Ltd.

  14. Software for browsing sectioned images of a dog body and generating a 3D model.

    PubMed

    Park, Jin Seo; Jung, Yong Wook

    2016-01-01

    The goals of this study were (1) to provide accessible and instructive browsing software for sectioned images and a portable document format (PDF) file that includes three-dimensional (3D) models of an entire dog body and (2) to develop techniques for segmentation and 3D modeling that would enable an investigator to perform these tasks without the aid of a computer engineer. To achieve these goals, relatively important or large structures in the sectioned images were outlined to generate segmented images. The sectioned and segmented images were then packaged into browsing software. In this software, structures in the sectioned images are shown in detail and in real color. After 3D models were made from the segmented images, the 3D models were exported into a PDF file. In this format, the 3D models could be manipulated freely. The browsing software and PDF file are available for study by students, for lecture for teachers, and for training for clinicians. These files will be helpful for anatomical study by and clinical training of veterinary students and clinicians. Furthermore, these techniques will be useful for researchers who study two-dimensional images and 3D models.

  15. A role for the anterior insular cortex in the global neuronal workspace model of consciousness.

    PubMed

    Michel, Matthias

    2017-03-01

    According to the global neuronal workspace model of consciousness, consciousness results from the global broadcast of information throughout the brain. The global neuronal workspace is mainly constituted by a fronto-parietal network. The anterior insular cortex is part of this global neuronal workspace, but the function of this region has not yet been defined within the global neuronal workspace model of consciousness. In this review, I hypothesize that the anterior insular cortex implements a cross-modal priority map, the function of which is to determine priorities for the processing of information and subsequent entrance in the global neuronal workspace.

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

    PubMed

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

    2015-06-01

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

  17. 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.

  18. 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.

  19. Software Toolbox for Low-frequency Conductivity and Current Density Imaging using MRI.

    PubMed

    Sajib, Saurav Z K; Katoch, Nitish; Kim, Hyung Joong; Kwon, Oh In; Woo, Eung Je

    2017-07-27

    Low-frequency conductivity and current density imaging using MRI includes magnetic resonance electrical impedance tomography (MREIT), diffusion tensor MREIT (DT-MREIT), conductivity tensor imaging (CTI), and magnetic resonance current density imaging (MRCDI). MRCDI and MREIT provide current density and isotropic conductivity images, respectively, using current-injection phase MRI techniques. DT-MREIT produces anisotropic conductivity tensor images by incorporating diffusion weighted MRI into MREIT. These current-injection techniques are finding clinical applications in diagnostic imaging and also in tDCS, DBS, and electroporation where treatment currents can function as imaging currents. To avoid adverse effects of nerve and muscle stimulations due to injected currents, conductivity tensor imaging (CTI) utilizes B1 mapping and multi-b diffusion weighted MRI to produce low-frequency anisotropic conductivity tensor images without injecting current. This paper describes numerical implementations of several key mathematical functions for conductivity and current density image reconstructions in MRCDI, MREIT, DT-MREIT, and CTI. To facilitate experimental studies of clinical applications, we developed a software toolbox for these low-frequency conductivity and current density imaging methods. This MR-based conductivity imaging (MRCI) toolbox includes 11 toolbox functions which can be used in the Matlab environment. The MRCI toolbox is available at http://iirc.khu.ac.kr/software.html. Its functions were tested by using several experimental data sets which are provided together with the toolbox. Users of the toolbox can focus on experimental designs and interpretations of reconstructed images instead of developing their own image reconstruction softwares. We expect more toolbox functions to be added from future research outcomes.

  20. 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.

  1. JMorph: Software for performing rapid morphometric measurements on digital images of fossil assemblages

    NASA Astrophysics Data System (ADS)

    Lelièvre, Peter G.; Grey, Melissa

    2017-08-01

    Quantitative morphometric analyses of form are widely used in palaeontology, especially for taxonomic and evolutionary research. These analyses can involve several measurements performed on hundreds or even thousands of samples. Performing measurements of size and shape on large assemblages of macro- or microfossil samples is generally infeasible or impossible with traditional instruments such as vernier calipers. Instead, digital image processing software is required to perform measurements via suitable digital images of samples. Many software packages exist for morphometric analyses but there is not much available for the integral stage of data collection, particularly for the measurement of the outlines of samples. Some software exists to automatically detect the outline of a fossil sample from a digital image. However, automatic outline detection methods may perform inadequately when samples have incomplete outlines or images contain poor contrast between the sample and staging background. Hence, a manual digitization approach may be the only option. We are not aware of any software packages that are designed specifically for efficient digital measurement of fossil assemblages with numerous samples, especially for the purposes of manual outline analysis. Throughout several previous studies, we have developed a new software tool, JMorph, that is custom-built for that task. JMorph provides the means to perform many different types of measurements, which we describe in this manuscript. We focus on JMorph's ability to rapidly and accurately digitize the outlines of fossils. JMorph is freely available from the authors.

  2. Image processing software for providing radiometric inputs to land surface climatology models

    NASA Technical Reports Server (NTRS)

    Newcomer, Jeffrey A.; Goetz, Scott J.; Strebel, Donald E.; Hall, Forrest G.

    1989-01-01

    During the First International Land Surface Climatology Project (ISLSCP) Field Experiment (FIFE), 80 gigabytes of image data were generated from a variety of satellite and airborne sensors in a multidisciplinary attempt to study energy and mass exchange between the land surface and the atmosphere. To make these data readily available to researchers with a range of image data handling experience and capabilities, unique image-processing software was designed to perform a variety of nonstandard image-processing manipulations and to derive a set of standard-format image products. The nonconventional features of the software include: (1) adding new layers of geographic coordinates, and solar and viewing conditions to existing data; (2) providing image polygon extraction and calibration of data to at-sensor radiances; and, (3) generating standard-format derived image products that can be easily incorporated into radiometric or climatology models. The derived image products consist of easily handled ASCII descriptor files, byte image data files, and additional per-pixel integer data files (e.g., geographic coordinates, and sun and viewing conditions). Details of the solutions to the image-processing problems, the conventions adopted for handling a variety of satellite and aircraft image data, and the applicability of the output products to quantitative modeling are presented. They should be of general interest to future experiment and data-handling design considerations.

  3. 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.

  4. Enhancement of the Shared Graphics Workspace.

    DTIC Science & Technology

    1986-05-01

    RESPONSIBLE INDIVIDUAL 22b. TELEPHONE (Include Area Code) 22c OFFICE SYMBOL Ginger Winn (202) 694-5919 DARPA DO FORM 1473, 84 MAR 83 APR edition may...photograph and the image is less sharp. Text images appear on the SGWS red -green-blue (RGB) monitor in black on amber, with a resolution of 1,024 x 512 pixels...boards no longer send extra characters when an operator presses a button for longer than usual. The system confused the operator by showing all options

  5. 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.

  6. An image-processing software package: UU and Fig for optical metrology applications

    NASA Astrophysics Data System (ADS)

    Chen, Lujie

    2013-06-01

    Modern optical metrology applications are largely supported by computational methods, such as phase shifting [1], Fourier Transform [2], digital image correlation [3], camera calibration [4], etc, in which image processing is a critical and indispensable component. While it is not too difficult to obtain a wide variety of image-processing programs from the internet; few are catered for the relatively special area of optical metrology. This paper introduces an image-processing software package: UU (data processing) and Fig (data rendering) that incorporates many useful functions to process optical metrological data. The cross-platform programs UU and Fig are developed based on wxWidgets. At the time of writing, it has been tested on Windows, Linux and Mac OS. The userinterface is designed to offer precise control of the underline processing procedures in a scientific manner. The data input/output mechanism is designed to accommodate diverse file formats and to facilitate the interaction with other independent programs. In terms of robustness, although the software was initially developed for personal use, it is comparably stable and accurate to most of the commercial software of similar nature. In addition to functions for optical metrology, the software package has a rich collection of useful tools in the following areas: real-time image streaming from USB and GigE cameras, computational geometry, computer vision, fitting of data, 3D image processing, vector image processing, precision device control (rotary stage, PZT stage, etc), point cloud to surface reconstruction, volume rendering, batch processing, etc. The software package is currently used in a number of universities for teaching and research.

  7. 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.

  8. 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.

  9. Open source software in a practical approach for post processing of radiologic images.

    PubMed

    Valeri, Gianluca; Mazza, Francesco Antonino; Maggi, Stefania; Aramini, Daniele; La Riccia, Luigi; Mazzoni, Giovanni; Giovagnoni, Andrea

    2015-03-01

    The purpose of this paper is to evaluate the use of open source software (OSS) to process DICOM images. We selected 23 programs for Windows and 20 programs for Mac from 150 possible OSS programs including DICOM viewers and various tools (converters, DICOM header editors, etc.). The programs selected all meet the basic requirements such as free availability, stand-alone application, presence of graphical user interface, ease of installation and advanced features beyond simple display monitor. Capabilities of data import, data export, metadata, 2D viewer, 3D viewer, support platform and usability of each selected program were evaluated on a scale ranging from 1 to 10 points. Twelve programs received a score higher than or equal to eight. Among them, five obtained a score of 9: 3D Slicer, MedINRIA, MITK 3M3, VolView, VR Render; while OsiriX received 10. OsiriX appears to be the only program able to perform all the operations taken into consideration, similar to a workstation equipped with proprietary software, allowing the analysis and interpretation of images in a simple and intuitive way. OsiriX is a DICOM PACS workstation for medical imaging and software for image processing for medical research, functional imaging, 3D imaging, confocal microscopy and molecular imaging. This application is also a good tool for teaching activities because it facilitates the attainment of learning objectives among students and other specialists.

  10. A Software Framework for the Analysis of Complex Microscopy Image Data

    PubMed Central

    Chao, Jerry; Ward, E. Sally

    2012-01-01

    Technological advances in both hardware and software have made possible the realization of sophisticated biological imaging experiments using the optical microscope. As a result, modern microscopy experiments are capable of producing complex image data sets. For a given data analysis task, the images in a set are arranged, based on the requirements of the task, by attributes such as the time and focus levels at which they were acquired. Importantly, different tasks performed over the course of an analysis are often facilitated by the use of different arrangements of the images. We present a software framework which supports the use of different logical image arrangements to analyze a physical set of images. Called the Microscopy Image Analysis Tool (MIATool), this framework realizes the logical arrangements using arrays of pointers to the images, thereby removing the need to replicate and manipulate the actual images in their storage medium. In order that they may be tailored to the specific requirements of disparate analysis tasks, these logical arrangements may differ in size and dimensionality, with no restrictions placed on the number of dimensions and the meaning of each dimension. MIATool additionally supports processing flexibility, extensible image processing capabilities, and data storage management. PMID:20423810

  11. Effect of software manipulation (Photoshop) of digitised retinal images on the grading of diabetic retinopathy

    PubMed Central

    George, L; Lusty, J; Owens, D; Ollerton, R

    1999-01-01

    AIMS—To determine whether software processing of digitised retinal images using a "sharpen" filter improves the ability to grade diabetic retinopathy.
METHODS—150 macula centred retinal images were taken as 35 mm colour transparencies representing a spectrum of diabetic retinopathy, digitised, and graded in random order before and after the application of a sharpen filter (Adobe Photoshop). Digital enhancement of contrast and brightness was performed and a X2 digital zoom was utilised. The grades from the unenhanced and enhanced digitised images were compared with the same retinal fields viewed as slides.
RESULTS—Overall agreement in retinopathy grade from the digitised images improved from 83.3% (125/150) to 94.0% (141/150) with sight threatening diabetic retinopathy (STDR) correctly identified in 95.5% (84/88) and 98.9% (87/88) of cases when using unenhanced and enhanced images respectively. In total, five images were overgraded and four undergraded from the enhanced images compared with 17 and eight images respectively when using unenhanced images.
CONCLUSION—This study demonstrates that the already good agreement in grading performance can be further improved by software manipulation or processing of digitised retinal images.

 PMID:10413691

  12. Effect of software manipulation (Photoshop) of digitised retinal images on the grading of diabetic retinopathy.

    PubMed

    George, L D; Lusty, J; Owens, D R; Ollerton, R L

    1999-08-01

    To determine whether software processing of digitised retinal images using a "sharpen" filter improves the ability to grade diabetic retinopathy. 150 macula centred retinal images were taken as 35 mm colour transparencies representing a spectrum of diabetic retinopathy, digitised, and graded in random order before and after the application of a sharpen filter (Adobe Photoshop). Digital enhancement of contrast and brightness was performed and a X2 digital zoom was utilised. The grades from the unenhanced and enhanced digitised images were compared with the same retinal fields viewed as slides. Overall agreement in retinopathy grade from the digitised images improved from 83.3% (125/150) to 94.0% (141/150) with sight threatening diabetic retinopathy (STDR) correctly identified in 95.5% (84/88) and 98.9% (87/88) of cases when using unenhanced and enhanced images respectively. In total, five images were overgraded and four undergraded from the enhanced images compared with 17 and eight images respectively when using unenhanced images. This study demonstrates that the already good agreement in grading performance can be further improved by software manipulation or processing of digitised retinal images.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. 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

  18. 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

  19. Onboard utilization of ground control points for image correction. Volume 4: Correlation analysis software design

    NASA Technical Reports Server (NTRS)

    1981-01-01

    The software utilized for image correction accuracy measurement is described. The correlation analysis program is written to allow the user various tools to analyze different correlation algorithms. The algorithms were tested using LANDSAT imagery in two different spectral bands. Three classification algorithms are implemented.

  20. 3-dimensional root phenotyping with a novel imaging and software platform

    USDA-ARS?s Scientific Manuscript database

    A novel imaging and software platform was developed for the high-throughput phenotyping of 3-dimensional root traits during seedling development. To demonstrate the platform’s capacity, plants of two rice (Oryza sativa) genotypes, Azucena and IR64, were grown in a transparent gellan gum system and ...

  1. 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

  2. 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

  3. 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.

  4. Software requirements and support for image-algebraic analysis, detection, and recognition of small targets

    NASA Astrophysics Data System (ADS)

    Schmalz, Mark S.; Ritter, Gerhard X.; Forsman, Robert H.; Yang, Chyuan-Huei T.; Hu, Wen-Chen; Porter, Ryan A.; McTaggart, Gary; Hranicky, James F.; Davis, James F.

    1995-06-01

    The detection of hazardous targets frequently requires a multispectral approach to image acquisition and analysis, which we have implemented in a software system called MATRE (multispectral automated target recognition and enhancement). MATRE provides capabilities of image enhancement, image database management, spectral signature extraction and visualization, statistical analysis of greyscale imagery, as well as 2D and 3D image processing operations. Our system is based upon a client-server architecture that is amenable to distributed implementation. In this paper, we discuss salient issues and requirements for multispectral recognition of hazardous targets, and show that our software fulfills or exceeds such requirements. MATRE's capabilities, as well as statistical and morphological analysis results, are exemplified with emphasis upon computational cost, ease of installation, and maintenance on various Unix platforms. Additionally, MATRE's image processing functions can be coded in vector-parallel form, for ease of implementation of SIMD-parallel processors. Our algorithms are expressed in terms of image algebra, a concise, rigorous notation that unifies linear and nonlinear mathematics in the image domain. An image algebra class library for the C + + language has been incorporated into the our system, which facilitates fast algorithm prototyping without the numerous drawbacks of descrete coding.

  5. 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

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

    PubMed

    Noumeir, Rita; Renaud, Bérubé

    2010-09-21

    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. 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. 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.

  7. 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.

  8. A software tool to measure the geometric distortion in x-ray image systems

    NASA Astrophysics Data System (ADS)

    Prieto, Gabriel; Guibelalde, Eduardo; Chevalier, Margarita

    2010-04-01

    A software tool is presented to measure the geometric distortion in images obtained with X-ray systems that provides a more objective method than the usual measurements over the image of a phantom with usual rulers. In a first step, this software has been applied to mammography images and makes use of the grid included into the CDMAM phantom (University Hospital Nijmegen). For digital images, this software tool automatically locates the grid crossing points and obtains a set of corners (up to 237) that are used by the program to determine 6 different squares, at top, bottom, left, right and central positions. The sixth square is the largest that can be fitted in the grid (widest possible square). The distortion is calculated as ((length of left diagonal - length of right diagonal)/ length of left diagonal) (%) for the six positions. The algorithm error is of the order of 0.3%. The method might be applied to other radiological systems without any major changes to adjust the program code to other phantoms. In this work a set of measurements for 54 CDMAM images, acquired in 11 different mammography systems from 6 manufacturers are presented. We can conclude that the distortion of all equipments is smaller than the recommendations for maximum distortions in primary displays (2%)

  9. WHIPPET: a collaborative software environment for medical image processing and analysis

    NASA Astrophysics Data System (ADS)

    Hu, Yangqiu; Haynor, David R.; Maravilla, Kenneth R.

    2007-03-01

    While there are many publicly available software packages for medical image processing, making them available to end users in clinical and research labs remains non-trivial. An even more challenging task is to mix these packages to form pipelines that meet specific needs seamlessly, because each piece of software usually has its own input/output formats, parameter sets, and so on. To address these issues, we are building WHIPPET (Washington Heterogeneous Image Processing Pipeline EnvironmenT), a collaborative platform for integrating image analysis tools from different sources. The central idea is to develop a set of Python scripts which glue the different packages together and make it possible to connect them in processing pipelines. To achieve this, an analysis is carried out for each candidate package for WHIPPET, describing input/output formats, parameters, ROI description methods, scripting and extensibility and classifying its compatibility with other WHIPPET components as image file level, scripting level, function extension level, or source code level. We then identify components that can be connected in a pipeline directly via image format conversion. We set up a TWiki server for web-based collaboration so that component analysis and task request can be performed online, as well as project tracking, knowledge base management, and technical support. Currently WHIPPET includes the FSL, MIPAV, FreeSurfer, BrainSuite, Measure, DTIQuery, and 3D Slicer software packages, and is expanding. Users have identified several needed task modules and we report on their implementation.

  10. 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.

  11. Integrating digital image management software for improved patient care and optimal practice management.

    PubMed

    Starr, Jon C

    2006-06-01

    Photographic images provide vital documentation of preoperative, intraoperative, and postoperative results in the clinical dermatologic surgery practice and can document histologic findings from skin biopsies, thereby enhancing patient care. Images may be printed as part of text documents, transmitted via electronic mail, or included in electronic medical records. To describe existing computer software that integrates digital photography and the medical record to improve patient care and practice management. A variety of computer applications are available to optimize the use of digital images in the dermatologic practice.

  12. 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

  13. 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.

  14. 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.

  15. A near-infrared fluorescence-based surgical navigation system imaging software for sentinel lymph node detection

    NASA Astrophysics Data System (ADS)

    Ye, Jinzuo; Chi, Chongwei; Zhang, Shuang; Ma, Xibo; Tian, Jie

    2014-02-01

    Sentinel lymph node (SLN) in vivo detection is vital in breast cancer surgery. A new near-infrared fluorescence-based surgical navigation system (SNS) imaging software, which has been developed by our research group, is presented for SLN detection surgery in this paper. The software is based on the fluorescence-based surgical navigation hardware system (SNHS) which has been developed in our lab, and is designed specifically for intraoperative imaging and postoperative data analysis. The surgical navigation imaging software consists of the following software modules, which mainly include the control module, the image grabbing module, the real-time display module, the data saving module and the image processing module. And some algorithms have been designed to achieve the performance of the software, for example, the image registration algorithm based on correlation matching. Some of the key features of the software include: setting the control parameters of the SNS; acquiring, display and storing the intraoperative imaging data in real-time automatically; analysis and processing of the saved image data. The developed software has been used to successfully detect the SLNs in 21 cases of breast cancer patients. In the near future, we plan to improve the software performance and it will be extensively used for clinical purpose.

  16. Open Source software and social networks: disruptive alternatives for medical imaging.

    PubMed

    Ratib, Osman; Rosset, Antoine; Heuberger, Joris

    2011-05-01

    In recent decades several major changes in computer and communication technology have pushed the limits of imaging informatics and PACS beyond the traditional system architecture providing new perspectives and innovative approach to a traditionally conservative medical community. Disruptive technologies such as the world-wide-web, wireless networking, Open Source software and recent emergence of cyber communities and social networks have imposed an accelerated pace and major quantum leaps in the progress of computer and technology infrastructure applicable to medical imaging applications. This paper reviews the impact and potential benefits of two major trends in consumer market software development and how they will influence the future of medical imaging informatics. Open Source software is emerging as an attractive and cost effective alternative to traditional commercial software developments and collaborative social networks provide a new model of communication that is better suited to the needs of the medical community. Evidence shows that successful Open Source software tools have penetrated the medical market and have proven to be more robust and cost effective than their commercial counterparts. Developed by developers that are themselves part of the user community, these tools are usually better adapted to the user's need and are more robust than traditional software programs being developed and tested by a large number of contributing users. This context allows a much faster and more appropriate development and evolution of the software platforms. Similarly, communication technology has opened up to the general public in a way that has changed the social behavior and habits adding a new dimension to the way people communicate and interact with each other. The new paradigms have also slowly penetrated the professional market and ultimately the medical community. Secure social networks allowing groups of people to easily communicate and exchange information

  17. 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.

  18. Counting pollen grains using readily available, free image processing and analysis software

    PubMed Central

    Costa, Clayton M.; Yang, Suann

    2009-01-01

    Background and Aims Although many methods exist for quantifying the number of pollen grains in a sample, there are few standard methods that are user-friendly, inexpensive and reliable. The present contribution describes a new method of counting pollen using readily available, free image processing and analysis software. Methods Pollen was collected from anthers of two species, Carduus acanthoides and C. nutans (Asteraceae), then illuminated on slides and digitally photographed through a stereomicroscope. Using ImageJ (NIH), these digital images were processed to remove noise and sharpen individual pollen grains, then analysed to obtain a reliable total count of the number of grains present in the image. A macro was developed to analyse multiple images together. To assess the accuracy and consistency of pollen counting by ImageJ analysis, counts were compared with those made by the human eye. Key Results and Conclusions Image analysis produced pollen counts in 60 s or less per image, considerably faster than counting with the human eye (5–68 min). In addition, counts produced with the ImageJ procedure were similar to those obtained by eye. Because count parameters are adjustable, this image analysis protocol may be used for many other plant species. Thus, the method provides a quick, inexpensive and reliable solution to counting pollen from digital images, not only reducing the chance of error but also substantially lowering labour requirements. PMID:19640891

  19. The accuracy of a designed software for automated localization of craniofacial landmarks on CBCT images.

    PubMed

    Shahidi, Shoaleh; Bahrampour, Ehsan; Soltanimehr, Elham; Zamani, Ali; Oshagh, Morteza; Moattari, Marzieh; Mehdizadeh, Alireza

    2014-09-16

    Two-dimensional projection radiographs have been traditionally considered the modality of choice for cephalometric analysis. To overcome the shortcomings of two-dimensional images, three-dimensional computed tomography (CT) has been used to evaluate craniofacial structures. However, manual landmark detection depends on medical expertise, and the process is time-consuming. The present study was designed to produce software capable of automated localization of craniofacial landmarks on cone beam (CB) CT images based on image registration and to evaluate its accuracy. The software was designed using MATLAB programming language. The technique was a combination of feature-based (principal axes registration) and voxel similarity-based methods for image registration. A total of 8 CBCT images were selected as our reference images for creating a head atlas. Then, 20 CBCT images were randomly selected as the test images for evaluating the method. Three experts twice located 14 landmarks in all 28 CBCT images during two examinations set 6 weeks apart. The differences in the distances of coordinates of each landmark on each image between manual and automated detection methods were calculated and reported as mean errors. The combined intraclass correlation coefficient for intraobserver reliability was 0.89 and for interobserver reliability 0.87 (95% confidence interval, 0.82 to 0.93). The mean errors of all 14 landmarks were <4 mm. Additionally, 63.57% of landmarks had a mean error of <3 mm compared with manual detection (gold standard method). The accuracy of our approach for automated localization of craniofacial landmarks, which was based on combining feature-based and voxel similarity-based methods for image registration, was acceptable. Nevertheless we recommend repetition of this study using other techniques, such as intensity-based methods.

  20. Workspace Analysis and Optimization of 3-PUU Parallel Mechanism in Medicine Base on Genetic Algorithm

    PubMed Central

    Hou, Yongchao; Zhao, Yang

    2015-01-01

    A novel 3-PUU parallel robot was put forward, on which kinematic analysis was conducted to obtain its inverse kinematics solution, and on this basis, the limitations of the sliding pair and the Hooke joint on the workspace were analyzed. Moreover, the workspace was solved through the three dimensional limit search method, and then optimization analysis was performed on the workspace of this parallel robot, which laid the foundations for the configuration design and further analysis of the parallel mechanism, with the result indicated that this type of robot was equipped with promising application prospect. In addition that, the workspace after optimization can meet more requirements of patients. PMID:26628930

  1. Workspace Analysis and Optimization of 3-PUU Parallel Mechanism in Medicine Base on Genetic Algorithm.

    PubMed

    Hou, Yongchao; Zhao, Yang

    2015-01-01

    A novel 3-PUU parallel robot was put forward, on which kinematic analysis was conducted to obtain its inverse kinematics solution, and on this basis, the limitations of the sliding pair and the Hooke joint on the workspace were analyzed. Moreover, the workspace was solved through the three dimensional limit search method, and then optimization analysis was performed on the workspace of this parallel robot, which laid the foundations for the configuration design and further analysis of the parallel mechanism, with the result indicated that this type of robot was equipped with promising application prospect. In addition that, the workspace after optimization can meet more requirements of patients.

  2. 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.

  3. 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).

  4. 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.

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

    PubMed

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

    2011-01-01

    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). 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. 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. 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. 0 2011 Ameri-

  6. 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.

  7. 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

  8. Making the PACS workstation a browser of image processing software: a feasibility study using inter-process communication techniques.

    PubMed

    Wang, Chunliang; Ritter, Felix; Smedby, Orjan

    2010-07-01

    To enhance the functional expandability of a picture archiving and communication systems (PACS) workstation and to facilitate the integration of third-part image-processing modules, we propose a browser-server style method. In the proposed solution, the PACS workstation shows the front-end user interface defined in an XML file while the image processing software is running in the background as a server. Inter-process communication (IPC) techniques allow an efficient exchange of image data, parameters, and user input between the PACS workstation and stand-alone image-processing software. Using a predefined communication protocol, the PACS workstation developer or image processing software developer does not need detailed information about the other system, but will still be able to achieve seamless integration between the two systems and the IPC procedure is totally transparent to the final user. A browser-server style solution was built between OsiriX (PACS workstation software) and MeVisLab (Image-Processing Software). Ten example image-processing modules were easily added to OsiriX by converting existing MeVisLab image processing networks. Image data transfer using shared memory added <10ms of processing time while the other IPC methods cost 1-5 s in our experiments. The browser-server style communication based on IPC techniques is an appealing method that allows PACS workstation developers and image processing software developers to cooperate while focusing on different interests.

  9. 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.

  10. 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.

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

    PubMed Central

    2011-01-01

    Background The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. Methods In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. Results The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the

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

    PubMed

    Markiewicz, Tomasz

    2011-03-30

    The Matlab software is a one of the most advanced development tool for application in engineering practice. From our point of view the most important is the image processing toolbox, offering many built-in functions, including mathematical morphology, and implementation of a many artificial neural networks as AI. It is very popular platform for creation of the specialized program for image analysis, also in pathology. Based on the latest version of Matlab Builder Java toolbox, it is possible to create the software, serving as a remote system for image analysis in pathology via internet communication. The internet platform can be realized based on Java Servlet Pages with Tomcat server as servlet container. In presented software implementation we propose remote image analysis realized by Matlab algorithms. These algorithms can be compiled to executable jar file with the help of Matlab Builder Java toolbox. The Matlab function must be declared with the set of input data, output structure with numerical results and Matlab web figure. Any function prepared in that manner can be used as a Java function in Java Servlet Pages (JSP). The graphical user interface providing the input data and displaying the results (also in graphical form) must be implemented in JSP. Additionally the data storage to database can be implemented within algorithm written in Matlab with the help of Matlab Database Toolbox directly with the image processing. The complete JSP page can be run by Tomcat server. The proposed tool for remote image analysis was tested on the Computerized Analysis of Medical Images (CAMI) software developed by author. The user provides image and case information (diagnosis, staining, image parameter etc.). When analysis is initialized, input data with image are sent to servlet on Tomcat. When analysis is done, client obtains the graphical results as an image with marked recognized cells and also the quantitative output. Additionally, the results are stored in a server

  13. Algorithms and Software for Improved CT Imaging: Promotional Slides for Industrial Clients

    DTIC Science & Technology

    2015-09-03

    Briefing Charts 3. DATES COVERED (From - To) 29 June 2015 – 03 September 2015 4. TITLE AND SUBTITLE Algorithms and Software for Improved CT Imaging...Number: #15477; Clearance Date: 03 September 2015 14. ABSTRACT Viewgraphs/Briefing Charts 15. SUBJECT TERMS N/A 16. SECURITY CLASSIFICATION OF...distribution is unlimited. Frequency spectrum of the columns of the sinogram oscillations due to mechanical resonances and other effects r θ Distribution

  14. 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.

  15. 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.

  16. 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

  17. Application of Scion image software to the simultaneous determination of curcuminoids in turmeric (Curcuma longa).

    PubMed

    Sotanaphun, Uthai; Phattanawasin, Panadda; Sriphong, Lawan

    2009-01-01

    Curcumin, desmethoxycurcumin and bisdesmethoxycurcumin are bioactive constituents of turmeric (Curcuma longa). Owing to their different potency, quality control of turmeric based on the content of each curcuminoid is more reliable than that based on total curcuminoids. However, to perform such an assay, high-cost instrument is needed. To develop a simple and low-cost method for the simultaneous quantification of three curcuminoids in turmeric using TLC and the public-domain software Scion Image. The image of a TLC chromatogram of turmeric extract was recorded using a digital scanner. The density of the TLC spot of each curcuminoid was analysed by the Scion Image software. The density value was transformed to concentration by comparison with the calibration curve of standard curcuminoids developed on the same TLC plate. The polynomial regression data for all curcuminoids showed good linear relationship with R(2) > 0.99 in the concentration range of 0.375-6 microg/spot. The limits of detection and quantitation were 43-73 and 143-242 ng/spot, respectively. The method gave adequate precision, accuracy and recovery. The contents of each curcuminoid determined using this method were not significantly different from those determined using the TLC densitometric method. TLC image analysis using Scion Image is shown to be a reliable method for the simultaneous analysis of the content of each curcuminoid in turmeric.

  18. 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

  19. A software tool for automatic classification and segmentation of 2D/3D medical images

    NASA Astrophysics Data System (ADS)

    Strzelecki, Michal; Szczypinski, Piotr; Materka, Andrzej; Klepaczko, Artur

    2013-02-01

    Modern medical diagnosis utilizes techniques of visualization of human internal organs (CT, MRI) or of its metabolism (PET). However, evaluation of acquired images made by human experts is usually subjective and qualitative only. Quantitative analysis of MR data, including tissue classification and segmentation, is necessary to perform e.g. attenuation compensation, motion detection, and correction of partial volume effect in PET images, acquired with PET/MR scanners. This article presents briefly a MaZda software package, which supports 2D and 3D medical image analysis aiming at quantification of image texture. MaZda implements procedures for evaluation, selection and extraction of highly discriminative texture attributes combined with various classification, visualization and segmentation tools. Examples of MaZda application in medical studies are also provided.

  20. 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.

  1. 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.

  2. Enhanced simulator software for image validation and interpretation for multimodal localization super-resolution fluorescence microscopy

    NASA Astrophysics Data System (ADS)

    Erdélyi, Miklós; Sinkó, József; Gajdos, Tamás.; Novák, Tibor

    2017-02-01

    Optical super-resolution techniques such as single molecule localization have become one of the most dynamically developed areas in optical microscopy. These techniques routinely provide images of fixed cells or tissues with sub-diffraction spatial resolution, and can even be applied for live cell imaging under appropriate circumstances. Localization techniques are based on the precise fitting of the point spread functions (PSF) to the measured images of stochastically excited, identical fluorescent molecules. These techniques require controlling the rate between the on, off and the bleached states, keeping the number of active fluorescent molecules at an optimum value, so their diffraction limited images can be detected separately both spatially and temporally. Because of the numerous (and sometimes unknown) parameters, the imaging system can only be handled stochastically. For example, the rotation of the dye molecules obscures the polarization dependent PSF shape, and only an averaged distribution - typically estimated by a Gaussian function - is observed. TestSTORM software was developed to generate image stacks for traditional localization microscopes, where localization meant the precise determination of the spatial position of the molecules. However, additional optical properties (polarization, spectra, etc.) of the emitted photons can be used for further monitoring the chemical and physical properties (viscosity, pH, etc.) of the local environment. The image stack generating program was upgraded by several new features, such as: multicolour, polarization dependent PSF, built-in 3D visualization, structured background. These features make the program an ideal tool for optimizing the imaging and sample preparation conditions.

  3. 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.

  4. A User Assessment of Workspaces in Selected Music Education Computer Laboratories.

    ERIC Educational Resources Information Center

    Badolato, Michael Jeremy

    A study of 120 students selected from the user populations of four music education computer laboratories was conducted to determine the applicability of current ergonomic and environmental design guidelines in satisfying the needs of users of educational computing workspaces. Eleven categories of workspace factors were organized into a…

  5. Shadow netWorkspace: An Open Source Intranet for Learning Communities

    ERIC Educational Resources Information Center

    Laffey, James M.; Musser, Dale

    2006-01-01

    Shadow netWorkspace (SNS) is a web application system that allows a school or any type of community to establish an intranet with network workspaces for all members and groups. The goal of SNS has been to make it easy for schools and other educational organizations to provide network services in support of implementing a learning community. SNS is…

  6. Open source software for the analysis of corneal deformation parameters on the images from the Corvis tonometer.

    PubMed

    Koprowski, Robert

    2015-04-11

    The software supplied with the Corvis tonometer (which is designed to measure intraocular pressure with the use of the air-puff method) is limited to providing basic numerical data. These data relate to the values of the measured intraocular pressure and, for example, applanation amplitudes. However, on the basis of a sequence of images obtained from the Corvis tonometer, it is possible to obtain much more information which is not available in its original software. This will be presented in this paper. The proposed software has been tested on 1400 images from the Corvis tonometer. The number of analysed 2D images (with a resolution of 200 × 576 pixels) in a sequence is arbitrary. However, in typical cases there are 140 images. The proposed software has been written in Matlab (Version 7.11.0.584, R2010b). The methods of image analysis and processing and in particular edge detection and the fast Fourier transform have been applied. The software allows for fully automatic (1) acquisition of 12 new parameters previously unavailable in the original software of the Corvis tonometer. It also enables off-line (2) manual and (3) automatic browsing of images in a sequence; 3D graph visualization of: (4) the corneal deformation and (5) eyeball response; 6) change of the colour palette; (7) filtration and (8) visualization of selected measured values on individual 2D images. In addition, the proposed software enables (9) to save the obtained results for further analysis and processing. The dedicated software described in this paper enables to obtain additional new features of corneal deformations during intraocular pressure measurement. The software can be applied in the diagnosis of corneal deformation vibrations, glaucoma diagnosis, evaluation of measurement repeatability and others. The software has no licensing restrictions and can be used both commercially and non-commercially without any limitations.

  7. [Development of DICOM image viewing software for efficient image reading and evaluation of distributed server system for diagnostic environment].

    PubMed

    Ishikawa, K

    2000-12-01

    To construct an efficient diagnostic environment using computer displays, the author investigated the time of network transmission using clinical images. In our hospital, we introduced optical-fiber 100Base-Fx Ethernet connections between 22 HIS-segments and one RIS-segment. Although Ethernet architecture is inexpensive, the speed of image transmission becomes 2371 KB/sec. (4.6 CT-slice/sec.) in the RIS-segment and 996 KB/sec. (1.9 CT-slice/sec.) from the RIS-segment to HIS-segments. Because one examination is transmitted in one minute, it does not disturb image reading. Otherwise, a distributed server system using inexpensive personal computers helps in constructing an efficient system. This investigation showed that commercially based Digital Imaging and Communications in Medicine(DICOM) servers and RSNA Central Test Node servers are not so different in transmission speed. The author programmed and developed DICOM transmission and viewing software for Macintosh computers. This viewer includes two inventions, dynamic tiling window system (DTWS) and window binding mode(WBM). On DTWS, windows, tiles, and images are independent objects, which are movable and resizable. The tile-matrix is changeable by mouse dragging, which realizes suitable tile rectangles for wide-low or narrow-high images. The arranging window tool prevents windows from scattering. Using WBM, any operation affects each window similarly. This means that the relationship of compared images is always equivalent. DTWS and WBM contribute greatly to a filmless diagnostic environment.

  8. Comparison of an imaging software and manual prediction of soft tissue changes after orthognathic surgery.

    PubMed

    Ahmad Akhoundi, M S; Shirani, G; Arshad, M; Heidar, H; Sodagar, A

    2012-01-01

    Accurate prediction of the surgical outcome is important in treating dentofacial deformities. Visualized treatment objectives usually involve manual surgical simulation based on tracing of cephalometric radiographs. Recent technical advancements have led to the use of computer assisted imaging systems in treatment planning for orthognathic surgical cases. The purpose of this study was to examine and compare the ability and reliability of digitization using Dolphin Imaging Software with traditional manual techniques and to compare orthognathic prediction with actual outcomes. Forty patients consisting of 35 women and 5 men (32 class III and 8 class II) with no previous surgery were evaluated by manual tracing and indirect digitization using Dolphin Imaging Software. Reliability of each method was assessed then the two techniques were compared using paired t test. The nasal tip presented the least predicted error and higher reliability. The least accurate regions in vertical plane were subnasal and upper lip, and subnasal and pogonion in horizontal plane. There were no statistically significant differences between the predictions of groups with and without genioplasty. Computer-generated image prediction was suitable for patient education and communication. However, efforts are still needed to improve accuracy and reliability of the prediction program and to include changes in soft tissue tension and muscle strain.

  9. A PC-based 3D imaging system: algorithms, software, and hardware considerations.

    PubMed

    Raya, S P; Udupa, J K; Barrett, W A

    1990-01-01

    Three-dimensional (3D) imaging in medicine is known to produce easily and quickly derivable medically relevant information, especially in complex situations. We intend to demonstrate in this paper, that with an appropriate choice of approaches and a proper design of algorithms and software, it is possible to develop a low-cost 3D imaging system that can provide a level of performance sufficient to meet the daily case load in an individual or even group-practice situation. We describe hardware considerations of a generic system and give an example of a specific system we used for our implementation. Given a 3D image as a stack of slices, we generate a packed binary cubic voxel array, by combining segmentation (density thresholding), interpolation, and packing in an efficient way. Since threshold-based segmentation is very often not perfect, object-like structures and noise clutter the binary scene. We utilize an effective mechanism to isolate the object from this clutter by tracking a specified, connected surface of the object. The surface description thus obtained is rendered to create a depiction of the surface on a 2D display screen. Efficient implementation of hidden-part removal and image-space shading and a simple and fast antialiasing technique provide a level of performance which otherwise would not have been possible in a PC environment. We outline our software emphasizing some design aspects and present some clinical examples.

  10. 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.

  11. 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.

  12. An advanced software suite for the processing and analysis of silicon luminescence images

    NASA Astrophysics Data System (ADS)

    Payne, D. N. R.; Vargas, C.; Hameiri, Z.; Wenham, S. R.; Bagnall, D. M.

    2017-06-01

    Luminescence imaging is a versatile characterisation technique used for a broad range of research and industrial applications, particularly for the field of photovoltaics where photoluminescence and electroluminescence imaging is routinely carried out for materials analysis and quality control. Luminescence imaging can reveal a wealth of material information, as detailed in extensive literature, yet these techniques are often only used qualitatively instead of being utilised to their full potential. Part of the reason for this is the time and effort required for image processing and analysis in order to convert image data to more meaningful results. In this work, a custom built, Matlab based software suite is presented which aims to dramatically simplify luminescence image processing and analysis. The suite includes four individual programs which can be used in isolation or in conjunction to achieve a broad array of functionality, including but not limited to, point spread function determination and deconvolution, automated sample extraction, image alignment and comparison, minority carrier lifetime calibration and iron impurity concentration mapping.

  13. [Accuracy of morphological simulation for orthognatic surgery. Assessment of a 3D image fusion software.

    PubMed

    Terzic, A; Schouman, T; Scolozzi, P

    2013-08-06

    The CT/CBCT data allows for 3D reconstruction of skeletal and untextured soft tissue volume. 3D stereophotogrammetry technology has strongly improved the quality of facial soft tissue surface texture. The combination of these two technologies allows for an accurate and complete reconstruction. The 3D virtual head may be used for orthognatic surgical planning, virtual surgery, and morphological simulation obtained with a software dedicated to the fusion of 3D photogrammetric and radiological images. The imaging material include: a multi-slice CT scan or broad field CBCT scan, a 3D photogrammetric camera. The operative image processing protocol includes the following steps: 1) pre- and postoperative CT/CBCT scan and 3D photogrammetric image acquisition; 2) 3D image segmentation and fusion of untextured CT/CBCT skin with the preoperative textured facial soft tissue surface of the 3D photogrammetric scan; 3) image fusion of the pre- and postoperative CT/CBCT data set virtual osteotomies, and 3D photogrammetric soft tissue virtual simulation; 4) fusion of virtual simulated 3D photogrammetric and real postoperative images, and assessment of accuracy using a color-coded scale to measure the differences between the two surfaces. Copyright © 2013. Published by Elsevier Masson SAS.

  14. 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.

  15. Software designs of image processing tasks with incremental refinement of computation.

    PubMed

    Anastasia, Davide; Andreopoulos, Yiannis

    2010-08-01

    Software realizations of computationally-demanding image processing tasks (e.g., image transforms and convolution) do not currently provide graceful degradation when their clock-cycles budgets are reduced, e.g., when delay deadlines are imposed in a multitasking environment to meet throughput requirements. This is an important obstacle in the quest for full utilization of modern programmable platforms' capabilities since worst-case considerations must be in place for reasonable quality of results. In this paper, we propose (and make available online) platform-independent software designs performing bitplane-based computation combined with an incremental packing framework in order to realize block transforms, 2-D convolution and frame-by-frame block matching. The proposed framework realizes incremental computation: progressive processing of input-source increments improves the output quality monotonically. Comparisons with the equivalent nonincremental software realization of each algorithm reveal that, for the same precision of the result, the proposed approach can lead to comparable or faster execution, while it can be arbitrarily terminated and provide the result up to the computed precision. Application examples with region-of-interest based incremental computation, task scheduling per frame, and energy-distortion scalability verify that our proposal provides significant performance scalability with graceful degradation.

  16. CONRAD--a software framework for cone-beam imaging in radiology.

    PubMed

    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

    2013-11-01

    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. 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. 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. As a common software framework, CONRAD enables the medical physics community to share algorithms and develop new ideas. In particular this offers new opportunities for scientific collaboration and quantitative performance comparison

  17. 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

  18. 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

  19. 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

  20. 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.

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

    PubMed Central

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

    2010-01-01

    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. PMID:21258475

  2. 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.

  3. 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...

  4. Comparative Evaluation of the Ostium After External and Nonendoscopic Endonasal Dacryocystorhinostomy Using Image Processing (Matlabs and Image J) Softwares.

    PubMed

    Ganguly, Anasua; Kaza, Hrishikesh; Kapoor, Aditya; Sheth, Jenil; Ali, Mohammad Hasnat; Tripathy, Devjyoti; Rath, Suryasnata

    The purpose of this study was to compare the characteristics of the ostium after external dacryocystorhinostomy and nonendoscopic endonasal dacryocystorhinostomy (NEN-DCR). This cross-sectional study included patients who underwent a successful external dacryocystorhinostomy or NEN-DCR and had ≥1 month follow up. Pictures of the ostium were captured with a nasal endoscope (4 mm, 30°) after inserting a lacrimal probe premarked at 2 mm. Image analyses were performed using Image J and Contour softwares. Of the 113 patients included, external dacryocystorhinostomy group had 53 patients and NEN-DCR group had 60 patients. The mean age of patients in the NEN-DCR group (38 years) was significantly (p < 0.05) lower than the external dacryocystorhinostomy group (50 years). There was no statistically significant difference (2 sample t test, p > 0.05) in mean follow up (6 vs. 4 months), maximum diameter of ostium (8 vs. 7 mm), perpendicular drawn to it (4 vs. 4 mm), area of ostium (43 vs. 36 mm), and the minimum distance between common internal punctum and edge of the ostium (1 vs. 1 mm) between the external and NEN-DCR groups. Image processing softwares offer simple and objective method to measure the ostium. While ostia are comparable in size, their relative position differs with posteriorly placed ostia in external compared with inferior in NEN-DCR.

  5. 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.

  6. 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.

  7. Comparison of perfusion- and diffusion-weighted imaging parameters in brain tumor studies processed using different software platforms.

    PubMed

    Milchenko, Mikhail V; Rajderkar, Dhanashree; LaMontagne, Pamela; Massoumzadeh, Parinaz; Bogdasarian, Ronald; Schweitzer, Gordon; Benzinger, Tammie; Marcus, Dan; Shimony, Joshua S; Fouke, Sarah Jost

    2014-10-01

    To compare quantitative imaging parameter measures from diffusion- and perfusion-weighted imaging magnetic resonance imaging (MRI) sequences in subjects with brain tumors that have been processed with different software platforms. Scans from 20 subjects with primary brain tumors were selected from the Comprehensive Neuro-oncology Data Repository at Washington University School of Medicine (WUSM) and the Swedish Neuroscience Institute. MR images were coregistered, and each subject's data set was processed by three software packages: 1) vendor-specific scanner software, 2) research software developed at WUSM, and 3) a commercially available, Food and Drug Administration-approved, processing platform (Nordic Ice). Regions of interest (ROIs) were chosen within the brain tumor and normal nontumor tissue. The results obtained using these methods were compared. For diffusion parameters, including mean diffusivity and fractional anisotropy, concordance was high when comparing different processing methods. For perfusion-imaging parameters, a significant variance in cerebral blood volume, cerebral blood flow, and mean transit time (MTT) values was seen when comparing the same raw data processed using different software platforms. Correlation was better with larger ROIs (radii ≥ 5 mm). Greatest variance was observed in MTT. Diffusion parameter values were consistent across different software processing platforms. Perfusion parameter values were more variable and were influenced by the software used. Variation in the MTT was especially large suggesting that MTT estimation may be unreliable in tumor tissues using current MRI perfusion methods. Copyright © 2014 AUR. Published by Elsevier Inc. All rights reserved.

  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. The i5k Workspace@NAL--enabling genomic data access, visualization and curation of arthropod genomes.

    PubMed

    Poelchau, Monica; Childers, Christopher; Moore, Gary; Tsavatapalli, Vijaya; Evans, Jay; Lee, Chien-Yueh; Lin, Han; Lin, Jun-Wei; Hackett, Kevin

    2015-01-01

    The 5000 arthropod genomes initiative (i5k) has tasked itself with coordinating the sequencing of 5000 insect or related arthropod genomes. The resulting influx of data, mostly from small research groups or communities with little bioinformatics experience, will require visualization, dissemination and curation, preferably from a centralized platform. The National Agricultural Library (NAL) has implemented the i5k Workspace@NAL (http://i5k.nal.usda.gov/) to help meet the i5k initiative's genome hosting needs. Any i5k member is encouraged to contact the i5k Workspace with their genome project details. Once submitted, new content will be accessible via organism pages, genome browsers and BLAST search engines, which are implemented via the open-source Tripal framework, a web interface for the underlying Chado database schema. We also implement the Web Apollo software for groups that choose to curate gene models. New content will add to the existing body of 35 arthropod species, which include species relevant for many aspects of arthropod genomic research, including agriculture, invasion biology, systematics, ecology and evolution, and developmental research. Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

  10. The i5k Workspace@NAL—enabling genomic data access, visualization and curation of arthropod genomes

    PubMed Central

    Poelchau, Monica; Childers, Christopher; Moore, Gary; Tsavatapalli, Vijaya; Evans, Jay; Lee, Chien-Yueh; Lin, Han; Lin, Jun-Wei; Hackett, Kevin

    2015-01-01

    The 5000 arthropod genomes initiative (i5k) has tasked itself with coordinating the sequencing of 5000 insect or related arthropod genomes. The resulting influx of data, mostly from small research groups or communities with little bioinformatics experience, will require visualization, dissemination and curation, preferably from a centralized platform. The National Agricultural Library (NAL) has implemented the i5k Workspace@NAL (http://i5k.nal.usda.gov/) to help meet the i5k initiative's genome hosting needs. Any i5k member is encouraged to contact the i5k Workspace with their genome project details. Once submitted, new content will be accessible via organism pages, genome browsers and BLAST search engines, which are implemented via the open-source Tripal framework, a web interface for the underlying Chado database schema. We also implement the Web Apollo software for groups that choose to curate gene models. New content will add to the existing body of 35 arthropod species, which include species relevant for many aspects of arthropod genomic research, including agriculture, invasion biology, systematics, ecology and evolution, and developmental research. PMID:25332403

  11. a New Digital Image Correlation Software for Displacements Field Measurement in Structural Applications

    NASA Astrophysics Data System (ADS)

    Ravanelli, R.; Nascetti, A.; Di Rita, M.; Belloni, V.; Mattei, D.; Nisticó, N.; Crespi, M.

    2017-07-01

    Recently, there has been a growing interest in studying non-contact techniques for strain and displacement measurement. Within photogrammetry, Digital Image Correlation (DIC) has received particular attention thanks to the recent advances in the field of lowcost, high resolution digital cameras, computer power and memory storage. DIC is indeed an optical technique able to measure full field displacements and strain by comparing digital images of the surface of a material sample at different stages of deformation and thus can play a major role in structural monitoring applications. For all these reasons, a free and open source 2D DIC software, named py2DIC, was developed at the Geodesy and Geomatics Division of DICEA, University of Rome La Sapienza. Completely written in python, the software is based on the template matching method and computes the displacement and strain fields. The potentialities of Py2DIC were evaluated by processing the images captured during a tensile test performed in the Lab of Structural Engineering, where three different Glass Fiber Reinforced Polymer samples were subjected to a controlled tension by means of a universal testing machine. The results, compared with the values independently measured by several strain gauges fixed on the samples, demonstrate the possibility to successfully characterize the deformation mechanism of the investigated material. Py2DIC is indeed able to highlight displacements at few microns level, in reasonable agreement with the reference, both in terms of displacements (again, at few microns in the average) and Poisson's module.

  12. 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.

  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. Collaborative immersive workspace through a shared augmented environment

    NASA Astrophysics Data System (ADS)

    Kiyokawa, Kiyoshi; Iwasa, Hidehiko; Takemura, Haruo; Yokoya, Naokazu

    1998-10-01

    We focus on a shared augmented environment (SAE) as an almost ideal face-to-face collaborative virtual workspace. In an SAE, multiple users can observe both a virtual world and real partners through optical see-through head mounted displays. This paper describes two experiments for verifying the effectiveness of an SAE compared with a conventional shared virtual environment (SVE) and exploring improvement of them. Through the experiments, the effectiveness of an SAE compared with an SVE was confirmed. It was also confirmed that enhancement of the shared environment with computer graphics, i.e. displaying a partner's body in an SVE, drawing a linear as a partner's viewing directions and emphasizing virtual objects to which a partner pay attention, improves workers' feeling and collaboration efficiency.

  15. Applying Workspace Limitations in a Velocity-Controlled Robotic Mechanism

    NASA Technical Reports Server (NTRS)

    Abdallah, Muhammad E. (Inventor); Hargrave, Brian (Inventor); Platt, Robert J., Jr. (Inventor)

    2014-01-01

    A robotic system includes a robotic mechanism responsive to velocity control signals, and a permissible workspace defined by a convex-polygon boundary. A host machine determines a position of a reference point on the mechanism with respect to the boundary, and includes an algorithm for enforcing the boundary by automatically shaping the velocity control signals as a function of the position, thereby providing smooth and unperturbed operation of the mechanism along the edges and corners of the boundary. The algorithm is suited for application with higher speeds and/or external forces. A host machine includes an algorithm for enforcing the boundary by shaping the velocity control signals as a function of the reference point position, and a hardware module for executing the algorithm. A method for enforcing the convex-polygon boundary is also provided that shapes a velocity control signal via a host machine as a function of the reference point position.

  16. 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

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

    PubMed

    Solves-Llorens, J A; Rupérez, M J; Monserrat, C; Feliu, E; García, M; Lloret, M

    2014-08-01

    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. 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. 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. 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 application can accelerate the

  18. XDesign: An open-source software package for designing X-ray imaging phantoms and experiments

    DOE PAGES

    Ching, Daniel J.; Gursoy, Dogˇa

    2017-02-21

    Here, the development of new methods or utilization of current X-ray computed tomography methods is impeded by the substantial amount of expertise required to design an X-ray computed tomography experiment from beginning to end. In an attempt to make material models, data acquisition schemes and reconstruction algorithms more accessible to researchers lacking expertise in some of these areas, a software package is described here which can generate complex simulated phantoms and quantitatively evaluate new or existing data acquisition schemes and image reconstruction algorithms for targeted applications.

  19. 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.

  20. 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.

  1. Interactions and Optimizations Analysis between Stiffness and Workspace of 3-UPU Robotic Mechanism

    NASA Astrophysics Data System (ADS)

    Zhang, Dan; Wei, Bin

    2017-04-01

    The interactions between stiffness and workspace performances are studied. The stiffness in x, y and z directions as well as the workspace of a 3-UPU mechanism are studied and optimized. The stiffness of the robotic system in every single moveable direction is measured and analyzed, and it is observed that in the case where one tries to make the x and y translational stiffness larger, the z directional stiffness will be reduced, i.e. the x and y translational stiffness contradicts with the one in z direction. Subsequently, the objective functions for the summation of the x and y translational stiffness and z directional stiffness are established and they are being optimized simultaneously. However, we later found that these two objectives are not in the same scale; a normalization of the objectives is thus taken into consideration. Meanwhile, the robotic system's workspace is studied and optimized. Through comparing the stiffness landscape and the workspace volume landscape, it is also observed that the z translational stiffness shows the same changing tendency with the workspace volume's changing tendency while the x and y translational stiffness shows the opposite changing tendency compared to the workspace volume's. Via employing the Pareto front theory and differential evolution, the summation of the x and y translational stiffness and the volume of the workspace are being simultaneously optimized. Finally, the mechanism is employed to synthesize an exercise-walking machine for stroke patients.

  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. 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.

  4. 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.

  5. MIA - A free and open source software for gray scale medical image analysis

    PubMed Central

    2013-01-01

    Background Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large. Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers. One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development. Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don’t provide an clear approach when one wants to shape a new command line tool from a prototype shell script. Results The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell

  6. MIA - A free and open source software for gray scale medical image analysis.

    PubMed

    Wollny, Gert; Kellman, Peter; Ledesma-Carbayo, María-Jesus; Skinner, Matthew M; Hublin, Jean-Jaques; Hierl, Thomas

    2013-10-11

    Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large.Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers.One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development.Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don't provide an clear approach when one wants to shape a new command line tool from a prototype shell script. The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by

  7. Magnetic resonance imaging diffusion tensor tractography: evaluation of anatomic accuracy of different fiber tracking software packages.

    PubMed

    Feigl, Guenther C; Hiergeist, Wolfgang; Fellner, Claudia; Schebesch, Karl-Michael M; Doenitz, Christian; Finkenzeller, Thomas; Brawanski, Alexander; Schlaier, Juergen

    2014-01-01

    Diffusion tensor imaging (DTI)-based tractography has become an integral part of preoperative diagnostic imaging in many neurosurgical centers, and other nonsurgical specialties depend increasingly on DTI tractography as a diagnostic tool. The aim of this study was to analyze the anatomic accuracy of visualized white matter fiber pathways using different, readily available DTI tractography software programs. Magnetic resonance imaging scans of the head of 20 healthy volunteers were acquired using a Siemens Symphony TIM 1.5T scanner and a 12-channel head array coil. The standard settings of the scans in this study were 12 diffusion directions and 5-mm slices. The fornices were chosen as an anatomic structure for the comparative fiber tracking. Identical data sets were loaded into nine different fiber tracking packages that used different algorithms. The nine software packages and algorithms used were NeuroQLab (modified tensor deflection [TEND] algorithm), Sörensen DTI task card (modified streamline tracking technique algorithm), Siemens DTI module (modified fourth-order Runge-Kutta algorithm), six different software packages from Trackvis (interpolated streamline algorithm, modified FACT algorithm, second-order Runge-Kutta algorithm, Q-ball [FACT algorithm], tensorline algorithm, Q-ball [second-order Runge-Kutta algorithm]), DTI Query (modified streamline tracking technique algorithm), Medinria (modified TEND algorithm), Brainvoyager (modified TEND algorithm), DTI Studio modified FACT algorithm, and the BrainLab DTI module based on the modified Runge-Kutta algorithm. Three examiners (a neuroradiologist, a magnetic resonance imaging physicist, and a neurosurgeon) served as examiners. They were double-blinded with respect to the test subject and the fiber tracking software used in the presented images. Each examiner evaluated 301 images. The examiners were instructed to evaluate screenshots from the different programs based on two main criteria: (i) anatomic

  8. IMART software for correction of motion artifacts in images collected in intravital microscopy

    PubMed Central

    Dunn, Kenneth W; Lorenz, Kevin S; Salama, Paul; Delp, Edward J

    2014-01-01

    Intravital microscopy is a uniquely powerful tool, providing the ability to characterize cell and organ physiology in the natural context of the intact, living animal. With the recent development of high-resolution microscopy techniques such as confocal and multiphoton microscopy, intravital microscopy can now characterize structures at subcellular resolution and capture events at sub-second temporal resolution. However, realizing the potential for high resolution requires remarkable stability in the tissue. Whereas the rigid structure of the skull facilitates high-resolution imaging of the brain, organs of the viscera are free to move with respiration and heartbeat, requiring additional apparatus for immobilization. In our experience, these methods are variably effective, so that many studies are compromised by residual motion artifacts. Here we demonstrate the use of IMART, a software tool for removing motion artifacts from intravital microscopy images collected in time series or in three dimensions. PMID:26090271

  9. 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

  10. 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.

  11. Higher-order continuation for the determination of robot workspace boundaries

    NASA Astrophysics Data System (ADS)

    Hentz, Gauthier; Charpentier, Isabelle; Renaud, Pierre

    2016-02-01

    In the medical and surgical fields, robotics may be of great interest for safer and more accurate procedures. Space constraints for a robotic assistant are however strict. Therefore, roboticists study non-conventional mechanisms with advantageous size/workspace ratios. The determination of mechanism workspace, and primarily its boundaries, is thus of major importance. This Note builds on boundary equation definition, continuation and automatic differentiation to propose a general, accurate, fast and automated method for the determination of mechanism workspace. The method is illustrated with a planar RRR mechanism and a three-dimensional Orthoglide parallel mechanism.

  12. 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

  13. 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.

  14. AnaSP: a software suite for automatic image analysis of multicellular spheroids.

    PubMed

    Piccinini, Filippo

    2015-04-01

    Today, more and more biological laboratories use 3D cell cultures and tissues grown in vitro as a 3D model of in vivo tumours and metastases. In the last decades, it has been extensively established that multicellular spheroids represent an efficient model to validate effects of drugs and treatments for human care applications. However, a lack of methods for quantitative analysis limits the usage of spheroids as models for routine experiments. Several methods have been proposed in literature to perform high throughput experiments employing spheroids by automatically computing different morphological parameters, such as diameter, volume and sphericity. Nevertheless, these systems are typically grounded on expensive automated technologies, that make the suggested solutions affordable only for a limited subset of laboratories, frequently performing high content screening analysis. In this work we propose AnaSP, an open source software suitable for automatically estimating several morphological parameters of spheroids, by simply analyzing brightfield images acquired with a standard widefield microscope, also not endowed with a motorized stage. The experiments performed proved sensitivity and precision of the segmentation method proposed, and excellent reliability of AnaSP to compute several morphological parameters of spheroids imaged in different conditions. AnaSP is distributed as an open source software tool. Its modular architecture and graphical user interface make it attractive also for researchers who do not work in areas of computer vision and suitable for both high content screenings and occasional spheroid-based experiments. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  15. HARPS-N: software path from the observation block to the image

    NASA Astrophysics Data System (ADS)

    Sosnowska, D.; Lodi, M.; Gao, X.; Buchschacher, N.; Vick, A.; Guerra, J.; Gonzalez, M.; Kelly, D.; Lovis, C.; Pepe, F.; Molinari, E.; Cameron, A. C.; Latham, D.; Udry, S.

    2012-09-01

    HARPS North is the twin of the HARPS (High Accuracy Radial velocity for Planetary Search) spectrograph operating in La Silla (Chile) recently installed on the TNG in La Palma observatory and used to follow-up, the "hot" candidates delivered by the Kepler satellite. HARPS-N is delivered with its own software that completely integrates with the TNG control system. A special care has been dedicated to develop tools that will assist the astronomers during the whole process of taking images: from the observation schedule to the raw image acquisition. All these tools are presented in the paper. In order to provide a stable and reliable system, the software has been developed keeping in mind concepts like failover and high-availability. HARPS-N is made of heterogeneous systems, from normal computer to real-time systems, that's why the standard message queue middleware (ActiveMQ) was chosen to provide the communications between different processes. The path of operations starting with the Observation Blocks and ending with the FITS frames is fully automated and could allow, in the future, the completely remote observing runs optimized for the time and quality constraints.

  16. A medical software system for volumetric analysis of cerebral pathologies in magnetic resonance imaging (MRI) data.

    PubMed

    Egger, Jan; Kappus, Christoph; Freisleben, Bernd; Nimsky, Christopher

    2012-08-01

    In this contribution, a medical software system for volumetric analysis of different cerebral pathologies in magnetic resonance imaging (MRI) data is presented. The software system is based on a semi-automatic segmentation algorithm and helps to overcome the time-consuming process of volume determination during monitoring of a patient. After imaging, the parameter settings-including a seed point-are set up in the system and an automatic segmentation is performed by a novel graph-based approach. Manually reviewing the result leads to reseeding, adding seed points or an automatic surface mesh generation. The mesh is saved for monitoring the patient and for comparisons with follow-up scans. Based on the mesh, the system performs a voxelization and volume calculation, which leads to diagnosis and therefore further treatment decisions. The overall system has been tested with different cerebral pathologies-glioblastoma multiforme, pituitary adenomas and cerebral aneurysms- and evaluated against manual expert segmentations using the Dice Similarity Coefficient (DSC). Additionally, intra-physician segmentations have been performed to provide a quality measure for the presented system.

  17. ASAP (Automatic Software for ASL Processing): A toolbox for processing Arterial Spin Labeling images.

    PubMed

    Mato Abad, Virginia; García-Polo, Pablo; O'Daly, Owen; Hernández-Tamames, Juan Antonio; Zelaya, Fernando

    2016-04-01

    The method of Arterial Spin Labeling (ASL) has experienced a significant rise in its application to functional imaging, since it is the only technique capable of measuring blood perfusion in a truly non-invasive manner. Currently, there are no commercial packages for processing ASL data and there is no recognized standard for normalizing ASL data to a common frame of reference. This work describes a new Automated Software for ASL Processing (ASAP) that can automatically process several ASL datasets. ASAP includes functions for all stages of image pre-processing: quantification, skull-stripping, co-registration, partial volume correction and normalization. To assess the applicability and validity of the toolbox, this work shows its application in the study of hypoperfusion in a sample of healthy subjects at risk of progressing to Alzheimer's disease. ASAP requires limited user intervention, minimizing the possibility of random and systematic errors, and produces cerebral blood flow maps that are ready for statistical group analysis. The software is easy to operate and results in excellent quality of spatial normalization. The results found in this evaluation study are consistent with previous studies that find decreased perfusion in Alzheimer's patients in similar regions and demonstrate the applicability of ASAP. Copyright © 2015 Elsevier Inc. All rights reserved.

  18. Optimising MR perfusion imaging: comparison of different software-based approaches in acute ischaemic stroke.

    PubMed

    Schaafs, Lars-Arne; Porter, David; Audebert, Heinrich J; Fiebach, Jochen B; Villringer, Kersten

    2016-11-01

    Perfusion imaging (PI) is susceptible to confounding factors such as motion artefacts as well as delay and dispersion (D/D). We evaluate the influence of different post-processing algorithms on hypoperfusion assessment in PI analysis software packages to improve the clinical accuracy of stroke PI. Fifty patients with acute ischaemic stroke underwent MRI imaging in the first 24 h after onset. Diverging approaches to motion and D/D correction were applied. The calculated MTT and CBF perfusion maps were assessed by volumetry of lesions and tested for agreement with a standard approach and with the final lesion volume (FLV) on day 6 in patients with persisting vessel occlusion. MTT map lesion volumes were significantly smaller throughout the software packages with correction of motion and D/D when compared to the commonly used approach with no correction (p = 0.001-0.022). Volumes on CBF maps did not differ significantly (p = 0.207-0.925). All packages with advanced post-processing algorithms showed a high level of agreement with FLV (ICC = 0.704-0.879). Correction of D/D had a significant influence on estimated lesion volumes and leads to significantly smaller lesion volumes on MTT maps. This may improve patient selection. • Assessment on hypoperfusion using advanced post-processing with correction for motion and D/D. • CBF appears to be more robust regarding differences in post-processing. • Tissue at risk is estimated more accurately by correcting software algorithms. • Advanced post-processing algorithms show a higher agreement with the final lesion volume.

  19. An open-source software tool for the generation of relaxation time maps in magnetic resonance imaging.

    PubMed

    Messroghli, Daniel R; Rudolph, Andre; Abdel-Aty, Hassan; Wassmuth, Ralf; Kühne, Titus; Dietz, Rainer; Schulz-Menger, Jeanette

    2010-07-30

    In magnetic resonance (MR) imaging, T1, T2 and T2* relaxation times represent characteristic tissue properties that can be quantified with the help of specific imaging strategies. While there are basic software tools for specific pulse sequences, until now there is no universal software program available to automate pixel-wise mapping of relaxation times from various types of images or MR systems. Such a software program would allow researchers to test and compare new imaging strategies and thus would significantly facilitate research in the area of quantitative tissue characterization. After defining requirements for a universal MR mapping tool, a software program named MRmap was created using a high-level graphics language. Additional features include a manual registration tool for source images with motion artifacts and a tabular DICOM viewer to examine pulse sequence parameters. MRmap was successfully tested on three different computer platforms with image data from three different MR system manufacturers and five different sorts of pulse sequences: multi-image inversion recovery T1; Look-Locker/TOMROP T1; modified Look-Locker (MOLLI) T1; single-echo T2/T2*; and multi-echo T2/T2*. Computing times varied between 2 and 113 seconds. Estimates of relaxation times compared favorably to those obtained from non-automated curve fitting. Completed maps were exported in DICOM format and could be read in standard software packages used for analysis of clinical and research MR data. MRmap is a flexible cross-platform research tool that enables accurate mapping of relaxation times from various pulse sequences. The software allows researchers to optimize quantitative MR strategies in a manufacturer-independent fashion. The program and its source code were made available as open-source software on the internet.

  20. ImFCS: a software for imaging FCS data analysis and visualization.

    PubMed

    Sankaran, Jagadish; Shi, Xianke; Ho, Liang Yoong; Stelzer, Ernst H K; Wohland, Thorsten

    2010-12-06

    The multiplexing of fluorescence correlation spectroscopy (FCS), especially in imaging FCS using fast, sensitive array detectors, requires the handling of large amounts of data. One can easily collect in excess of 100,000 FCS curves a day, too many to be treated manually. Therefore, ImFCS, an open-source software which relies on standard image files was developed and provides a wide range of options for the calculation of spatial and temporal auto- and cross-correlations, as well as differences in Cross-Correlation Functions (ΔCCF). ImFCS permits fitting of standard models to correlation functions and provides optimized histograms of fitted parameters. Applications include the measurement of diffusion and flow with Imaging Total Internal Reflection FCS (ITIR-FCS) and Single Plane Illumination Microscopy FCS (SPIM-FCS) in biologically relevant samples. As a compromise between ITIR-FCS and SPIM-FCS, we extend the applications to Imaging Variable Angle-FCS (IVA-FCS) where sub-critical oblique illumination provides sample sectioning close to the cover slide.

  1. 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.

  2. 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

  3. 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.

  4. Software-based approach toward vendor independent real-time photoacoustic imaging using ultrasound beamformed data

    NASA Astrophysics Data System (ADS)

    Zhang, Haichong K.; Huang, Howard; Lei, Chen; Kim, Younsu; Boctor, Emad M.

    2017-03-01

    Photoacoustic (PA) imaging has shown its potential for many clinical applications, but current research and usage of PA imaging are constrained by additional hardware costs to collect channel data, as the PA signals are incorrectly processed in existing clinical ultrasound systems. This problem arises from the fact that ultrasound systems beamform the PA signals as echoes from the ultrasound transducer instead of directly from illuminated sources. Consequently, conventional implementations of PA imaging rely on parallel channel acquisition from research platforms, which are not only slow and expensive, but are also mostly not approved by the FDA for clinical use. In previous studies, we have proposed the synthetic-aperture based photoacoustic re-beamformer (SPARE) that uses ultrasound beamformed radio frequency (RF) data as the input, which is readily available in clinical ultrasound scanners. The goal of this work is to implement the SPARE beamformer in a clinical ultrasound system, and to experimentally demonstrate its real-time visualization. Assuming a high pulsed repetition frequency (PRF) laser is used, a PZT-based pseudo PA source transmission was synchronized with the ultrasound line trigger. As a result, the frame-rate increases when limiting the image field-of-view (FOV), with 50 to 20 frames per second achieved for FOVs from 35 mm to 70 mm depth, respectively. Although in reality the maximum PRF of laser firing limits the PA image frame rate, this result indicates that the developed software is capable of displaying PA images with the maximum possible frame-rate for certain laser system without acquiring channel data.

  5. Assessment of global longitudinal strain using standardized myocardial deformation imaging: a modality independent software approach.

    PubMed

    Riffel, Johannes H; Keller, Marius G P; Aurich, Matthias; Sander, Yannick; Andre, Florian; Giusca, Sorin; Aus dem Siepen, Fabian; Seitz, Sebastian; Galuschky, Christian; Korosoglou, Grigorios; Mereles, Derliz; Katus, Hugo A; Buss, Sebastian J

    2015-07-01

    Myocardial deformation measurement is superior to left ventricular ejection fraction in identifying early changes in myocardial contractility and prediction of cardiovascular outcome. The lack of standardization hinders its clinical implementation. The aim of the study is to investigate a novel standardized deformation imaging approach based on the feature tracking algorithm for the assessment of global longitudinal (GLS) and global circumferential strain (GCS) in echocardiography and cardiac magnetic resonance imaging (CMR). 70 subjects undergoing CMR were consecutively investigated with echocardiography within a median time of 30 min. GLS and GCS were analyzed with a post-processing software incorporating the same standardized algorithm for both modalities. Global strain was defined as the relative shortening of the whole endocardial contour length and calculated according to the strain formula. Mean GLS values were -16.2 ± 5.3 and -17.3 ± 5.3 % for echocardiography and CMR, respectively. GLS did not differ significantly between the two imaging modalities, which showed strong correlation (r = 0.86), a small bias (-1.1 %) and narrow 95 % limits of agreement (LOA ± 5.4 %). Mean GCS values were -17.9 ± 6.3 and -24.4 ± 7.8 % for echocardiography and CMR, respectively. GCS was significantly underestimated by echocardiography (p < 0.001). A weaker correlation (r = 0.73), a higher bias (-6.5 %) and wider LOA (± 10.5 %) were observed for GCS. GLS showed a strong correlation (r = 0.92) when image quality was good, while correlation dropped to r = 0.82 with poor acoustic windows in echocardiography. GCS assessment revealed only a strong correlation (r = 0.87) when echocardiographic image quality was good. No significant differences for GLS between two different echocardiographic vendors could be detected. Quantitative assessment of GLS using a standardized software algorithm allows the direct comparison of values acquired irrespective of the imaging modality. GLS may

  6. Using interactive software to teach image-based clinical laboratory tests in developing countries: a pilot trial in Nepal.

    PubMed

    Mallapaty, Gabriele; Kim, Sara; Astion, Michael L

    2003-05-01

    This study explores the feasibility of using computer tutorials to train laboratory personnel in Nepal. Training incorporated three software programs that teach microscope-based laboratory tests (peripheral blood smears, urinalysis, Gram stains). Forty-seven participants attended training sessions and completed a questionnaire. The participants' overall perception was: 1) the software was superior to formal lectures for learning image-based laboratory tests (43 participants, 92%); 2) the software would enhance job performance (43 participants, 92%); 3) more subjects should be taught using software (40 participants, 85%); and 4) the software helped participants learn new materials (38 participants, 81%). Considering that 79% of the participants were novice computer users, it is noteworthy that 38 (81%) participants thought the method of instruction was easy to understand. Factors contributing to learning included: 1) the resemblance of the computer images to actual microscope images derived from patient samples (37 participants, 68%); 2) the use of multiple examples of cells and other microscopic structures (28 participants, 60%); 3) the ability to interact with images and animations (23 participants, 49%); 4) the step-by-step explanation of laboratory techniques (21 participants, 45%); and 5) the self-pacing of the tutorial (12 participants, 26%). Overall, the pilot study suggests that educational software could help train clinical laboratory personnel in developing countries.

  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. An open source software for analysis of dynamic contrast enhanced magnetic resonance images: UMMPerfusion revisited.

    PubMed

    Zöllner, Frank G; Daab, Markus; Sourbron, Steven P; Schad, Lothar R; Schoenberg, Stefan O; Weisser, Gerald

    2016-01-14

    Perfusion imaging has become an important image based tool to derive the physiological information in various applications, like tumor diagnostics and therapy, stroke, (cardio-) vascular diseases, or functional assessment of organs. However, even after 20 years of intense research in this field, perfusion imaging still remains a research tool without a broad clinical usage. One problem is the lack of standardization in technical aspects which have to be considered for successful quantitative evaluation; the second problem is a lack of tools that allow a direct integration into the diagnostic workflow in radiology. Five compartment models, namely, a one compartment model (1CP), a two compartment exchange (2CXM), a two compartment uptake model (2CUM), a two compartment filtration model (2FM) and eventually the extended Toft's model (ETM) were implemented as plugin for the DICOM workstation OsiriX. Moreover, the plugin has a clean graphical user interface and provides means for quality management during the perfusion data analysis. Based on reference test data, the implementation was validated against a reference implementation. No differences were found in the calculated parameters. We developed open source software to analyse DCE-MRI perfusion data. The software is designed as plugin for the DICOM Workstation OsiriX. It features a clean GUI and provides a simple workflow for data analysis while it could also be seen as a toolbox providing an implementation of several recent compartment models to be applied in research tasks. Integration into the infrastructure of a radiology department is given via OsiriX. Results can be saved automatically and reports generated automatically during data analysis ensure certain quality control.

  9. BAMS2 Workspace: a comprehensive and versatile neuroinformatic platform for collating and processing neuroanatomical connections

    PubMed Central

    Bota, Mihail; Talpalaru, Ştefan; Hintiryan, Houri; Dong, Hong-Wei; Swanson, Larry W.

    2014-01-01

    We present in this paper a novel neuroinformatic platform, the BAMS2 Workspace (http://brancusi1.usc.edu), designed for storing and processing information about gray matter region axonal connections. This de novo constructed module allows registered users to directly collate their data by using a simple and versatile visual interface. It also allows construction and analysis of sets of connections associated with gray matter region nomenclatures from any designated species. The Workspace includes a set of tools allowing the display of data in matrix and networks formats, and the uploading of processed information in visual, PDF, CSV, and Excel formats. Finally, the Workspace can be accessed anonymously by third party systems to create individualized connectivity networks. All features of the BAMS2 Workspace are described in detail, and are demonstrated with connectivity reports collated in BAMS and associated with the rat sensory-motor cortex, medial frontal cortex, and amygdalar regions. PMID:24668342

  10. A collaborative resource management workspace and project management application for data collection, analysis and visualization: OpenNRM

    NASA Astrophysics Data System (ADS)

    Osti, A.

    2013-12-01

    During the process of research and design for OpenNRM, we imagined a place where diverse groups of people and communities could effectively and efficiently collaborate to manage large-scale environmental problems and projects. Our research revealed the need to combine a variety of software components. Users can explore and analyze a topic while simultaneously develop stories and solve problems in a way that the end result is consumable by their colleagues and the general public. To do this we brought together software modules that are typically separate: Document and Asset Management, GIS and Interactive Mapping, WIKI and Information Libraries, Data Catalogs and Services, Project Management Tools and Storytelling templates. These components, along with others are supported by extensive data catalogs (NWIS, Storet, CDEC, Cuahsi), data analysis tools and web services for a turn-key workspace that will allow you to quickly build project communities and data stories. In this presentation we will show you how our investigation into these collaborative efforts are implemented and working for some of our clients, including the State of California's Sacramento San Joaquin Bay-Delta and San Joaquin River Basin. The case study will display the use of the OpenNRM workspace for real time environmental conditions management, data visualization, project operations, environmental restoration, high frequency monitoring and data reporting. We will demonstrate how scientists and policy makers are working together to tell the story of this complicated and divisive system and how they are becoming better managers of that system. Using the genius of web services, we will show you how OpenNRM was designed to allow you to build your own community while easily sharing data stories, project data, monitoring results, document libraries, interactive maps and datasets with others. We will get into more technical detail by presenting how our data interpolation tools can show high frequency

  11. 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.

  12. 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. © 2013 The Authors. BJU International © 2013 BJU International.

  13. A Method to Determine an Organization’s Compatibility with Hybrid Workspaces

    DTIC Science & Technology

    2014-03-27

    tasks. However, hybrid workspaces are still an emerging concept and represent a radical departure from traditional workplace setups. Current use of...the speed of communication in the workplace , the physical layout of the workplace is still centered around the traditional concept of assigning...this freedom may lead to failure. One of the oldest examples of a workplace centered around hybrid workspace concepts , constructed in the 1940s

  14. 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

  15. 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

  16. 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.

  17. Optimal design of a 3-leg 6-DOF parallel manipulator for a specific workspace

    NASA Astrophysics Data System (ADS)

    Fu, Jianxun; Gao, Feng

    2016-07-01

    Researchers seldom study optimum design of a six-degree-of-freedom(DOF) parallel manipulator with three legs based upon the given workspace. An optimal design method of a novel three-leg six-DOF parallel manipulator(TLPM) is presented. The mechanical structure of this robot is introduced, with this structure the kinematic constrain equations is decoupled. Analytical solutions of the forward kinematics are worked out, one configuration of this robot, including position and orientation of the end-effector are graphically displayed. Then, on the basis of several extreme positions of the kinematic performances, the task workspace is given. An algorithm of optimal designing is introduced to find the smallest dimensional parameters of the proposed robot. Examples illustrate the design results, and a design stability index is introduced, which ensures that the robot remains a safe distance from the boundary of sits actual workspace. Finally, one prototype of the robot is developed based on this method. This method can easily find appropriate kinematic parameters that can size a robot having the smallest workspace enclosing a predefined task workspace. It improves the design efficiency, ensures that the robot has a small mechanical size possesses a large given workspace volume, and meets the lightweight design requirements.

  18. Upper extremity 3D reachable workspace analysis in dystrophinopathy using Kinect

    PubMed Central

    Han, Jay J.; Kurillo, Gregorij; Abresch, Richard T.; de Bie, Evan; Nicorici, Alina; Bajcsy, Ruzena

    2015-01-01

    Introduction An innovative upper extremity 3D reachable workspace outcome measure acquired using Kinect sensor is applied towards Duchenne/Becker muscular dystrophy (DMD/BMD). The validity, sensitivity, and clinical meaningfulness of the novel outcome is examined. Methods Upper extremity function assessment (Brooke scale, NeuroQOL questionnaire) and Kinect-based reachable workspace analyses were conducted in 43 individuals with dystrophinopathy (30-DMD, 13-BMD; ages 7–60) and 46 controls (ages 6–68). Results The reachable workspace measure reliably captured a wide-range of upper extremity impairments encountered in both pediatric and adult, as well as ambulatory and non-ambulatory individuals with dystrophinopathy. Reduced reachable workspaces were noted for the dystrophinopathy cohort compared to controls, and they correlated with Brooke grades. Additionally, progressive reduction in reachable workspace directly correlated with worsening ability to perform activities of daily living, as self-reported on the NeuroQOL. Discussion This study demonstrates the utility and potential of the novel sensor-acquired reachable workspace outcome measure in dystrophinopathy. PMID:25597487

  19. 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

  20. 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.

  1. Dose imaging with gel-dosemeter layers: optical analysis and dedicated software.

    PubMed

    Gambarini, G; Carrara, M; Gay, S; Tomatis, S

    2006-01-01

    In radiotherapy involving thermal and epithermal neutrons, the knowledge of dose distributions, with separation of the contribution of each secondary radiation component, is of utmost importance. Layers of Fricke-Xylenol-Orange-infused gel dosemeters give the possibility of achieving such requirements because, owing to the layer-geometry, enriching or depleting the gel matrix of suitable isotopes does not sensibly alter neutron transport. The dosimetry method has been critically re-examined with the aim of improving its suitability to boron neutron capture therapy (BNCT) requirements, as it applies to the protocol of measurement and analysis, the sensitivity of the method and the range of the linearity of the dosemeters. Software has been developed and studied to obtain automatically the images of the various dose components with the established separation procedure.

  2. 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.

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. Measuring the Pain Area: An Intra- and Inter-Rater Reliability Study Using Image Analysis Software.

    PubMed

    Dos Reis, Felipe Jose Jandre; de Barros E Silva, Veronica; de Lucena, Raphaela Nunes; Mendes Cardoso, Bruno Alexandre; Nogueira, Leandro Calazans

    2016-01-01

    Pain drawings have frequently been used for clinical information and research. The aim of this study was to investigate intra- and inter-rater reliability of area measurements performed on pain drawings. Our secondary objective was to verify the reliability when using computers with different screen sizes, both with and without mouse hardware. Pain drawings were completed by patients with chronic neck pain or neck-shoulder-arm pain. Four independent examiners participated in the study. Examiners A and B used the same computer with a 16-inch screen and wired mouse hardware. Examiner C used a notebook with a 16-inch screen and no mouse hardware, and Examiner D used a computer with an 11.6-inch screen and a wireless mouse. Image measurements were obtained using GIMP and NIH ImageJ computer programs. The length of all the images was measured using GIMP software to a set scale in ImageJ. Thus, each marked area was encircled and the total surface area (cm(2) ) was calculated for each pain drawing measurement. A total of 117 areas were identified and 52 pain drawings were analyzed. The intrarater reliability between all examiners was high (ICC = 0.989). The inter-rater reliability was also high. No significant differences were observed when using different screen sizes or when using or not using the mouse hardware. This suggests that the precision of these measurements is acceptable for the use of this method as a measurement tool in clinical practice and research. © 2014 World Institute of Pain.

  9. 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.

  10. Real-time telemedicine using shared three-dimensional workspaces over ATM

    NASA Astrophysics Data System (ADS)

    Cahoon, Peter; Forsey, David R.; Hutchison, Susan

    1999-03-01

    During the past five years a high speed ATM network has been developed at UBC that provides a campus testbed, a local testbed to the hospitals, and a National testbed between here and the BADLAB in Ottawa. This testbed has been developed to combine a commercial shared audio/video/whiteboard environment coupled with a shared interactive 3-dimensional solid model. This solid model ranges from a skull reconstructed from a CT scan with muscles and an overlying skin, to a model of the ventricle system of the human brain. Typical interactions among surgeon, radiologist and modeler consist of having image slices of the original scan shared by all and the ability to adjust the surface of the model to conform to each individuals perception of what the final object should look like. The purpose of this interaction can range from forensic reconstruction from partial remains to pre-maxillofacial surgery. A joint project with the forensic unit of the R.C.M.P. in Ottawa using the BADLAB is now in the stages of testing this methodology on a real case beginning with a CT scan of partial remains. A second study underway with the department of Maxiofacial reconstruction at Dalhousie University in Halifax Nova Scotia and concerns a subject who is about to undergo orthognathic surgery, in particular a mandibular advancement. This subject has been MRI scanned, a solid model constructed of the mandible and the virtual surgery constructed on the model. This model and the procedure have been discussed and modified by the modeler and the maxillofacial specialist using these shared workspaces. The procedure will be repeated after the actual surgery to verify the modeled procedure. The advantage of this technique is that none of the specialists need be in the same room, or city. Given the scarcity of time and specialists this methodology shows great promise. In November of this last year a shared live demonstration of this facial modeler was done between Vancouver and Dalhousie University in

  11. Digital map and situation surface: a team-oriented multidisplay workspace for network enabled situation analysis

    NASA Astrophysics Data System (ADS)

    Peinsipp-Byma, E.; Geisler, Jürgen; Bader, Thomas

    2009-05-01

    System concepts for network enabled image-based ISR (intelligence, surveillance, reconnaissance) is the major mission of Fraunhofer IITB's applied research in the area of defence and security solutions. For the TechDemo08 as part of the NATO CNAD POW Defence against terrorism Fraunhofer IITB advanced a new multi display concept to handle the shear amount and high complexity of ISR data acquired by networked, distributed surveillance systems with the objective to support the generation of a common situation picture. Amount and Complexity of ISR data demands an innovative man-machine interface concept for humans to deal with it. The IITB's concept is the Digital Map & Situation Surface. This concept offers to the user a coherent multi display environment combining a horizontal surface for the situation overview from the bird's eye view, an attached vertical display for collateral information and so-called foveatablets as personalized magic lenses in order to obtain high resolved and role-specific information about a focused areaof- interest and to interact with it. In the context of TechDemo08 the Digital Map & Situation Surface served as workspace for team-based situation visualization and analysis. Multiple sea- and landside surveillance components were connected to the system.

  12. Global workspace theory of consciousness: toward a cognitive neuroscience of human experience.

    PubMed

    Baars, Bernard J

    2005-01-01

    Global workspace (GW) theory emerged from the cognitive architecture tradition in cognitive science. Newell and co-workers were the first to show the utility of a GW or "blackboard" architecture in a distributed set of knowledge sources, which could cooperatively solve problems that no single constituent could solve alone. The empirical connection with conscious cognition was made by Baars (1988, 2002). GW theory generates explicit predictions for conscious aspects of perception, emotion, motivation, learning, working memory, voluntary control, and self systems in the brain. It has similarities to biological theories such as Neural Darwinism and dynamical theories of brain functioning. Functional brain imaging now shows that conscious cognition is distinctively associated with wide spread of cortical activity, notably toward frontoparietal and medial temporal regions. Unconscious comparison conditions tend to activate only local regions, such as visual projection areas. Frontoparietal hypometabolism is also implicated in unconscious states, including deep sleep, coma, vegetative states, epileptic loss of consciousness, and general anesthesia. These findings are consistent with the GW hypothesis, which is now favored by a number of scientists and philosophers.

  13. 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.

  14. Xmipp 3.0: an improved software suite for image processing in electron microscopy.

    PubMed

    de la Rosa-Trevín, J M; Otón, J; Marabini, R; Zaldívar, A; Vargas, J; Carazo, J M; Sorzano, C O S

    2013-11-01

    Xmipp is a specialized software package for image processing in electron microscopy, and that is mainly focused on 3D reconstruction of macromolecules through single-particles analysis. In this article we present Xmipp 3.0, a major release which introduces several improvements and new developments over the previous version. A central improvement is the concept of a project that stores the entire processing workflow from data import to final results. It is now possible to monitor, reproduce and restart all computing tasks as well as graphically explore the complete set of interrelated tasks associated to a given project. Other graphical tools have also been improved such as data visualization, particle picking and parameter "wizards" that allow the visual selection of some key parameters. Many standard image formats are transparently supported for input/output from all programs. Additionally, results have been standardized, facilitating the interoperation between different Xmipp programs. Finally, as a result of a large code refactoring, the underlying C++ libraries are better suited for future developments and all code has been optimized. Xmipp is an open-source package that is freely available for download from: http://xmipp.cnb.csic.es. Copyright © 2013 Elsevier Inc. All rights reserved.

  15. Development of imaging mass spectrometry (IMS) dataset extractor software, IMS convolution.

    PubMed

    Hayasaka, Takahiro; Goto-Inoue, Naoko; Ushijima, Masaru; Yao, Ikuko; Yuba-Kubo, Akiko; Wakui, Masatoshi; Kajihara, Shigeki; Matsuura, Masaaki; Setou, Mitsutoshi

    2011-07-01

    Imaging mass spectrometry (IMS) is a powerful tool for detecting and visualizing biomolecules in tissue sections. The technology has been applied to several fields, and many researchers have started to apply it to pathological samples. However, it is very difficult for inexperienced users to extract meaningful signals from enormous IMS datasets, and the procedure is time-consuming. We have developed software, called IMS Convolution with regions of interest (ROI), to automatically extract meaningful signals from IMS datasets. The processing is based on the detection of common peaks within the ordered area in the IMS dataset. In this study, the IMS dataset from a mouse eyeball section was acquired by a mass microscope that we recently developed, and the peaks extracted by manual and automatic procedures were compared. The manual procedure extracted 16 peaks with higher intensity in mass spectra averaged in whole measurement points. On the other hand, the automatic procedure using IMS Convolution easily and equally extracted peaks without any effort. Moreover, the use of ROIs with IMS Convolution enabled us to extract the peak on each ROI area, and all of the 16 ion images on mouse eyeball tissue were from phosphatidylcholine species. Therefore, we believe that IMS Convolution with ROIs could automatically extract the meaningful peaks from large-volume IMS datasets for inexperienced users as well as for researchers who have performed the analysis.

  16. A Monte Carlo software bench for simulation of spectral k-edge CT imaging: Initial results.

    PubMed

    Nasirudin, Radin A; Penchev, Petar; Mei, Kai; Rummeny, Ernst J; Fiebich, Martin; Noël, Peter B

    2015-06-01

    Spectral Computed Tomography (SCT) systems equipped with photon counting detectors (PCD) are clinically desired, since such systems provide not only additional diagnostic information but also radiation dose reductions by a factor of two or more. The current unavailability of clinical PCDs makes a simulation of such systems necessary. In this paper, we present a Monte Carlo-based simulation of a SCT equipped with a PCD. The aim of this development is to facilitate research on potential clinical applications. Our MC simulator takes into account scattering interactions within the scanned object and has the ability to simulate scans with and without scatter and a wide variety of imaging parameters. To demonstrate the usefulness of such a MC simulator for development of SCT applications, a phantom with contrast targets covering a wide range of clinically significant iodine concentrations is simulated. With those simulations the impact of scatter and exposure on image quality and material decomposition results is investigated. Our results illustrate that scatter radiation plays a significant role in visual as well as quantitative results. Scatter radiation can reduce the accuracy of contrast agent concentration by up to 15%. We present a reliable and robust software bench for simulation of SCTs equipped with PCDs. Copyright © 2015 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  17. Pluri-IQ: Quantification of Embryonic Stem Cell Pluripotency through an Image-Based Analysis Software.

    PubMed

    Perestrelo, Tânia; Chen, Weitong; Correia, Marcelo; Le, Christopher; Pereira, Sandro; Rodrigues, Ana S; Sousa, Maria I; Ramalho-Santos, João; Wirtz, Denis

    2017-08-08

    Image-based assays, such as alkaline phosphatase staining or immunocytochemistry for pluripotent markers, are common methods used in the stem cell field to assess pluripotency. Although an increased number of image-analysis approaches have been described, there is still a lack of software availability to automatically quantify pluripotency in large images after pluripotency staining. To address this need, we developed a robust and rapid image processing software, Pluri-IQ, which allows the automatic evaluation of pluripotency in large low-magnification images. Using mouse embryonic stem cells (mESC) as a model, we combined an automated segmentation algorithm with a supervised machine-learning platform to classify colonies as pluripotent, mixed, or differentiated. In addition, Pluri-IQ allows the automatic comparison between different culture conditions. This efficient user-friendly open-source software can be easily implemented in images derived from pluripotent cells or cells that express pluripotent markers (e.g., OCT4-GFP) and can be routinely used, decreasing image assessment bias. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

  18. Position, singularity and workspace analysis of 3-PSR-O spatial parallel manipulator

    NASA Astrophysics Data System (ADS)

    Shao, Jiejie; Chen, Wenyu; Fu, Xin

    2015-04-01

    Although the parallel mechanisms have the advantages of high accuracy, velocity, stiffness, and payload capacity, the shortcomings of the space utilization and workspace limit the applications in the confined space. A novel 3 degrees of freedom spatial parallel manipulator 3-PSR-O (prismatic-spherical-revolute) is proposed, which possesses a compact architecture and extended workspace while maintaining the inherent advantages of the parallel mechanisms. The direct-inverse position, singularity and workspace are investigated. The mapping method is adopted in the position analysis, and the closed form solution is derived in the form of a six order equation. The singularity analysis of the mechanism is also carried out based on the geometrical constraints, including six singularity boundaries. A feature boundary, which is independent of the prismatic joints' stroke limit, is obtained by integrating the six singularity boundaries. According to the formation of the reachable workspace, a concept of basic workspace is also introduced and presented in the analytical way. By demarcating the basic workspace along the central height with the feature boundary, the reachable workspace can be derived and analyzed more efficiently. Finally, a comparative study on the space utilization between the 3-PSP parallel mechanism and the new mechanism is also presented. The area of feature boundary of the new mechanism is about 140% of the 3-PSP parallel mechanism, while its installation radius is only 1/2 of the 3-PSP parallel mechanism. The proposed parallel mechanism shows great space utilization, and is ideally suited for applications in confined space occasions such as immersion lithography, nano-imprint etc.

  19. 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.

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

    PubMed

    Czekierda, Łukasz; Malawski, Filip; Wyszkowski, Przemysław

    2015-10-01

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

  1. Looking to 2050: The USGS Integrated Software for Imagers and Spectrometers (ISIS)

    NASA Astrophysics Data System (ADS)

    Becker, T. L.; Edmundson, K. L.; Sides, S.; Hare, T. M.; Laura, J. R.

    2017-02-01

    Astrogeology Science Center develops and maintains software (ISIS) in support of planetary data for a diverse set of missions. We plan to provide support through the future while adapting to changes in hardware, software, and science requirements.

  2. 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.

  3. Accuracy and feasibility of three different methods for software-based image fusion in whole-body PET and CT.

    PubMed

    Putzer, Daniel; Henninger, Benjamin; Kovacs, Peter; Uprimny, Christian; Kendler, Dorota; Jaschke, Werner; Bale, Reto J

    2016-06-01

    Even as PET/CT provides valuable diagnostic information in a great number of clinical indications, availability of hybrid PET/CT scanners is mainly limited to clinical centers. A software-based image fusion would facilitate combined image reading of CT and PET data sets if hardware image fusion is not available. To analyze the relevance of retrospective image fusion of separately acquired PET and CT data sets, we studied the accuracy, practicability and reproducibility of three different image registration techniques. We evaluated whole-body 18F-FDG-PET and CT data sets of 71 oncologic patients. Images were fused retrospectively using Stealth Station System, Treon (Medtronic Inc., Louisville, CO, USA) equipped with Cranial4 Software. External markers fixed to a vacuum mattress were used as reference for exact repositioning. Registration was repeated using internal anatomic landmarks and Automerge software, assessing accuracy for all three methods, measuring distances of liver representation in CT and PET with reference to a common coordinate system. On first measurement of image fusions with external markers, 53 were successful, 16 feasible and 2 not successful. Using anatomic landmarks, 42 were successful, 26 feasible and 3 not successful. Using Automerge Software only 13 were successful. The mean distance between center points in PET and CT was 7.69±4.96 mm on first, and 7.65±4.2 mm on second measurement. Results with external markers correlate very well and inaccuracies are significantly lower (P<0.001) than results using anatomical landmarks (10.38±6.13 mm and 10.83±6.23 mm). Analysis revealed a significantly faster alignment using external markers (P<0.001). External fiducials in combination with immobilization devices and breathing protocols allow for highly accurate image fusion cost-effectively and significantly less time, posing an attractive alternative for PET/CT interpretation when a hybrid scanner is not available.

  4. Multislice mapping and quantification of brain perfusion MR imaging data: a comparative study of homemade and commercial software.

    PubMed

    Ariöz, Umut; Oğuz, Kader Karli; Sentürk, Senem; Cila, Ayşenur

    2005-12-01

    We developed a homemade computer program for analysis of perfusion weighted MR imaging (PW-MRI) data in order to produce colored multislice rCBV, rCBF, and MTT maps. We then compared those maps with others produced by a commercially available program, obtained from the same PW-MRI data, to determine the feasibility of using our program in clinical practice. Studies of 20 patients were performed on a high field MR scanner. Imaging protocol consisted of perfusion study (EPI, TR/TE: 1430/46 msec, 10 mm gap, matrix: 128x128, FOV: 240 cm, NEX: 1). Twenty ml of Gd-DTPA was administered at a rate of 4-5 ml/sec beginning at the 5th acquisition of 50 dynamic series. MATLAB software was used for writing codes of both mathematical equations and the graphical user interface. All images were in DICOM standard. For validation of the results, all maps were compared with another commercially available program, which is widely being used in daily practice, and was installed on the MR scanner. Ability to define the lesion contours and extension, and artifacts at the bone-soft tissue interface were the criteria used for statistical evaluation. Field definition was equally good in 38% of the patient scans for both software programs; our homemade software was better in 23% of the cases and the commercial software was better in 31%. In 6% of the results, either software program was not sufficient. For the elimination of artifacts, our homemade software was 100% successful in every case. Our homemade program is a user friendly one that gives comparable results with those of a commonly used commercial one. However, this program should be tested with different categories of diseases and a larger patient population and then compared with different commercial software programs to be validated more clearly.

  5. 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.

  6. Agreement between clinical estimation and a new quantitative analysis by Photoshop software in fundus and angiographic image variables.

    PubMed

    Ramezani, Alireza; Ahmadieh, Hamid; Azarmina, Mohsen; Soheilian, Masoud; Dehghan, Mohammad H; Mohebbi, Mohammad R

    2009-12-01

    To evaluate the validity of a new method for the quantitative analysis of fundus or angiographic images using Photoshop 7.0 (Adobe, USA) software by comparing with clinical evaluation. Four hundred and eighteen fundus and angiographic images of diabetic patients were evaluated by three retina specialists and then by computing using Photoshop 7.0 software. Four variables were selected for comparison: amount of hard exudates (HE) on color pictures, amount of HE on red-free pictures, severity of leakage, and the size of the foveal avascular zone (FAZ). The coefficient of agreement (Kappa) between the two methods in the amount of HE on color and red-free photographs were 85% (0.69) and 79% (0.59), respectively. The agreement for severity of leakage was 72% (0.46). In the two methods for the evaluation of the FAZ size using the magic and lasso software tools, the agreement was 54% (0.09) and 89% (0.77), respectively. Agreement in the estimation of the FAZ size by the lasso magnetic tool was excellent and was almost as good in the quantification of HE on color and on red-free images. Considering the agreement of this new technique for the measurement of variables in fundus images using Photoshop software with the clinical evaluation, this method seems to have sufficient validity to be used for the quantitative analysis of HE, leakage, and FAZ size on the angiograms of diabetic patients.

  7. UltraTrack: Software for semi-automated tracking of muscle fascicles in sequences of B-mode ultrasound images.

    PubMed

    Farris, Dominic James; Lichtwark, Glen A

    2016-05-01

    Dynamic measurements of human muscle fascicle length from sequences of B-mode ultrasound images have become increasingly prevalent in biomedical research. Manual digitisation of these images is time consuming and algorithms for automating the process have been developed. Here we present a freely available software implementation of a previously validated algorithm for semi-automated tracking of muscle fascicle length in dynamic ultrasound image recordings, "UltraTrack". UltraTrack implements an affine extension to an optic flow algorithm to track movement of the muscle fascicle end-points throughout dynamically recorded sequences of images. The underlying algorithm has been previously described and its reliability tested, but here we present the software implementation with features for: tracking multiple fascicles in multiple muscles simultaneously; correcting temporal drift in measurements; manually adjusting tracking results; saving and re-loading of tracking results and loading a range of file formats. Two example runs of the software are presented detailing the tracking of fascicles from several lower limb muscles during a squatting and walking activity. We have presented a software implementation of a validated fascicle-tracking algorithm and made the source code and standalone versions freely available for download. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  8. MSiReader v1.0: Evolving Open-Source Mass Spectrometry Imaging Software for Targeted and Untargeted Analyses.

    PubMed

    Bokhart, Mark T; Nazari, Milad; Garrard, Kenneth P; Muddiman, David C

    2017-09-20

    A major update to the mass spectrometry imaging (MSI) software MSiReader is presented, offering a multitude of newly added features critical to MSI analyses. MSiReader is a free, open-source, and vendor-neutral software written in the MATLAB platform and is capable of analyzing most common MSI data formats. A standalone version of the software, which does not require a MATLAB license, is also distributed. The newly incorporated data analysis features expand the utility of MSiReader beyond simple visualization of molecular distributions. The MSiQuantification tool allows researchers to calculate absolute concentrations from quantification MSI experiments exclusively through MSiReader software, significantly reducing data analysis time. An image overlay feature allows the incorporation of complementary imaging modalities to be displayed with the MSI data. A polarity filter has also been incorporated into the data loading step, allowing the facile analysis of polarity switching experiments without the need for data parsing prior to loading the data file into MSiReader. A quality assurance feature to generate a mass measurement accuracy (MMA) heatmap for an analyte of interest has also been added to allow for the investigation of MMA across the imaging experiment. Most importantly, as new features have been added performance has not degraded, in fact it has been dramatically improved. These new tools and the improvements to the performance in MSiReader v1.0 enable the MSI community to evaluate their data in greater depth and in less time. Graphical Abstract ᅟ.

  9. Software for Collaborative Use of Large Interactive Displays

    NASA Technical Reports Server (NTRS)

    Trimble, Jay; Shab, Thodore; Wales, Roxana; Vera, Alonso; Tollinger, Irene; McCurdy, Michael; Lyubimov, Dmitriy

    2006-01-01

    The MERBoard Collaborative Workspace, which is currently being deployed to support the Mars Exploration Rover (MER) Missions, is the first instantiation of a new computing architecture designed to support collaborative and group computing using computing devices situated in NASA mission operations room. It is a software system for generation of large-screen interactive displays by multiple users

  10. [The relation of workspace and installation space of epicyclic kinematics with six degrees of freedom].

    PubMed

    Pott, Peter P; Schwarz, Markus L R

    2007-10-01

    The kinematics of a robotic device significantly determines its installation space when it comes to technical realisation. With regard to the deployment of robotic manipulators in surgery, manipulators with a preferably small installation space are needed. This study describes six versions of novel epicyclic kinematics with six degrees of freedom (DOF). At first, the kinematics functionality was analysed using Gruebler's formula. Subsequently, the quantitative determination of the relation of workspace and installation space was performed using Matlab algorithms. To qualitatively describe the shape of the workspace, the Matlab visualisation features were utilised. For comparison, the well-known Hexapod was used. The assessed kinematics had 6-DOF-functionality. It became apparent that one version of the epicyclic kinematics having two 3-DOF disk systems mounted in a parallel way featured a particularly good relation of workspace and installation space. Compared to the Hexapod, this is approximately four times better. The shape of the workspaces of all epicyclic kinematics assessed was convex and compact. It could be shown that a novel epicyclic kinematics has a notably advantageous relation of workspace and installation space. Apparently, it seems to be well suited for the deployment in robotic machines for surgical procedures.

  11. Three-dimensional representation software as image enhancement tool in small-bowel capsule endoscopy: a feasibility study.

    PubMed

    Koulaouzidis, Anastasios; Karargyris, Alexandros; Rondonotti, Emanuele; Noble, Colin L; Douglas, Sarah; Alexandridis, Efstratios; Zahid, Ali M; Bathgate, Andrew J; Trimble, Ken C; Plevris, John N

    2013-11-01

    Three-dimensional imaging in capsule endoscopy is not currently feasible due to hardware limitations. However, software algorithms that enable three-dimensional reconstruction in capsule endoscopy are available. Feasibility study. A phantom was designed to test the accuracy of three-dimensional reconstruction. Thereafter, 192 small-bowel capsule endoscopy images (of vascular: 50; inflammatory: 73; protruding structures: 69) were reviewed with the aid of a purpose-built three-dimensional reconstruction software. Seven endoscopists rated visualisation improved or non-improved. Subgroup analyses performed for diagnostic category, diagnosis, image surface morphology and colour and SBCE equipment used (PillCam(®) vs. MiroCam(®)). Overall, phantom experiments showed that the three-dimensional reconstruction software was accurate at 90% of red, 70% of yellow and 45% of white phantom models. Enhanced visualisation for 56% of vascular, 23% of inflammatory and <10% of protruding structures was noted (P=0.007, 0.172 and 0.008, respectively). Furthermore, three-dimensional software application enhanced 53.7% of red, 21.8% of white, 17.3% of red and white, and 9.2% of images of lesions with colour similar to that of the surrounding mucosa, P<0.0001. Application of a three-dimensional reconstruction software in capsule endoscopy leads to image enhancement for a significant proportion of vascular, but less so for inflammatory and protruding lesions. Until optics technology allows hardware-enabled three-dimensional reconstruction, it seems a plausible alternative. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  12. Design and evaluation of a THz time domain imaging system using standard optical design software.

    PubMed

    Brückner, Claudia; Pradarutti, Boris; Müller, Ralf; Riehemann, Stefan; Notni, Gunther; Tünnermann, Andreas

    2008-09-20

    A terahertz (THz) time domain imaging system is analyzed and optimized with standard optical design software (ZEMAX). Special requirements to the illumination optics and imaging optics are presented. In the optimized system, off-axis parabolic mirrors and lenses are combined. The system has a numerical aperture of 0.4 and is diffraction limited for field points up to 4 mm and wavelengths down to 750 microm. ZEONEX is used as the lens material. Higher aspherical coefficients are used for correction of spherical aberration and reduction of lens thickness. The lenses were manufactured by ultraprecision machining. For optimization of the system, ray tracing and wave-optical methods were combined. We show how the ZEMAX Gaussian beam analysis tool can be used to evaluate illumination optics. The resolution of the THz system was tested with a wire and a slit target, line gratings of different period, and a Siemens star. The behavior of the temporal line spread function can be modeled with the polychromatic coherent line spread function feature in ZEMAX. The spectral and temporal resolutions of the line gratings are compared with the respective modulation transfer function of ZEMAX. For maximum resolution, the system has to be diffraction limited down to the smallest wavelength of the spectrum of the THz pulse. Then, the resolution on time domain analysis of the pulse maximum can be estimated with the spectral resolution of the center of gravity wavelength. The system resolution near the optical axis on time domain analysis of the pulse maximum is 1 line pair/mm with an intensity contrast of 0.22. The Siemens star is used for estimation of the resolution of the whole system. An eight channel electro-optic sampling system was used for detection. The resolution on time domain analysis of the pulse maximum of all eight channels could be determined with the Siemens star to be 0.7 line pairs/mm.

  13. 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.

  14. 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).

  15. 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.

  16. 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. Copyright © 2015 Elsevier Inc. All rights reserved.

  17. 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.

  18. 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.

  19. 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.

  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. 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.

  2. Creating the optimal workspace for hospital staff using human centred design.

    PubMed

    Cawood, T; Saunders, E; Drennan, C; Cross, N; Nicholl, D; Kenny, A; Meates, D; Laing, R

    2016-07-01

    We were tasked with creating best possible non-clinical workspace solutions for approximately 450 hospital staff across 11 departments encompassing medical, nursing, allied health, administrative and other support staff. We used a Human-Centred Design process, involving 'Hear, Create and Deliver' stages. We used observations, contextual enquiry and role-specific workshops to understand needs, key interactions and drivers of behaviour. Co-design workshops were then used to explore and prototype-test concepts for the final design. With extensive employee engagement and design process expertise, an innovative solution was created that focussed on meeting the functional workspace needs of a diverse group of staff requiring a range of different spaces, incorporating space constraints and equity. This project demonstrated the strength of engaging employees in an expert-led Human-Centred Design process. We believe this is a successful blueprint process for other institutions to embrace when facing similar workspace design challenges. © 2016 Royal Australasian College of Physicians.

  3. Workspace Safe Operation of a Force- or Impedance-Controlled Robot

    NASA Technical Reports Server (NTRS)

    Abdallah, Muhammad E. (Inventor); Hargrave, Brian (Inventor); Yamokoski, John D. (Inventor); Strawser, Philip A. (Inventor)

    2013-01-01

    A method of controlling a robotic manipulator of a force- or impedance-controlled robot within an unstructured workspace includes imposing a saturation limit on a static force applied by the manipulator to its surrounding environment, and may include determining a contact force between the manipulator and an object in the unstructured workspace, and executing a dynamic reflex when the contact force exceeds a threshold to thereby alleviate an inertial impulse not addressed by the saturation limited static force. The method may include calculating a required reflex torque to be imparted by a joint actuator to a robotic joint. A robotic system includes a robotic manipulator having an unstructured workspace and a controller that is electrically connected to the manipulator, and which controls the manipulator using force- or impedance-based commands. The controller, which is also disclosed herein, automatically imposes the saturation limit and may execute the dynamic reflex noted above.

  4. A redundant, 6-DOF parallel manipulator structure with improved workspace and dexterity

    SciTech Connect

    Stoughton, R.S.; Salerno, R.; Canfield, S.; Reinholtz, C.

    1994-08-01

    This paper presents a novel manipulator structure which combines two known parallel manipulator structures--a Stewart Platform (SP), and a double octahedral Variable Geometry Truss (VGT). The combined VGT + SP structure is redundant, using nine actuators to realize six-DOF motion. Combining the two structures allows the translational and orientational workspaces of the two individual structures to sum together to a much larger workspace than is generally achievable with parallel manipulator structures. In addition, the VGT portion of the structure allows the configuration of the Stewart Platform to be changed ``on the fly`` from one with a large workspace to one with high dexterity. A useful application of this structure is at the distal end of a truss-based manipulator, where it can serve as a dexterous wrist while preserving an internal passageway for cabling and/or conveyance systems.

  5. 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.

  6. 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%.

  7. ARAM: an automated image analysis software to determine rosetting parameters and parasitaemia in Plasmodium samples.

    PubMed

    Kudella, Patrick Wolfgang; Moll, Kirsten; Wahlgren, Mats; Wixforth, Achim; Westerhausen, Christoph

    2016-04-18

    Rosetting is associated with severe malaria and a primary cause of death in Plasmodium falciparum infections. Detailed understanding of this adhesive phenomenon may enable the development of new therapies interfering with rosette formation. For this, it is crucial to determine parameters such as rosetting and parasitaemia of laboratory strains or patient isolates, a bottleneck in malaria research due to the time consuming and error prone manual analysis of specimens. Here, the automated, free, stand-alone analysis software automated rosetting analyzer for micrographs (ARAM) to determine rosetting rate, rosette size distribution as well as parasitaemia with a convenient graphical user interface is presented. Automated rosetting analyzer for micrographs is an executable with two operation modes for automated identification of objects on images. The default mode detects red blood cells and fluorescently labelled parasitized red blood cells by combining an intensity-gradient with a threshold filter. The second mode determines object location and size distribution from a single contrast method. The obtained results are compared with standardized manual analysis. Automated rosetting analyzer for micrographs calculates statistical confidence probabilities for rosetting rate and parasitaemia. Automated rosetting analyzer for micrographs analyses 25 cell objects per second reliably delivering identical results compared to manual analysis. For the first time rosette size distribution is determined in a precise and quantitative manner employing ARAM in combination with established inhibition tests. Additionally ARAM measures the essential observables parasitaemia, rosetting rate and size as well as location of all detected objects and provides confidence intervals for the determined observables. No other existing software solution offers this range of function. The second, non-malaria specific, analysis mode of ARAM offers the functionality to detect arbitrary objects

  8. MR urography in children. Part 2: how to use ImageJ MR urography processing software.

    PubMed

    Vivier, Pierre-Hugues; Dolores, Michael; Taylor, Melissa; Dacher, Jean-Nicolas

    2010-05-01

    MR urography (MRU) is an emerging technique particularly useful in paediatric uroradiology. The most common indication is the investigation of hydronephrosis. Combined static and dynamic contrast-enhanced MRU (DCE-MRU) provides both morphological and functional information in a single examination. However, specific post-processing must be performed and to our knowledge, dedicated software is not available in conventional workstations. Investigators involved in MRU classically use homemade software that is not freely accessible. For these reasons, we have developed a software program that is freely downloadable on the National Institute of Health (NIH) website. We report and describe in this study the features of this software program.

  9. Development of a Prototype Robotic System for Radiosurgery with Upper Hemispherical Workspace

    PubMed Central

    Seo, Yong-chil; Kim, Chang-hoi; Park, Jongwon; Choi, Yoo Rark; Lee, Sung Uk; Bae, Yeong-Geol; Kim, Seungho

    2017-01-01

    This paper introduces a specialized robotic system under development for radiosurgery using a small-sized linear accelerator. The robotic system is a 5-DOF manipulator that can be installed above a patient to make an upper hemispherical workspace centered in a target point. In order to determine the optimal lengths of the link, we consider the requirements for the workspace of a linear accelerator for radiosurgery. A more suitable kinematic structure than conventional industrial manipulators is proposed, and the kinematic analysis is also provided. A graphic simulator is implemented and used for dynamic analysis. Based on those results, a prototype manipulator and its control system are under development.

  10. Computation of robot configuration and workspaces via the Fourier transform on the discrete-motion group

    SciTech Connect

    Kyatkin, A.B.; Chirikjian, G.S.

    1999-06-01

    The authors apply the Fourier transform on the discrete-motion group to the problem of computing the configuration-space obstacles of mobile robots which move among static obstacles, the problem of finding the workspace density of binary manipulators with many actuators, and the problem of determining workspace boundaries of manipulators with continuous-motion actuators. They develop and implement Fourier transforms for the discrete-motion group of the plane. These transforms allow them to apply fast Fourier transform methods to the computation of convolution-like integrals that arise in robot kinematics and motion planning. The results of the implementation are discussed for particular examples.

  11. 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").

  12. 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

  13. SU-F-I-43: A Software-Based Statistical Method to Compute Low Contrast Detectability in Computed Tomography Images

    SciTech Connect

    Chacko, M; Aldoohan, S

    2016-06-15

    Purpose: The low contrast detectability (LCD) of a CT scanner is its ability to detect and display faint lesions. The current approach to quantify LCD is achieved using vendor-specific methods and phantoms, typically by subjectively observing the smallest size object at a contrast level above phantom background. However, this approach does not yield clinically applicable values for LCD. The current study proposes a statistical LCD metric using software tools to not only to assess scanner performance, but also to quantify the key factors affecting LCD. This approach was developed using uniform QC phantoms, and its applicability was then extended under simulated clinical conditions. Methods: MATLAB software was developed to compute LCD using a uniform image of a QC phantom. For a given virtual object size, the software randomly samples the image within a selected area, and uses statistical analysis based on Student’s t-distribution to compute the LCD as the minimal Hounsfield Unit’s that can be distinguished from the background at the 95% confidence level. Its validity was assessed by comparison with the behavior of a known QC phantom under various scan protocols and a tissue-mimicking phantom. The contributions of beam quality and scattered radiation upon the computed LCD were quantified by using various external beam-hardening filters and phantom lengths. Results: As expected, the LCD was inversely related to object size under all scan conditions. The type of image reconstruction kernel filter and tissue/organ type strongly influenced the background noise characteristics and therefore, the computed LCD for the associated image. Conclusion: The proposed metric and its associated software tools are vendor-independent and can be used to analyze any LCD scanner performance. Furthermore, the method employed can be used in conjunction with the relationships established in this study between LCD and tissue type to extend these concepts to patients’ clinical CT

  14. 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

    This paper involves easy accessible integrated web-based analysis of satellite images with a plug-in based open source software. The paper is targeted to both users and developers of geospatial software. Guided by a use case scenario, we describe the ILWIS software and its toolbox to access satellite images through the GEONETCast broadcasting system. The last two decades have shown a major shift from stand-alone software systems to networked ones, often client/server applications using distributed geo-(web-)services. This allows organisations to combine without much effort their own data with remotely available data and processing functionality. Key to this integrated spatial data analysis is a low-cost access to data from within a user-friendly and flexible software. Web-based open source software solutions are more often a powerful option for developing countries. The Integrated Land and Water Information System (ILWIS) is a PC-based GIS & Remote Sensing software, comprising a complete package of image processing, spatial analysis and digital mapping and was developed as commercial software from the early nineties onwards. Recent project efforts have migrated ILWIS into a modular, plug-in-based open source software, and provide web-service support for OGC-based web mapping and processing. The core objective of the ILWIS Open source project is to provide a maintainable framework for researchers and software developers to implement training components, scientific toolboxes and (web-) services. The latest plug-ins have been developed for multi-criteria decision making, water resources analysis and spatial statistics analysis. The development of this framework is done since 2007 in the context of 52°North, which is an open initiative that advances the development of cutting edge open source geospatial software, using the GPL license. GEONETCast, as part of the emerging Global Earth Observation System of Systems (GEOSS), puts essential environmental data at the

  15. Effects of photographic distance on tree crown atributes calculated using urbancrowns image analysis software

    Treesearch

    Mason F. Patterson; P. Eric Wiseman; Matthew F. Winn; Sang-mook Lee; Philip A. Araman

    2011-01-01

    UrbanCrowns is a software program developed by the USDA Forest Service that computes crown attributes using a side-view digital photograph and a few basic field measurements. From an operational standpoint, it is not known how well the software performs under varying photographic conditions for trees of diverse size, which could impact measurement reproducibility and...

  16. 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

  17. Quantitative comparison and evaluation of software packages for assessment of abdominal adipose tissue distribution by magnetic resonance imaging.

    PubMed

    Bonekamp, S; Ghosh, P; Crawford, S; Solga, S F; Horska, A; Brancati, F L; Diehl, A M; Smith, S; Clark, J M

    2008-01-01

    To examine five available software packages for the assessment of abdominal adipose tissue with magnetic resonance imaging, compare their features and assess the reliability of measurement results. Feature evaluation and test-retest reliability of softwares (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision) used in manual, semi-automated or automated segmentation of abdominal adipose tissue. A random sample of 15 obese adults with type 2 diabetes. Axial T1-weighted spin echo images centered at vertebral bodies of L2-L3 were acquired at 1.5 T. Five software packages were evaluated (NIHImage, SliceOmatic, Analyze, HippoFat and EasyVision), comparing manual, semi-automated and automated segmentation approaches. Images were segmented into cross-sectional area (CSA), and the areas of visceral (VAT) and subcutaneous adipose tissue (SAT). Ease of learning and use and the design of the graphical user interface (GUI) were rated. Intra-observer accuracy and agreement between the software packages were calculated using intra-class correlation. Intra-class correlation coefficient was used to obtain test-retest reliability. Three of the five evaluated programs offered a semi-automated technique to segment the images based on histogram values or a user-defined threshold. One software package allowed manual delineation only. One fully automated program demonstrated the drawbacks of uncritical automated processing. The semi-automated approaches reduced variability and measurement error, and improved reproducibility. There was no significant difference in the intra-observer agreement in SAT and CSA. The VAT measurements showed significantly lower test-retest reliability. There were some differences between the software packages in qualitative aspects, such as user friendliness. Four out of five packages provided essentially the same results with respect to the inter- and intra-rater reproducibility. Our results using SliceOmatic, Analyze or NIHImage were comparable and could

  18. Global workspace dynamics: cortical "binding and propagation" enables conscious contents.

    PubMed

    Baars, Bernard J; Franklin, Stan; Ramsoy, Thomas Zoega

    2013-01-01

    A global workspace (GW) is a functional hub of binding and propagation in a population of loosely coupled signaling elements. In computational applications, GW architectures recruit many distributed, specialized agents to cooperate in resolving focal ambiguities. In the brain, conscious experiences may reflect a GW function. For animals, the natural world is full of unpredictable dangers and opportunities, suggesting a general adaptive pressure for brains to resolve focal ambiguities quickly and accurately. GW theory aims to understand the differences between conscious and unconscious brain events. In humans and related species the cortico-thalamic (C-T) core is believed to underlie conscious aspects of perception, thinking, learning, feelings of knowing (FOK), felt emotions, visual imagery, working memory, and executive control. Alternative theoretical perspectives are also discussed. The C-T core has many anatomical hubs, but conscious percepts are unitary and internally consistent at any given moment. Over time, conscious contents constitute a very large, open set. This suggests that a brain-based GW capacity cannot be localized in a single anatomical hub. Rather, it should be sought in a functional hub - a dynamic capacity for binding and propagation of neural signals over multiple task-related networks, a kind of neuronal cloud computing. In this view, conscious contents can arise in any region of the C-T core when multiple input streams settle on a winner-take-all equilibrium. The resulting conscious gestalt may ignite an any-to-many broadcast, lasting ∼100-200 ms, and trigger widespread adaptation in previously established networks. To account for the great range of conscious contents over time, the theory suggests an open repertoire of binding coalitions that can broadcast via theta/gamma or alpha/gamma phase coupling, like radio channels competing for a narrow frequency band. Conscious moments are thought to hold only 1-4 unrelated items; this small

  19. 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

  20. CellSeT: novel software to extract and analyze structured networks of plant cells from confocal images.

    PubMed

    Pound, Michael P; French, Andrew P; Wells, Darren M; Bennett, Malcolm J; Pridmore, Tony P

    2012-04-01

    It is increasingly important in life sciences that many cell-scale and tissue-scale measurements are quantified from confocal microscope images. However, extracting and analyzing large-scale confocal image data sets represents a major bottleneck for researchers. To aid this process, CellSeT software has been developed, which utilizes tissue-scale structure to help segment individual cells. We provide examples of how the CellSeT software can be used to quantify fluorescence of hormone-responsive nuclear reporters, determine membrane protein polarity, extract cell and tissue geometry for use in later modeling, and take many additional biologically relevant measures using an extensible plug-in toolset. Application of CellSeT promises to remove subjectivity from the resulting data sets and facilitate higher-throughput, quantitative approaches to plant cell research.

  1. 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.

  2. [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.

  3. Biological Visualization, Imaging and Simulation(Bio-VIS) at NASA Ames Research Center: Developing New Software and Technology for Astronaut Training and Biology Research in Space

    NASA Technical Reports Server (NTRS)

    Smith, Jeffrey

    2003-01-01

    The Bio- Visualization, Imaging and Simulation (BioVIS) Technology Center at NASA's Ames Research Center is dedicated to developing and applying advanced visualization, computation and simulation technologies to support NASA Space Life Sciences research and the objectives of the Fundamental Biology Program. Research ranges from high resolution 3D cell imaging and structure analysis, virtual environment simulation of fine sensory-motor tasks, computational neuroscience and biophysics to biomedical/clinical applications. Computer simulation research focuses on the development of advanced computational tools for astronaut training and education. Virtual Reality (VR) and Virtual Environment (VE) simulation systems have become important training tools in many fields from flight simulation to, more recently, surgical simulation. The type and quality of training provided by these computer-based tools ranges widely, but the value of real-time VE computer simulation as a method of preparing individuals for real-world tasks is well established. Astronauts routinely use VE systems for various training tasks, including Space Shuttle landings, robot arm manipulations and extravehicular activities (space walks). Currently, there are no VE systems to train astronauts for basic and applied research experiments which are an important part of many missions. The Virtual Glovebox (VGX) is a prototype VE system for real-time physically-based simulation of the Life Sciences Glovebox where astronauts will perform many complex tasks supporting research experiments aboard the International Space Station. The VGX consists of a physical display system utilizing duel LCD projectors and circular polarization to produce a desktop-sized 3D virtual workspace. Physically-based modeling tools (Arachi Inc.) provide real-time collision detection, rigid body dynamics, physical properties and force-based controls for objects. The human-computer interface consists of two magnetic tracking devices

  4. Use of ImageJ software for histomorphometric evaluation of normal and severely affected canine ear canals

    PubMed Central

    Zur, Gila; Klement, Eyal

    2015-01-01

    Morphological studies comparing normal and diseased ear canals use primarily subjective scoring. The aim of this study was to compare normal and severely affected ears in dogs with objective measurements using ImageJ software. Ear canals were harvested from cadavers with normal ears and from dogs that underwent total ear canal ablation for unresolved otitis. Histopathology samples from ear canals were evaluated by semi-quantitative scoring and also by using ImageJ-software for histomorphometric measurements. The normal ears were compared to the severely affected ears using the 2 methods. The 2 methods were significantly (P < 0.0001) correlated for epidermal hyperplasia, ceruminous gland dilation, and hyperplasia and tissue inflammation, which were significantly greater in the severely affected ears (P < 0.0001). This study demonstrated that there is a very high correlation between the 2 methods for the most markedly affected components of otitis externa and that ImageJ software can be efficiently used to measure and evaluate ear canal histomorphometry. PMID:26424913

  5. 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

  6. Development and evaluation of an open-source software package "CGITA" for quantifying tumor heterogeneity with molecular images.

    PubMed

    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

    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. 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. 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.). 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.

  7. Three-Dimensional Root Phenotyping with a Novel Imaging and Software Platform1[C][W][OA

    PubMed Central

    Clark, Randy T.; MacCurdy, Robert B.; Jung, Janelle K.; Shaff, Jon E.; McCouch, Susan R.; Aneshansley, Daniel J.; Kochian, Leon V.

    2011-01-01

    A novel imaging and software platform was developed for the high-throughput phenotyping of three-dimensional root traits during seedling development. To demonstrate the platform’s capacity, plants of two rice (Oryza sativa) genotypes, Azucena and IR64, were grown in a transparent gellan gum system and imaged daily for 10 d. Rotational image sequences consisting of 40 two-dimensional images were captured using an optically corrected digital imaging system. Three-dimensional root reconstructions were generated and analyzed using a custom-designed software, RootReader3D. Using the automated and interactive capabilities of RootReader3D, five rice root types were classified and 27 phenotypic root traits were measured to characterize these two genotypes. Where possible, measurements from the three-dimensional platform were validated and were highly correlated with conventional two-dimensional measurements. When comparing gellan gum-grown plants with those grown under hydroponic and sand culture, significant differences were detected in morphological root traits (P < 0.05). This highly flexible platform provides the capacity to measure root traits with a high degree of spatial and temporal resolution and will facilitate novel investigations into the development of entire root systems or selected components of root systems. In combination with the extensive genetic resources that are now available, this platform will be a powerful resource to further explore the molecular and genetic determinants of root system architecture. PMID:21454799

  8. 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.

  9. Reachable Workspace and Performance of Upper Limb (PUL) in Duchenne muscular dystrophy

    PubMed Central

    Han, Jay J.; de Bie, Evan; Nicorici, Alina; Abresch, Richard T.; Anthonisen, Colleen; Bajcsy, Ruzena; Kurillo, Gregorij; McDonald, Craig M.

    2015-01-01

    Introduction The Kinect-based reachable workspace relative surface area (RSA) is compared with the Performance of Upper Limb (PUL) assessment in Duchenne muscular dystrophy (DMD). Methods 29 individuals with DMD (ages: 7–23, Brooke: 1–5) underwent both Kinect-based reachable workspace RSA and PUL assessments. RSAs were also collected from 24 age-matched controls. Total and quadrant RSAs were compared with the PUL total, shoulder-, middle-, and distal-dimension scores. Results The total reachable workspace RSA correlated well with the total PUL score (Spearman ρ=−0.602, P<0.001), and with each of the PUL dimensional scores: shoulder (ρ=−0.624, P<0.001), middle (ρ=−0.564, P=0.001), and distal (ρ=−0.630, P<0.001). With quadrant RSA, reachability in a particular quadrant was closely associated with respective PUL dimensional-level function (lateral-upper quadrant for shoulder-, lateral-upper/lower quadrants for middle-, and lateral-lower quadrant for distal-level function). Discussion This study demonstrates concurrent validity of the reachable workspace outcome measure (RSA) with the DMD-specific upper extremity outcome measure (PUL). PMID:26342193

  10. Exploring the Effectiveness of an Online Writing Workspace to Support Literacy in a Social Studies Classroom

    ERIC Educational Resources Information Center

    Carlin-Menter, Shannon

    2013-01-01

    The purpose of this exploratory study was to analyze the writing experiences of eighth-grade students in three social studies classrooms while using a Web 2.0 online writing workspace. Participants included one social studies teacher and 69 eighth-grade students in a selective admission public high school. Furthermore, three of the eighth-grade…

  11. Revolute manipulator workspace optimization using a modified bacteria foraging algorithm: A comparative study

    NASA Astrophysics Data System (ADS)

    Panda, S.; Mishra, D.; Biswal, B. B.; Tripathy, M.

    2014-02-01

    Robotic manipulators with three-revolute (3R) motions to attain desired positional configurations are very common in industrial robots. The capability of these robots depends largely on the workspace of the manipulator in addition to other parameters. In this study, an evolutionary optimization algorithm based on the foraging behaviour of the Escherichia coli bacteria present in the human intestine is utilized to optimize the workspace volume of a 3R manipulator. The new optimization method is modified from the original algorithm for faster convergence. This method is also useful for optimization problems in a highly constrained environment, such as robot workspace optimization. The new approach for workspace optimization of 3R manipulators is tested using three cases. The test results are compared with standard results available using other optimization algorithms, i.e. the differential evolution algorithm, the genetic algorithm and the particle swarm optimization algorithm. The present method is found to be superior to the other methods in terms of computational efficiency.

  12. Collaborative Knowledge Building: A Learning Module in Shadow netWorkspace[TM] Learning System.

    ERIC Educational Resources Information Center

    Lin, Yi-Mei; Peng, Hsinyi; Gottdenker, Joshua

    Shadow netWorkspace[TM](SNS) is designed and developed as a free, open source, network-based work environment specifically for use in K-12 schools to support schools and learning. This paper describes a learning module utilizing features of SNS and articulates how teacher and students can collaboratively learn and work to build knowledge. The…

  13. Investigating Uses and Perceptions of an Online Collaborative Workspace for the Dissertation Process

    ERIC Educational Resources Information Center

    Rockinson-Szapkiw, Amanda J.

    2012-01-01

    The intent of this study was to investigate 93 doctoral candidates' perceptions and use of an online collaboration workspace and content management server, Microsoft Office SharePoint, for dissertation process. All candidates were enrolled in an Ed.D. programme in the United States. Descriptive statistics demonstrate that candidates frequently use…

  14. Workspace analysis and design improvement of a carotid flow measurement system.

    PubMed

    Carbone, G; Nakadate, R; Solis, J; Ceccarelli, M; Takanishi, A; Minagawa, E; Sugawara, M; Niki, K

    2010-11-01

    Heart and cerebrovascular diseases such as arteriosclerosis and myocardial ischemia dysfunction are currently among the main causes of death in developed countries. Recently, wave intensity (WI), which is an index used to obtain the force of cardiac contraction, has been investigated as a method for early-stage diagnosis of the above-mentioned diseases. Nevertheless, experimental tests have proven that the manual measurements of WI by means of commercial ultrasonic diagnostic systems require too much time and can be affected by the operator's skills. For this purpose, the introduction of robotic-assisted technology has advantages in terms of repetitiveness and accuracy of the measurement procedure. Therefore, at Waseda University, the development of a carotid blood flow measurement system has been proposed to support doctors while using ultrasound diagnostic equipment to measure the WI. This robotic system is composed of a serial robot with a wrist having a six-degree-of-freedom (6-DOF) parallel mechanism. The main focus is to obtain a suitable workspace performance of the 6-DOF parallel mechanism wrist. In this paper, a workspace analysis is carried out on a wrist prototype built for the Waseda-Tokyo Women's Medical Aloka Blood Flow Measurement System No.1 Refined (WTA-1R). Then, mechanical design enhancements are proposed and validated to provide a suitable workspace performance both as reachable workspace and dexterity, and a refined prototype WTA-1RII has been built.

  15. Investigating Uses and Perceptions of an Online Collaborative Workspace for the Dissertation Process

    ERIC Educational Resources Information Center

    Rockinson-Szapkiw, Amanda J.

    2012-01-01

    The intent of this study was to investigate 93 doctoral candidates' perceptions and use of an online collaboration workspace and content management server, Microsoft Office SharePoint, for dissertation process. All candidates were enrolled in an Ed.D. programme in the United States. Descriptive statistics demonstrate that candidates frequently use…

  16. Investigating Learning Space for Research Workspaces in Higher Education in Malaysia

    ERIC Educational Resources Information Center

    Yusof, Norhafezah; Hashim, Rosna Awang; Kian, Chan Kok

    2016-01-01

    Purpose: The purpose of this paper is to investigate learning space for research workspaces in Higher Education Institutions (HEIs) in Malaysia based on the evaluations by experts and university research workers on a practical model for creating an effective research learning space. It examines expert analyses of the notion of a suitable research…

  17. An adaptive workspace hypothesis about the neural correlates of consciousness: insights from neuroscience and meditation studies.

    PubMed

    Raffone, Antonino; Srinivasan, Narayanan

    2009-01-01

    While enormous progress has been made to identify neural correlates of consciousness (NCC), crucial NCC aspects are still very controversial. A major hurdle is the lack of an adequate definition and characterization of different aspects of conscious experience and also its relationship to attention and metacognitive processes like monitoring. In this paper, we therefore attempt to develop a unitary theoretical framework for NCC, with an interdependent characterization of endogenous attention, access consciousness, phenomenal awareness, metacognitive consciousness, and a non-referential form of unified consciousness. We advance an adaptive workspace hypothesis about the NCC based on the global workspace model emphasizing transient resonant neurodynamics and prefrontal cortex function, as well as meditation-related characterizations of conscious experiences. In this hypothesis, transient dynamic links within an adaptive coding net in prefrontal cortex, especially in anterior prefrontal cortex, and between it and the rest of the brain, in terms of ongoing intrinsic and long-range signal exchanges, flexibly regulate the interplay between endogenous attention, access consciousness, phenomenal awareness, and metacognitive consciousness processes. Such processes are established in terms of complementary aspects of an ongoing transition between context-sensitive global workspace assemblies, modulated moment-to-moment by body and environment states. Brain regions associated to momentary interoceptive and exteroceptive self-awareness, or first-person experiential perspective as emphasized in open monitoring meditation, play an important modulatory role in adaptive workspace transitions.

  18. 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.

  19. 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

  20. Mapping and correction of the CMM workspace error with the use of an electronic gyroscope and neural networks--practical application.

    PubMed

    Swornowski, Pawel J

    2013-01-01

    The article presents the application of neural networks in determining and correction of the deformation of a coordinate measuring machine (CMM) workspace. The information about the CMM errors is acquired using an ADXRS401 electronic gyroscope. A test device (PS-20 module) was built and integrated with a commercial measurement system based on the SP25M passive scanning probe and with a PH10M module (Renishaw). The proposed solution was tested on a Kemco 600 CMM and on a DEA Global Clima CMM. In the former case, correction of the CMM errors was performed using the source code of WinIOS software owned by The Institute of Advanced Manufacturing Technology, Cracow, Poland and in the latter on an external PC. Optimum parameters of full and simplified mapping of a given layer of the CMM workspace were determined for practical applications. The proposed method can be employed for the interim check (ISO 10360-2 procedure) or to detect local CMM deformations, occurring when the CMM works at high scanning speeds (>20 mm/s). © Wiley Periodicals, Inc.

  1. 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.

  2. 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.

  3. 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

  4. 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

  5. SmartGrain: High-Throughput Phenotyping Software for Measuring Seed Shape through Image Analysis1[C][W][OA

    PubMed Central

    Tanabata, Takanari; Shibaya, Taeko; Hori, Kiyosumi; Ebana, Kaworu; Yano, Masahiro

    2012-01-01

    Seed shape and size are among the most important agronomic traits because they affect yield and market price. To obtain accurate seed size data, a large number of measurements are needed because there is little difference in size among seeds from one plant. To promote genetic analysis and selection for seed shape in plant breeding, efficient, reliable, high-throughput seed phenotyping methods are required. We developed SmartGrain software for high-throughput measurement of seed shape. This software uses a new image analysis method to reduce the time taken in the preparation of seeds and in image capture. Outlines of seeds are automatically recognized from digital images, and several shape parameters, such as seed length, width, area, and perimeter length, are calculated. To validate the software, we performed a quantitative trait locus (QTL) analysis for rice (Oryza sativa) seed shape using backcrossed inbred lines derived from a cross between japonica cultivars Koshihikari and Nipponbare, which showed small differences in seed shape. SmartGrain removed areas of awns and pedicels automatically, and several QTLs were detected for six shape parameters. The allelic effect of a QTL for seed length detected on chromosome 11 was confirmed in advanced backcross progeny; the cv Nipponbare allele increased seed length and, thus, seed weight. High-throughput measurement with SmartGrain reduced sampling error and made it possible to distinguish between lines with small differences in seed shape. SmartGrain could accurately recognize seed not only of rice but also of several other species, including Arabidopsis (Arabidopsis thaliana). The software is free to researchers. PMID:23054566

  6. 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.

  7. An audit of half-count myocardial perfusion imaging using resolution recovery software.

    PubMed

    Lawson, Richard S; White, Duncan; Nijran, Kuldip; Cade, Sarah C; Hall, David O; Kenny, Bob; Knight, Andy; Livieratos, Lefteris; Murray, Anthony; Towey, David

    2014-05-01

    The Nuclear Medicine Software Quality Group of the Institute of Physics and Engineering in Medicine has conducted a multicentre, multivendor audit to evaluate the use of resolution recovery software from several manufacturers when applied to myocardial perfusion data with half the normal counts acquired under a variety of clinical protocols in a range of departments. The objective was to determine whether centres could obtain clinical results with half-count data processed with resolution recovery software that were equivalent to those obtained using their normal protocols. Sixteen centres selected 50 routine myocardial perfusion studies each, from which the Nuclear Medicine Software Quality Group generated simulated half-count studies using Poisson resampling. These half-count studies were reconstructed using resolution recovery and the clinical reports compared with the original reports from the full-count data. A total of 769 patient studies were processed and compared. Eight centres found only a small number of clinically relevant discrepancies between the two reports, whereas eight had an unacceptably high number of discrepancies. There were no significant differences in acquisition parameters between the two groups, although centres finding a high number of discrepancies were more likely to perform both rest and stress scans on normal studies. Half of the participating centres could potentially make use of resolution recovery to reduce the administered activity for myocardial perfusion scans without changing their routine acquisition protocols. The other half could consider adjusting the reconstruction parameters used with their resolution recovery software if they wish to use reduced activity successfully.

  8. Periprosthetic Artifact Reduction Using Virtual Monochromatic Imaging Derived From Gemstone Dual-Energy Computed Tomography and Dedicated Software.

    PubMed

    Reynoso, Exequiel; Capunay, Carlos; Rasumoff, Alejandro; Vallejos, Javier; Carpio, Jimena; Lago, Karen; Carrascosa, Patricia

    2016-01-01

    The aim of this study was to explore the usefulness of combined virtual monochromatic imaging and metal artifact reduction software (MARS) for the evaluation of musculoskeletal periprosthetic tissue. Measurements were performed in periprosthetic and remote regions in 80 patients using a high-definition scanner. Polychromatic images with and without MARS and virtual monochromatic images were obtained. Periprosthetic polychromatic imaging (PI) showed significant differences compared with remote areas among the 3 tissues explored (P < 0.0001). No significant differences were observed between periprosthetic and remote tissues using monochromatic imaging with MARS (P = 0.053 bone, P = 0.32 soft tissue, and P = 0.13 fat). However, such differences were significant using PI with MARS among bone (P = 0.005) and fat (P = 0.02) tissues. All periprosthetic areas were noninterpretable using PI, compared with 11 (9%) using monochromatic imaging. The combined use of virtual monochromatic imaging and MARS reduced periprosthetic artifacts, achieving attenuation levels comparable to implant-free tissue.

  9. Novel development tool for software pipeline optimization for VLIW-DSPs used in real-time image processing

    NASA Astrophysics Data System (ADS)

    Fuertler, Johannes; Mayer, Konrad J.; Krattenthaler, Werner; Bajla, Ivan

    2003-04-01

    Although the hardware platform is often seen as the most important element of real-time imaging systems, software optimization can also provide remarkable reduction of overall computational costs. The recommended code development flow for digital signal processors based on the TMS320C6000(TM) architecture usually involves three phases: development of C code, refinement of C code, and programming linear assembly code. Each step requires a different level of knowledge of processor internals. The developer is not directly involved in the automatic scheduling process. In some cases, however, this may result in unacceptable code performance. A better solution can be achieved by scheduling the assembly code by hand. Unfortunately, scheduling of software pipelines by hand not only requires expert skills but is also time consuming, and moreover, prone to errors. To overcome these drawbacks we have designed an innovative development tool - the Software Pipeline Optimization Tool (SPOT(TM)). The SPOT is based on visualization of the scheduled assembly code by a two-dimensional interactive schedule editor, which is equipped with feedback mechanisms deduced from analysis of data dependencies and resource allocation conflicts. The paper addresses optimization techniques available by the application of the SPOT. Furthermore, the benefit of the SPOT is documented by more than 20 optimized image processing algorithms.

  10. 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.

  11. 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).

  12. Evaluation of two software tools dedicated to an automatic analysis of the CT scanner image spatial resolution.

    PubMed

    Torfeh, Tarraf; Beaumont, Stéphane; Guédon, Jean Pierre; Denis, Eloïse

    2007-01-01

    An evaluation of two software tools dedicated to an automatic analysis of the CT scanner image spatial resolution is presented in this paper. The methods evaluated consist of calculating the Modulation Transfer Function (MTF) of the CT scanners; the first uses an image of an impulse source, while the second method proposed by Droege and Morin uses an image of cyclic bar patterns. Two Digital Test Objects (DTO) are created to this purpose. These DTOs are then blurred by doing a convolution with a two-dimensional Gaussian Point Spread Function (PSF(Ref)), which has a well known Full Width at Half Maximum (FWHM). The evaluation process consists then of comparing the Fourier transform of the PSF on the one hand, and the two mentioned methods on the other hand.

  13. 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.

  14. Imaging and quantification of endothelial cell loss in eye bank prepared DMEK grafts using trainable segmentation software.

    PubMed

    Jardine, Griffin J; Holiman, Jeffrey D; Stoeger, Christopher G; Chamberlain, Winston D

    2014-09-01

    To improve accuracy and efficiency in quantifying the endothelial cell loss (ECL) in eye bank preparation of corneal endothelial grafts. Eight cadaveric corneas were subjected to Descemet Membrane Endothelial Keratoplasty (DMEK) preparation. The endothelial surfaces were stained with a viability stain, calcein AM dye (CAM) and then captured by a digital camera. The ECL rates were quantified in these images by three separate readers using trainable segmentation, a plug-in feature from the imaging software, Fiji. Images were also analyzed by Adobe Photoshop for comparison. Mean times required to process the images were measured between the two modalities. The mean ECL (with standard deviation) as analyzed by Fiji was 22.5% (6.5%) and Adobe was 18.7% (7.0%; p = 0.04). The mean time required to process the images through the two different imaging methods was 19.9 min (7.5) for Fiji and 23.4 min (12.9) for Adobe (p = 0.17). Establishing an accurate, efficient and reproducible means of quantifying ECL in graft preparation and surgical techniques can provide insight to the safety, long-term potential of the graft tissues as well as provide a quality control measure for eye banks and surgeons. Trainable segmentation in Fiji software using CAM is a novel approach to measuring ECL that captured a statistically significantly higher percentage of ECL comparable to Adobe and was more accurate in standardized testing. Interestingly, ECL as determined using both methods in eye bank-prepared DMEK grafts exceeded 18% on average.

  15. Exploiting the potential of free software to evaluate root canal biomechanical preparation outcomes through micro-CT images.

    PubMed

    Neves, A A; Silva, E J; Roter, J M; Belladona, F G; Alves, H D; Lopes, R T; Paciornik, S; De-Deus, G A

    2015-11-01

    To propose an automated image processing routine based on free software to quantify root canal preparation outcomes in pairs of sound and instrumented roots after micro-CT scanning procedures. Seven mesial roots of human mandibular molars with different canal configuration systems were studied: (i) Vertucci's type 1, (ii) Vertucci's type 2, (iii) two individual canals, (iv) Vertucci's type 6, canals (v) with and (vi) without debris, and (vii) canal with visible pulp calcification. All teeth were instrumented with the BioRaCe system and scanned in a Skyscan 1173 micro-CT before and after canal preparation. After reconstruction, the instrumented stack of images (IS) was registered against the preoperative sound stack of images (SS). Image processing included contrast equalization and noise filtering. Sound canal volumes were obtained by a minimum threshold. For the IS, a fixed conservative threshold was chosen as the best compromise between instrumented canal and dentine whilst avoiding debris, resulting in instrumented canal plus empty spaces. Arithmetic and logical operations between sound and instrumented stacks were used to identify debris. Noninstrumented dentine was calculated using a minimum threshold in the IS and subtracting from the SS and total debris. Removed dentine volume was obtained by subtracting SS from IS. Quantitative data on total debris present in the root canal space after instrumentation, noninstrumented areas and removed dentine volume were obtained for each test case, as well as three-dimensional volume renderings. After standardization of acquisition, reconstruction and image processing micro-CT images, a quantitative approach for calculation of root canal biomechanical outcomes was achieved using free software. © 2014 International Endodontic Journal. Published by John Wiley & Sons Ltd.

  16. 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.

  17. Novel Three-Dimensional Image Fusion Software to Facilitate Guidance of Complex Cardiac Catheterization : 3D image fusion for interventions in CHD.

    PubMed

    Goreczny, Sebastian; Dryzek, Pawel; Morgan, Gareth J; Lukaszewski, Maciej; Moll, Jadwiga A; Moszura, Tomasz

    2017-08-01

    We report initial experience with novel three-dimensional (3D) image fusion software for guidance of transcatheter interventions in congenital heart disease. Developments in fusion imaging have facilitated the integration of 3D roadmaps from computed tomography or magnetic resonance imaging datasets. The latest software allows live fusion of two-dimensional (2D) fluoroscopy with pre-registered 3D roadmaps. We reviewed all cardiac catheterizations guided with this software (Philips VesselNavigator). Pre-catheterization imaging and catheterization data were collected focusing on fusion of 3D roadmap, intervention guidance, contrast and radiation exposure. From 09/2015 until 06/2016, VesselNavigator was applied in 34 patients for guidance (n = 28) or planning (n = 6) of cardiac catheterization. In all 28 patients successful 2D-3D registration was performed. Bony structures combined with the cardiovascular silhouette were used for fusion in 26 patients (93%), calcifications in 9 (32%), previously implanted devices in 8 (29%) and low-volume contrast injection in 7 patients (25%). Accurate initial 3D roadmap alignment was achieved in 25 patients (89%). Six patients (22%) required realignment during the procedure due to distortion of the anatomy after introduction of stiff equipment. Overall, VesselNavigator was applied successfully in 27 patients (96%) without any complications related to 3D image overlay. VesselNavigator was useful in guidance of nearly all of cardiac catheterizations. The combination of anatomical markers and low-volume contrast injections allowed reliable 2D-3D registration in the vast majority of patients.

  18. Determining of a robot workspace using the integration of a CAD system with a virtual control system

    NASA Astrophysics Data System (ADS)

    Herbuś, K.; Ociepka, P.

    2016-08-01

    The paper presents a method for determining the workspace of an industrial robot using an approach consisting in integration a 3D model of an industrial robot with a virtual control system. The robot model with his work environment, prepared for motion simulation, was created in the “Motion Simulation” module of the Siemens PLM NX software. In the mentioned model components of the “link” type were created which map the geometrical form of particular elements of the robot and the components of “joint” type mapping way of cooperation of components of the “link” type. In the paper is proposed the solution in which the control process of a virtual robot is similar to the control process of a real robot using the manual control panel (teach pendant). For this purpose, the control application “JOINT” was created, which provides the manipulation of a virtual robot in accordance with its internal control system. The set of procedures stored in an .xlsx file is the element integrating the 3D robot model working in the CAD/CAE class system with the elaborated control application.

  19. 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.

  20. Simple and cost-effective hardware and software for functional brain mapping using intrinsic optical signal imaging.

    PubMed

    Harrison, Thomas C; Sigler, Albrecht; Murphy, Timothy H

    2009-09-15

    We describe a simple and low-cost system for intrinsic optical signal (IOS) imaging using stable LED light sources, basic microscopes, and commonly available CCD cameras. IOS imaging measures activity-dependent changes in the light reflectance of brain tissue, and can be performed with a minimum of specialized equipment. Our system uses LED ring lights that can be mounted on standard microscope objectives or video lenses to provide a homogeneous and stable light source, with less than 0.003% fluctuation across images averaged from 40 trials. We describe the equipment and surgical techniques necessary for both acute and chronic mouse preparations, and provide software that can create maps of sensory representations from images captured by inexpensive 8-bit cameras or by 12-bit cameras. The IOS imaging system can be adapted to commercial upright microscopes or custom macroscopes, eliminating the need for dedicated equipment or complex optical paths. This method can be combined with parallel high resolution imaging techniques such as two-photon microscopy.

  1. 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.

  2. 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

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

    PubMed Central

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

    2014-01-01

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

  4. Advanced Cell Classifier: User-Friendly Machine-Learning-Based Software for Discovering Phenotypes in High-Content Imaging Data.

    PubMed

    Piccinini, Filippo; Balassa, Tamas; Szkalisity, Abel; Molnar, Csaba; Paavolainen, Lassi; Kujala, Kaisa; Buzas, Krisztina; Sarazova, Marie; Pietiainen, Vilja; Kutay, Ulrike; Smith, Kevin; Horvath, Peter

    2017-06-28

    High-content, imaging-based screens now routinely generate data on a scale that precludes manual verification and interrogation. Software applying machine learning has become an essential tool to automate analysis, but these methods require annotated examples to learn from. Efficiently exploring large datasets to find relevant examples remains a challenging bottleneck. Here, we present Advanced Cell Classifier (ACC), a graphical software package for phenotypic analysis that addresses these difficulties. ACC applies machine-learning and image-analysis methods to high-content data generated by large-scale, cell-based experiments. It features methods to mine microscopic image data, discover new phenotypes, and improve recognition performance. We demonstrate that these features substantially expedite the training process, successfully uncover rare phenotypes, and improve the accuracy of the analysis. ACC is extensively documented, designed to be user-friendly for researchers without machine-learning expertise, and distributed as a free open-source tool at www.cellclassifier.org. Copyright © 2017 Elsevier Inc. All rights reserved.

  5. New technique to count mosquito adults: using ImageJ software to estimate number of mosquito adults in a trap.

    PubMed

    Kesavaraju, Banugopan; Dickson, Sammie

    2012-12-01

    A new technique is described here to count mosquitoes using open-source software. We wanted to develop a protocol that would estimate the total number of mosquitoes from a picture using ImageJ. Adult mosquitoes from CO2-baited traps were spread on a tray and photographed. The total number of mosquitoes in a picture was estimated using various calibrations on ImageJ, and results were compared with manual counting to identify the ideal calibration. The average trap count was 1,541, and the average difference between the manual count and the best calibration was 174.11 +/- 21.59, with 93% correlation. Subsequently, contents of a trap were photographed 5 different times after they were shuffled between each picture to alter the picture pattern of adult mosquitoes. The standard error among variations stayed below 50, indicating limited variation for total count between pictures of the same trap when the pictures were processed through ImageJ. These results indicate the software could be utilized efficiently to estimate total number of mosquitoes from traps.

  6. A software tool for interactive generation, representation, and systematical storage of transfer functions for 3D medical images.

    PubMed

    Alper Selver, M; Fischer, Felix; Kuntalp, Mehmet; Hillen, Walter

    2007-06-01

    As being a tool that assigns optical parameters, i.e. color, transparency, used in interactive visualization, transfer functions have very important effects on the quality of volume rendered medical images. However, finding accurate transfer functions is a very difficult, tedious, and time consuming task because of the variety of all possibilities. By addressing this problem, a software module, which can be easily plugged into any visualization program, is developed based on the specific expectations of medical experts. Its design includes both a new user interface to ease the interactive generation of the volume rendered medical images and a volumetric histogram based method for initial generation of transfer functions. In addition, a novel file system has been implemented to represent 3D medical images using transfer functions based on the DICOM standard. For evaluation of the system by various medical experts, the software is installed into a DICOM viewer. Based on the feedback obtained from the medical experts, several improvements are made, especially to increase the flexibility of the program. The final version of the implemented system shortens the transfer function design process and is applicable to various application areas.

  7. The MicroAnalysis Toolkit: X-ray Fluorescence Image Processing Software

    SciTech Connect

    Webb, S. M.

    2011-09-09

    The MicroAnalysis Toolkit is an analysis suite designed for the processing of x-ray fluorescence microprobe data. The program contains a wide variety of analysis tools, including image maps, correlation plots, simple image math, image filtering, multiple energy image fitting, semi-quantitative elemental analysis, x-ray fluorescence spectrum analysis, principle component analysis, and tomographic reconstructions. To be as widely useful as possible, data formats from many synchrotron sources can be read by the program with more formats available by request. An overview of the most common features will be presented.

  8. Preprocessing with Photoshop Software on Microscopic Images of A549 Cells in Epithelial-Mesenchymal Transition.

    PubMed

    Ren, Zhou-Xin; Yu, Hai-Bin; Shen, Jun-Ling; Li, Ya; Li, Jian-Sheng

    2015-06-01

    To establish a preprocessing method for cell morphometry in microscopic images of A549 cells in epithelial-mesenchymal transition (EMT). Adobe Photoshop CS2 (Adobe Systems, Inc.) was used for preprocessing the images. First, all images were processed for size uniformity and high distinguishability between the cell and background area. Then, a blank image with the same size and grids was established and cross points of the grids were added into a distinct color. The blank image was merged into a processed image. In the merged images, the cells with 1 or more cross points were chosen, and then the cell areas were enclosed and were replaced in a distinct color. Except for chosen cellular areas, all areas were changed into a unique hue. Three observers quantified roundness of cells in images with the image preprocess (IPP) or without the method (Controls), respectively. Furthermore, 1 observer measured the roundness 3 times with the 2 methods, respectively. The results between IPPs and Controls were compared for repeatability and reproducibility. As compared with the Control method, among 3 observers, use of the IPP method resulted in a higher number and a higher percentage of same-chosen cells in an image. The relative average deviation values of roundness, either for 3 observers or 1 observer, were significantly higher in Controls than in IPPs (p < 0.01 or 0.001). The values of intraclass correlation coefficient, both in Single Type or Average, were higher in IPPs than in Controls both for 3 observers and 1 observer. Processed with Adobe Photoshop, a chosen cell from an image was more objective, regular, and accurate, creating an increase of reproducibility and repeatability on morphometry of A549 cells in epithelial to mesenchymal transition.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Software-based mitigation of image degradation due to atmospheric turbulence

    NASA Astrophysics Data System (ADS)

    Huebner, Claudia S.; Scheifling, Corinne

    2010-10-01

    Motion-Compensated Averaging (MCA) with blind deconvolution has proven successful in mitigating turbulence effects like image dancing and blurring. In this paper an image quality control according to the "Lucky Imaging" principle is combined with the MCA-procedure, weighting good frames more heavily than bad ones, skipping a given percentage of extremely degraded frames entirely. To account for local isoplanatism, when image dancing will effect local displacements between consecutive frames rather than global shifts only, a locally operating MCA variant with block matching, proposed in earlier work, is employed. In order to reduce loss of detail due to normal averaging, various combinations of temporal mode, median and mean are tested as reference image. The respective restoration results by means of a weighted blind deconvolution algorithm are presented and evaluated.

  15. Software-based PET-MR image coregistration: combined PET-MRI for the rest of us!

    PubMed

    Robertson, Matthew S; Liu, Xinyang; Plishker, William; Zaki, George F; Vyas, Pranav K; Safdar, Nabile M; Shekhar, Raj

    2016-10-01

    With the introduction of hybrid positron emission tomography/magnetic resonance imaging (PET/MRI), a new imaging option to acquire multimodality images with complementary anatomical and functional information has become available. Compared with hybrid PET/computed tomography (CT), hybrid PET/MRI is capable of providing superior anatomical detail while removing the radiation exposure associated with CT. The early adoption of hybrid PET/MRI, however, has been limited. To provide a viable alternative to the hybrid PET/MRI hardware by validating a software-based solution for PET-MR image coregistration. A fully automated, graphics processing unit-accelerated 3-D deformable image registration technique was used to align PET (acquired as PET/CT) and MR image pairs of 17 patients (age range: 10 months-21 years, mean: 10 years) who underwent PET/CT and body MRI (chest, abdomen or pelvis), which were performed within a 28-day (mean: 10.5 days) interval. MRI data for most of these cases included single-station post-contrast axial T1-weighted images. Following registration, maximum standardized uptake value (SUVmax) values observed in coregistered PET (cPET) and the original PET were compared for 82 volumes of interest. In addition, we calculated the target registration error as a measure of the quality of image coregistration, and evaluated the algorithm's performance in the context of interexpert variability. The coregistration execution time averaged 97±45 s. The overall relative SUVmax difference was 7% between cPET-MRI and PET/CT. The average target registration error was 10.7±6.6 mm, which compared favorably with the typical voxel size (diagonal distance) of 8.0 mm (typical resolution: 0.66 mm × 0.66 mm × 8 mm) for MRI and 6.1 mm (typical resolution: 3.65 mm × 3.65 mm × 3.27 mm) for PET. The variability in landmark identification did not show statistically significant differences between the algorithm and a typical expert. We have

  16. Useful diagnostic biometabolic data obtained by PET/CT and MR fusion imaging using open source software.

    PubMed

    Antonica, Filippo; Asabella, Artor Niccoli; Ferrari, Cristina; Rubini, Domenico; Notaristefano, Antonio; Nicoletti, Adriano; Altini, Corinna; Merenda, Nunzio; Mossa, Emilio; Guarini, Attilio; Rubini, Giuseppe

    2014-01-01

    In the last decade numerous attempts were considered to co-register and integrate different imaging data. Like PET/CT the integration of PET to MR showed great interest. PET/MR scanners are recently tested on different distrectual or systemic pathologies. Unfortunately PET/MR scanners are expensive and diagnostic protocols are still under studies and investigations. Nuclear Medicine imaging highlights functional and biometabolic information but has poor anatomic details. The aim of this study is to integrate MR and PET data to produce distrectual or whole body fused images acquired from different scanners even in different days. We propose an offline method to fuse PET with MR data using an open-source software that has to be inexpensive, reproducible and capable to exchange data over the network. We also evaluate global quality, alignment quality, and diagnostic confidence of fused PET-MR images. We selected PET/CT studies performed in our Nuclear Medicine unit, MR studies provided by patients on DICOM CD media or network received. We used Osirix 5.7 open source version. We aligned CT slices with the first MR slice, pointed and marked for co-registration using MR-T1 sequence and CT as reference and fused with PET to produce a PET-MR image. A total of 100 PET/CT studies were fused with the following MR studies: 20 head, 15 thorax, 24 abdomen, 31 pelvis, 10 whole body. An interval of no more than 15 days between PET and MR was the inclusion criteria. PET/CT, MR and fused studies were evaluated by two experienced radiologist and two experienced nuclear medicine physicians. Each one filled a five point based evaluation scoring scheme based on image quality, image artifacts, segmentation errors, fusion misalignment and diagnostic confidence. Our fusion method showed best results for head, thorax and pelvic districts in terms of global quality, alignment quality and diagnostic confidence,while for the abdomen and pelvis alignement quality and global quality resulted

  17. Online Workspace to Connect Scientists with NASA's Science E/PO Efforts and Practitioners

    NASA Astrophysics Data System (ADS)

    Shipp, Stephanie; Bartolone , Lindsay; Peticolas, Laura; Woroner, Morgan; Dalton, Heather; Schwerin, Theresa; Smith, Denise

    2014-11-01

    There is a growing awareness of the need for a scientifically literate public in light of challenges facing society today, and also a growing concern about the preparedness of our future workforce to meet those challenges. Federal priorities for science, technology, engineering, and math (STEM) education call for improvement of teacher training, increased youth and public engagement, greater involvement of underrepresented populations, and investment in undergraduate and graduate education. How can planetary scientists contribute to these priorities? How can they “make their work and findings comprehensible, appealing, and available to the public” as called for in the Planetary Decadal Survey?NASA’s Science Mission Directorate (SMD) Education and Public Outreach (E/PO) workspace provides the SMD E/PO community of practice - scientists and educators funded to conduct SMD E/PO or those using NASA’s science discoveries in E/PO endeavors - with an online environment in which to communicate, collaborate, and coordinate activities, thus helping to increase effectiveness of E/PO efforts. The workspace offers interested scientists avenues to partner with SMD E/PO practitioners and learn about E/PO projects and impacts, as well as to advertise their own efforts to reach a broader audience. Through the workspace, scientists can become aware of opportunities for involvement and explore resources to improve professional practice, including literature reviews of best practices for program impact, mechanisms for engaging diverse audiences, and large- and small-scale program evaluation. Scientists will find “how to” manuals for getting started and increasing impact with public presentations, classroom visits, and other audiences, as well as primers with activity ideas and resources that can augment E/PO interactions with different audiences. The poster will introduce the workspace to interested scientists and highlight pathways to resources of interest that can help

  18. The Human-Information Workspace (HI-Space): Ambient Table Top Entertainment

    SciTech Connect

    Cowell, Andrew J.; May, Richard A.; Cramer, Nick O.; Matthias Rauterberg

    2004-09-01

    This paper introduces the Human Information Workspace (HISpace) as a test-bed for evaluating new information exploration mechanisms. In moving from dated interaction devices and small computer monitors, we aim to utilize more natural surfaces such as tables and walls as our interaction space. In testing our theories, we have produced a number of gaming applications as test cases. Here, we report on our most popular application, Virtual Hockey.

  19. Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples

    PubMed Central

    MacLeod, R.S.; Stinstra, J.G.; Lew, S.; Whitaker, R.T.; Swenson, D.J.; Cole, M.J.; Krüger, J.; Brooks, D.H.; Johnson, C.R.

    2009-01-01

    Many simulation studies in biomedicine are based on a similar sequence of processing steps, starting from images and running through geometric model generation, assignment of tissue properties, numerical simulation and visualization of the results—a process known as image-based geometric modelling and simulation. We present an overview of software systems for implementing such a sequence both within highly integrated problem-solving environments and in the form of loosely integrated pipelines. Loose integration in this case indicates that individual programs function largely independently but communicate through files of a common format and support simple scripting, so as to automate multiple executions wherever possible. We then describe three specific applications of such pipelines to translational biomedical research in electrophysiology. PMID:19414456

  20. Subject-specific, multiscale simulation of electrophysiology: a software pipeline for image-based models and application examples.

    PubMed

    MacLeod, R S; Stinstra, J G; Lew, S; Whitaker, R T; Swenson, D J; Cole, M J; Krüger, J; Brooks, D H; Johnson, C R

    2009-06-13

    Many simulation studies in biomedicine are based on a similar sequence of processing steps, starting from images and running through geometric model generation, assignment of tissue properties, numerical simulation and visualization of the results--a process known as image-based geometric modelling and simulation. We present an overview of software systems for implementing such a sequence both within highly integrated problem-solving environments and in the form of loosely integrated pipelines. Loose integration in this case indicates that individual programs function largely independently but communicate through files of a common format and support simple scripting, so as to automate multiple executions wherever possible. We then describe three specific applications of such pipelines to translational biomedical research in electrophysiology.

  1. Longitudinal evaluation of upper extremity reachable workspace in ALS by Kinect sensor.

    PubMed

    de Bie, Evan; Oskarsson, Bjorn; Joyce, Nanette C; Nicorici, Alina; Kurillo, Gregorij; Han, Jay J

    2017-02-01

    Our objective was to evaluate longitudinal changes in Microsoft Kinect measured upper extremity reachable workspace relative surface area (RSA) versus the revised Amyotrophic Lateral Sclerosis Functional Rating Scale (ALSFRS-R), ALSFRS-R upper extremity sub-scale and Forced Vital Capacity (FVC) in a cohort of patients diagnosed with amyotrophic lateral sclerosis (ALS). Ten patients diagnosed with ALS (ages 52-76 years, ALSFRS-R: 8-41 at entry) were tested using single 3D depth sensor, Microsoft Kinect, to measure reachable workspace RSA across five visits spanning one year. Changes in RSA, ALSFRS-R, ALSFRS-R upper extremity sub-scale, and FVC were assessed using a linear mixed model. Results showed that upper lateral quadrant RSA declined significantly in one year by approximately 19% (p <0.01) while all other quadrants and total RSA did not change significantly in this time-period. Simultaneously, ALSFRS-R upper extremity sub-scale worsened significantly by 25% (p <0.01). In conclusion, upper extremity reachable workspace RSA as a novel ALS outcome measure is capable of objectively quantifying declines in upper extremity ability over time in patients with ALS with more granularity than other common outcome measures. RSA may serve as a clinical endpoint for the evaluation of upper extremity targeted therapeutics.

  2. Mathematically gifted adolescents mobilize enhanced workspace configuration of theta cortical network during deductive reasoning.

    PubMed

    Zhang, L; Gan, J Q; Wang, H

    2015-03-19

    Previous studies have established the importance of the fronto-parietal brain network in the information processing of reasoning. At the level of cortical source analysis, this eletroencepalogram (EEG) study investigates the functional reorganization of the theta-band (4-8Hz) neurocognitive network of mathematically gifted adolescents during deductive reasoning. Depending on the dense increase of long-range phase synchronizations in the reasoning process, math-gifted adolescents show more significant adaptive reorganization and enhanced "workspace" configuration in the theta network as compared with average-ability control subjects. The salient areas are mainly located in the anterior cortical vertices of the fronto-parietal network. Further correlation analyses have shown that the enhanced workspace configuration with respect to the global topological metrics of the theta network in math-gifted subjects is correlated with the intensive frontal midline theta (fm theta) response that is related to strong neural effort for cognitive events. These results suggest that by investing more cognitive resources math-gifted adolescents temporally mobilize an enhanced task-related global neuronal workspace, which is manifested as a highly integrated fronto-parietal information processing network during the reasoning process.

  3. Dosimetry software Hermes Internal Radiation Dosimetry: from quantitative image reconstruction to voxel-level absorbed dose distribution.

    PubMed

    Hippeläinen, Eero T; Tenhunen, Mikko J; Mäenpää, Hanna O; Heikkonen, Jorma J; Sohlberg, Antti O

    2017-05-01

    The aim of this work is to validate a software package called Hermes Internal Radiation Dosimetry (HIRD) for internal dose assessment tailored for clinical practice. The software includes all the necessary steps to perform voxel-level absorbed dose calculations including quantitative reconstruction, image coregistration and volume of interest tools. The basics of voxel-level dosimetry methods and implementations to HIRD software are reviewed. Then, HIRD is validated using simulated SPECT/CT data and data from Lu-DOTATATE-treated patients by comparing absorbed kidney doses with OLINDA/EXM-based dosimetry. In addition, electron and photon dose components are studied separately in an example patient case. The simulation study showed that HIRD can reproduce time-activity curves accurately and produce absorbed doses with less than 10% error for the kidneys, liver and spleen. From the patient data, the absorbed kidney doses calculated using HIRD and using OLINDA/EXM were highly correlated (Pearson's correlation coefficient, r=0.98). From Bland-Altman plot analysis, an average absorbed dose difference of -2% was found between the methods. In addition, we found that in Lu-DOTATATE-treated patients, photons can contribute over 10% of the kidney's total dose and is partly because of cross-irradiation from high-uptake lesions close to the kidneys. HIRD is a straightforward voxel-level internal dosimetry software. Its clinical utility was verified with simulated and clinical Lu-DOTATATE-treated patient data. Patient studies also showed that photon contribution towards the total dose can be relatively high and voxel-level dose calculations can be valuable in cases where the target organ is in close proximity to high-uptake organs.

  4. 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.

  5. 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.

  6. The disagreement between the ideal observer and human observers in hardware and software imaging system optimization: theoretical explanations and evidence

    NASA Astrophysics Data System (ADS)

    He, Xin

    2017-03-01

    The ideal observer is widely used in imaging system optimization. One practical question remains open: do the ideal and human observers have the same preference in system optimization and evaluation? Based on the ideal observer's mathematical properties proposed by Barrett et. al. and the empirical properties of human observers investigated by Myers et. al., I attempt to pursue the general rules regarding the applicability of the ideal observer in system optimization. Particularly, in software optimization, the ideal observer pursues data conservation while humans pursue data presentation or perception. In hardware optimization, the ideal observer pursues a system with the maximum total information, while humans pursue a system with the maximum selected (e.g., certain frequency bands) information. These different objectives may result in different system optimizations between human and the ideal observers. Thus, an ideal observer optimized system is not necessarily optimal for humans. I cite empirical evidence in search and detection tasks, in hardware and software evaluation, in X-ray CT, pinhole imaging, as well as emission computed tomography to corroborate the claims. (Disclaimer: the views expressed in this work do not necessarily represent those of the FDA)

  7. Assessing accumulated hard-tissue debris using micro-computed tomography and free software for image processing and analysis.

    PubMed

    De-Deus, Gustavo; Marins, Juliana; Neves, Aline de Almeida; Reis, Claudia; Fidel, Sandra; Versiani, Marco A; Alves, Haimon; Lopes, Ricardo Tadeu; Paciornik, Sidnei

    2014-02-01

    The accumulation of debris occurs after root canal preparation procedures specifically in fins, isthmus, irregularities, and ramifications. The aim of this study was to present a step-by-step description of a new method used to longitudinally identify, measure, and 3-dimensionally map the accumulation of hard-tissue debris inside the root canal after biomechanical preparation using free software for image processing and analysis. Three mandibular molars presenting the mesial root with a large isthmus width and a type II Vertucci's canal configuration were selected and scanned. The specimens were assigned to 1 of 3 experimental approaches: (1) 5.25% sodium hypochlorite + 17% EDTA, (2) bidistilled water, and (3) no irrigation. After root canal preparation, high-resolution scans of the teeth were accomplished, and free software packages were used to register and quantify the amount of accumulated hard-tissue debris in either canal space or isthmus areas. Canal preparation without irrigation resulted in 34.6% of its volume filled with hard-tissue debris, whereas the use of bidistilled water or NaOCl followed by EDTA showed a reduction in the percentage volume of debris to 16% and 11.3%, respectively. The closer the distance to the isthmus area was the larger the amount of accumulated debris regardless of the irrigating protocol used. Through the present method, it was possible to calculate the volume of hard-tissue debris in the isthmuses and in the root canal space. Free-software packages used for image reconstruction, registering, and analysis have shown to be promising for end-user application. Copyright © 2014. Published by Elsevier Inc.

  8. Automated Scoring of Chromogenic Media for Detection of Methicillin-Resistant Staphylococcus aureus by Use of WASPLab Image Analysis Software.

    PubMed

    Faron, Matthew L; Buchan, Blake W; Vismara, Chiara; Lacchini, Carla; Bielli, Alessandra; Gesu, Giovanni; Liebregts, Theo; van Bree, Anita; Jansz, Arjan; Soucy, Genevieve; Korver, John; Ledeboer, Nathan A

    2016-03-01

    Recently, systems have been developed to create total laboratory automation for clinical microbiology. These systems allow for the automation of specimen processing, specimen incubation, and imaging of bacterial growth. In this study, we used the WASPLab to validate software that discriminates and segregates positive and negative chromogenic methicillin-resistant Staphylococcus aureus (MRSA) plates by recognition of pigmented colonies. A total of 57,690 swabs submitted for MRSA screening were enrolled in the study. Four sites enrolled specimens following their standard of care. Chromogenic agar used at these sites included MRSASelect (Bio-Rad Laboratories, Redmond, WA), chromID MRSA (bioMérieux, Marcy l'Etoile, France), and CHROMagar MRSA (BD Diagnostics, Sparks, MD). Specimens were plated and incubated using the WASPLab. The digital camera took images at 0 and 16 to 24 h and the WASPLab software determined the presence of positive colonies based on a hue, saturation, and value (HSV) score. If the HSV score fell within a defined threshold, the plate was called positive. The performance of the digital analysis was compared to manual reading. Overall, the digital software had a sensitivity of 100% and a specificity of 90.7% with the specificity ranging between 90.0 and 96.0 across all sites. The results were similar using the three different agars with a sensitivity of 100% and specificity ranging between 90.7 and 92.4%. These data demonstrate that automated digital analysis can be used to accurately sort positive from negative chromogenic agar cultures regardless of the pigmentation produced. Copyright © 2016 Faron et al.

  9. Automated Scoring of Chromogenic Media for Detection of Methicillin-Resistant Staphylococcus aureus by Use of WASPLab Image Analysis Software

    PubMed Central

    Faron, Matthew L.; Vismara, Chiara; Lacchini, Carla; Bielli, Alessandra; Gesu, Giovanni; Liebregts, Theo; van Bree, Anita; Jansz, Arjan; Soucy, Genevieve; Korver, John

    2015-01-01

    Recently, systems have been developed to create total laboratory automation for clinical microbiology. These systems allow for the automation of specimen processing, specimen incubation, and imaging of bacterial growth. In this study, we used the WASPLab to validate software that discriminates and segregates positive and negative chromogenic methicillin-resistant Staphylococcus aureus (MRSA) plates by recognition of pigmented colonies. A total of 57,690 swabs submitted for MRSA screening were enrolled in the study. Four sites enrolled specimens following their standard of care. Chromogenic agar used at these sites included MRSASelect (Bio-Rad Laboratories, Redmond, WA), chromID MRSA (bioMérieux, Marcy l'Etoile, France), and CHROMagar MRSA (BD Diagnostics, Sparks, MD). Specimens were plated and incubated using the WASPLab. The digital camera took images at 0 and 16 to 24 h and the WASPLab software determined the presence of positive colonies based on a hue, saturation, and value (HSV) score. If the HSV score fell within a defined threshold, the plate was called positive. The performance of the digital analysis was compared to manual reading. Overall, the digital software had a sensitivity of 100% and a specificity of 90.7% with the specificity ranging between 90.0 and 96.0 across all sites. The results were similar using the three different agars with a sensitivity of 100% and specificity ranging between 90.7 and 92.4%. These data demonstrate that automated digital analysis can be used to accurately sort positive from negative chromogenic agar cultures regardless of the pigmentation produced. PMID:26719443

  10. WINVICAR - A Windows Based Image Analysis Software Package Suitable for Manipulating EOS Data

    NASA Astrophysics Data System (ADS)

    Hook, S.; Alley, R.; Orton, M. N.

    2002-12-01

    WINVICAR is a collection of approximately 150 programs developed for processing of image data on the Windows platform. WINVICAR is a derivative of the VICAR package developed for image processing on the Unix and VAX/VMS platforms. The programs in the WINVICAR package can be run either at the command prompt or via a graphical user interface (GUI). The programs can also be scripted in batch files. The GUI interface requires that Microsoft Internet Explorer and the Microsoft Windows Scripting be installed on the computer. WINVICAR works on the more recent versions of the Windows operating system. The WINVICAR package includes a customized radiative transfer code for determining and compensating for atmospheric effects in image data. WINVICAR includes numerous programs developed specifically for manipulating data from certain NASA imaging instruments such as the MASTER airborne simulator. MASTER is an airborne imaging system designed to simulate and help validate data from the Moderate Resolution Imaging Spectroradiometer (MODIS) and Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) instruments on NASA Spacecraft. Although the WINVICAR package contains numerous general-purpose image-processing programs for completeness, its primary purpose is to allow users to manipulate data from certain NASA airborne and spaceborne imaging instruments. The WINVICAR package is distributed through the WINVICAR website: http://winvicar.jpl.nasa.gov Acknowledgements The work described in this paper was carried out in part at the Jet Propulsion Laboratory, California Institute of Technology, under a contract with the National Aeronautics and Space Administration as part of the Earth Observing System Mission to Planet Earth Program. Reference herein to any specific commercial product, process, or service by trade names, trademark, manufacturer or otherwise does not imply endorsement by the United States or the Jet Propulsion Laboratory, California Institute of

  11. plusTipTracker: Quantitative image analysis software for the measurement of microtubule dynamics.

    PubMed

    Applegate, Kathryn T; Besson, Sebastien; Matov, Alexandre; Bagonis, Maria H; Jaqaman, Khuloud; Danuser, Gaudenz

    2011-11-01

    Here we introduce plusTipTracker, a Matlab-based open source software package that combines automated tracking, data analysis, and visualization tools for movies of fluorescently-labeled microtubule (MT) plus end binding proteins (+TIPs). Although +TIPs mark only phases of MT growth, the plusTipTracker software allows inference of additional MT dynamics, including phases of pause and shrinkage, by linking collinear, sequential growth tracks. The algorithm underlying the reconstruction of full MT trajectories relies on the spatially and temporally global tracking framework described in Jaqaman et al. (2008). Post-processing of track populations yields a wealth of quantitative phenotypic information about MT network architecture that can be explored using several visualization modalities and bioinformatics tools included in plusTipTracker. Graphical user interfaces enable novice Matlab users to track thousands of MTs in minutes. In this paper, we describe the algorithms used by plusTipTracker and show how the package can be used to study regional differences in the relative proportion of MT subpopulations within a single cell. The strategy of grouping +TIP growth tracks for the analysis of MT dynamics has been introduced before (Matov et al., 2010). The numerical methods and analytical functionality incorporated in plusTipTracker substantially advance this previous work in terms of flexibility and robustness. To illustrate the enhanced performance of the new software we thus compare computer-assembled +TIP-marked trajectories to manually-traced MT trajectories from the same movie used in Matov et al. (2010). Copyright © 2011 Elsevier Inc. All rights reserved.

  12. Novel collaboration and situational awareness environment for leaders and their support staff via self assembling software.

    SciTech Connect

    Bouchard, Ann Marie; Osbourn, Gordon Cecil; Bartholomew, John Warren

    2008-02-01

    This is the final report on the Sandia Fellow LDRD, project 117865, 08-0281. This presents an investigation of self-assembling software intended to create shared workspace environment to allow online collaboration and situational awareness for use by high level managers and their teams.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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. Copyright © 2011 Associazione Italiana di Fisica Medica. Published by Elsevier Ltd. All rights reserved.

  18. 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.

  19. AutoRoot: open-source software employing a novel image analysis approach to support fully-automated plant phenotyping.

    PubMed

    Pound, Michael P; Fozard, Susan; Torres Torres, Mercedes; Forde, Brian G; French, Andrew P

    2017-01-01

    Computer-based phenotyping of plants has risen in importance in recent years. Whilst much software has been written to aid phenotyping using image analysis, to date the vast majority has been only semi-automatic. However, such interaction is not desirable in high throughput approaches. Here, we present a system designed to analyse plant images in a completely automated manner, allowing genuine high throughput measurement of root traits. To do this we introduce a new set of proxy traits. We test the system on a new, automated image capture system, the Microphenotron, which is able to image many 1000s of roots/h. A simple experiment is presented, treating the plants with differing chemical conditions to produce different phenotypes. The automated imaging setup and the new software tool was used to measure proxy traits in each well. A correlation matrix was calculated across automated and manual measures, as a validation. Some particular proxy measures are very highly correlated with the manual measures (e.g. proxy length to manual length, r(2) > 0.9). This suggests that while the automated measures are not directly equivalent to classic manual measures, they can be used to indicate phenotypic differences (hence the term, proxy). In addition, the raw discriminative power of the new proxy traits was examined. Principal component analysis was calculated across all proxy measures over two phenotypically-different groups of plants. Many of the proxy traits can be used to separate the data in the two conditions. The new proxy traits proposed tend to correlate well with equivalent manual measures, where these exist. Additionally, the new measures display strong discriminative power. It is suggested that for particular phenotypic differences, different traits will be relevant, and not all will have meaningful manual equivalent measures. However, approaches such as PCA can be used to interrogate the resulting data to identify differences between datasets. Select images can

  20. 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.

  1. 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.

  2. 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).

  3. 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.

  4. 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.

  5. Improved modified pressure imaging and software for egg micro-crack detection and egg quality grading

    USDA-ARS?s Scientific Manuscript database

    Cracks in the egg shell increase a food safety risk. Especially, eggs with very fine, hairline cracks (micro-cracks) are often undetected during the grading process because they are almost impossible to detect visually. A modified pressure imaging system was developed to detect eggs with micro-crack...

  6. Liver steatosis assessment: correlations among pathology, radiology, clinical data and automated image analysis software.

    PubMed

    Lee, Michael J; Bagci, Pelin; Kong, Jun; Vos, Miriam B; Sharma, Puneet; Kalb, Bobby; Saltz, Joel H; Martin, Diego R; Adsay, N Volkan; Farris, Alton B

    2013-06-01

    Quantitating hepatic steatosis is important in many liver diseases and liver transplantation. Since steatosis estimation by pathologists has inherent intra- and inter-observer variability, we compared and contrasted computerized techniques with magnetic resonance imaging measurements, pathologist visual scoring, and clinical parameters. Computerized methods applied to whole slide images included a commercial positive pixel count algorithm and a custom algorithm programmed at our institution. For all liver samples (n=59), including pediatric, adult, frozen section, and permanent specimens, statistically significant correlations were observed between pathology, radiology, and each image analysis modality (r=0.75-0.97, p<0.0001), with the strongest correlations in the pediatric cohort. Statistically significant relationships were observed between each method and with body mass index (r=0.37-0.56, p from <0.0001 to <0.05) and with albumin (r=0.55-0.64, p<0.05) but not with alanine aminotransferase or aspartate aminotransferase. Although pathologist assessments correlated (r=0.64-0.86, 0.92-0.97, and 0.78-0.91 for microvesicular, macrovesicular, and overall steatosis, respectively), the absolute values of hepatic steatosis visual assessment were susceptible to intra- and inter-observer variability, particularly for microvesicular steatosis. Image analysis, pathologist assessments, radiology measurements, and several clinical parameters all showed correlations in this study, providing evidence for the utility of each method in different clinical and research settings. Copyright © 2013 Elsevier GmbH. All rights reserved.

  7. 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.

  8. 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.

  9. Quantification of Abdominal Fat in Obese and Healthy Adolescents Using 3 Tesla Magnetic Resonance Imaging and Free Software for Image Analysis.

    PubMed

    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

    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. 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. 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). 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.

  10. 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

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

    PubMed

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

    2015-03-01

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

  12. 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.

  13. Object oriented design provides flexible framework for electrophysiolgy software toolbox - biomed 2010.

    PubMed

    Gruner, Charlotte M

    2010-01-01

    This work describes a software platform to support an expandible toolbox for electrophysiology data analysis. The current focus of the toolbox, known as NeuroMAX is spike-sorting and spike-time analysis tools. A key feature of the toolbox is the ability for a user to connect tools into a workspace toolchain in a flexible, intelligent feed-forward manner that allows a tool to use any previously computed data set as input. Tool parameters can be saved and applied to other data sets. Tools and workspaces can be accessed to process data either directly from the MATLAB command line or from the NeuroMAX GUI. This work discusses the object-oriented design of the toolbox, including the data classes, workspace classes, and tool classes created to achieve this functionality.

  14. [Development of software for three-dimensional reconstruction and automatic quantification of intravascular ultrasound images. Initial experience].

    PubMed

    Sanz, Roberto; Bodí, Vicente; Sanchís, Juan; Moratal, David; Núñez, Julio; Palau, Patricia; García, Diego; Rieta, José J; Sanchís, Juan M; Chorro, Francisco J; Llácer, Angel

    2006-09-01

    Quantification of intravascular ultrasound (IVUS) images is essential in ischemic heart disease and interventional cardiology. Manual analysis is very slow and expensive. We describe an automated computerized method of analysis that requires only minimal initial input from a specialist. This study was carried out by interventional cardiologists and biomedical engineers working in close collaboration. We developed software in which it was necessary only to identify the media-adventitia boundary in a few images taken from the whole sequence. A three-dimensional reconstruction was then generated from each sequence, from which measurements of areas and volumes could be derived automatically. In total, 2300 randomly selected images from video sequences of 11 patients were analyzed. Results obtained using the proposed method differed only minimally from those obtained with the manual method: for vessel area measurements, the variability was 0.08 (0.07) (mean absolute error [standard deviation] normalized to the actual value; this corresponds to an error of 0.08 mm(2) per mm(2) of vessel area); for lumen area, 0.11 (0.11) (normalized), and for plaque volume, 0.5 (0.3) (normalized). Regions with severe lesions (<4 mm(2)) were correctly identified in more than 90% of cases. Specialist time needed for each reconstruction was 10 (8) minutes (vs 60 [10] minutes for manual analysis; P< .0001). The computerized method used dramatically reduced the time and effort needed for IVUS sequence analysis, and the automated measurements obtained were very promising.

  15. Inter-Rater and Intra-Rater Repeatability and Reliability of EOS 3-Dimensional Imaging Analysis Software.

    PubMed

    Demzik, Alysen L; Alvi, Hasham M; Delagrammaticas, Dimitri E; Martell, John M; Beal, Matthew D; Manning, David W

    2016-05-01

    Quantifying ideal component position for the acetabulum and stem during total hip arthroplasty (THA) has been described by many methods. A new imaging method using low-dose digital stereoradiography, the EOS imaging system, is a biplanar low-dose X-ray system that allows for 3-dimensional modeling of lower limbs and semiautomated measurement of pelvic parameters and implant alignment. Twenty-five patients who underwent primary THA by a single surgeon between October 2014 and December 2014 were retrospectively selected. Only patients with unilateral THA without associated spine pathologies were included, totaling 16 right hips and 9 left hips. There were 8 men and 17 women in the cohort, with a mean age of 67 years (range, 53-82). Three individuals performed measurements of pelvic parameters and implant alignment on 3 separate occasions. An interclass correlation of >0.75 was accepted as evidence of excellent agreement and a confirmation of measurement reliability. Before reviewing patient radiographs, 4 pelvic phantom models were analyzed using the EOS 3-dimensional software to verify accuracy. All anatomic and implant measurements performed by the 3 independent reviewers showed interobserver and intraobserver agreement with interclass correlation >0.75. Three-dimensional modeling of hip implants with the EOS imaging system is a reasonable option for the evaluation of component position after THA. Copyright © 2016 Elsevier Inc. All rights reserved.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. Software programmable multi-mode interface for nuclear-medical imaging

    SciTech Connect

    Zubal, I.G.; Rowe, R.W.; Bizais, Y.J.C.; Bennett, G.W.; Brill, A.B.

    1982-01-01

    An innovative multi-port interface allows gamma camera events (spatial coordinates and energy) to be acquired concurrently with a sampling of physiological patient data. The versatility of the interface permits all conventional static, dynamic, and tomographic imaging modes, in addition to multi-hole coded aperture acquisition. The acquired list mode data may be analyzed or gated on the basis of various camera, isotopic, or physiological parameters.

  3. 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 respo