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Software and Algorithms for Biomedical Image Data Processing and Visualization

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 as product inspection or assembly of parts in space and industry.

Talukder, Ashit

NASA Tech Briefs, September 2003

Topics include: Oxygen-Partial-Pressure Sensor for Aircraft Oxygen Mask; Three-Dimensional Venturi Sensor for Measuring Extreme Winds; Swarms of Micron-Sized Sensors; Monitoring Volcanoes by Use of Air-Dropped Sensor Packages; Capacitive Sensors for Measuring Masses of Cryogenic Fluids; UHF Microstrip Antenna Array for Synthetic- Aperture Radar; Multimode Broad-Band Patch Antennas; 164-GHz MMIC HEMT Frequency Doubler; GPS Position and Heading Circuitry for Ships; Software for Managing Parametric Studies; Software Aids Visualization of Computed Unsteady Flow; Software for Testing Electroactive Structural Components; Advanced Software for Analysis of High-Speed Rolling-Element Bearings; Web Program for Development of GUIs for Cluster Computers; XML-Based Generator of C++ Code for Integration With GUIs; Oxide Protective Coats for Ir/Re Rocket Combustion Chambers; Simplified Waterproofing of Aerogels; Improved Thermal-Insulation Systems for Low Temperatures; Device for Automated Cutting and Transfer of Plant Shoots; Extension of Liouville Formalism to Postinstability Dynamics; Advances in Thrust-Based Emergency Control of an Airplane; Ultrasonic/Sonic Mechanisms for Drilling and Coring; Exercise Device Would Exert Selectable Constant Resistance; Improved Apparatus for Measuring Distance Between Axles; Six Classes of Diffraction-Based Optoelectronic Instruments; Modernizing Fortran 77 Legacy Codes; Active State Model for Autonomous Systems; Shields for Enhanced Protection Against High-Speed Debris; Scaling of Two-Phase Flows to Partial-Earth Gravity; Neutral-Axis Springs for Thin-Wall Integral Boom Hinges.

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AirSTAR Hardware and Software Design for Beyond Visual Range Flight Research

The National Aeronautics and Space Administration (NASA) Airborne Subscale Transport Aircraft Research (AirSTAR) Unmanned Aerial System (UAS) is a facility developed to study the flight dynamics of vehicles in emergency conditions, in support of aviation safety research. The system was upgraded to have its operational range significantly expanded, going beyond the line of sight of a ground-based pilot. A redesign of the airborne flight hardware was undertaken, as well as significant changes to the software base, in order to provide appropriate autonomous behavior in response to a number of potential failures and hazards. Ground hardware and system monitors were also upgraded to include redundant communication links, including ADS-B based position displays and an independent flight termination system. The design included both custom and commercially available avionics, combined to allow flexibility in flight experiment design while still benefiting from tested configurations in reversionary flight modes. A similar hierarchy was employed in the software architecture, to allow research codes to be tested, with a fallback to more thoroughly validated flight controls. As a remotely piloted facility, ground systems were also developed to ensure the flight modes and system state were communicated to ground operations personnel in real-time. Presented in this paper is a general overview of the concept of operations for beyond visual range flight, and a detailed review of the airborne hardware and software design. This discussion is held in the context of the safety and procedural requirements that drove many of the design decisions for the AirSTAR UAS Beyond Visual Range capability.

Laughter, Sean

Reimagining Disassembly Interfaces With Visualization: Combining Instruction Tracing and Control Flow With DisViz

In applications where efficiency is critical, developers may examine their compiled binaries, seeking to understand how the compiler transformed their source code and what performance implications that transformation may have. This analysis is challenging due to the vast number of disassembled binary instructions and the many-to-many mappings between them and the source code. These problems are exacerbated as source code size increases, giving the compiler more freedom to map and disperse binary instructions across the disassembly space. Interfaces for disassembly typically display instructions as an unstructured listing or sacrifice the order of execution. Here, we design a new visual interface for disassembly code that combines execution order with control flow structure, enabling analysts to both trace through code and identify familiar aspects of the computation. Central to our approach is a novel layout of instructions grouped into basic blocks that displays a looping structure in an intuitive way. We add to this disassembly representation a unique block-based mini-map that leverages our layout and shows context across thousands of disassembly instructions. Finally, we embed our disassembly visualization in a web-based tool, DisViz, which adds dynamic linking with source code across the entire application. DizViz was developed in collaboration with program analysis experts following design study methodology and was validated through evaluation sessions with ten participants from four institutions. Participants successfully completed the evaluation tasks, hypothesized about compiler optimizations, and noted the utility of our new disassembly view. Our evaluation suggests that our new integrated view helps application developers in understanding and navigating disassembly code.

Computer science

Astronomer's Proposal Tool

Astronomer's Proposal Tool (APT) is a computer program that assists astronomers in preparing their Phase 1 and Phase 2 Hubble Space Telescope science programs. APT is a successor to the Remote Proposal Submission System 2 (RPS2) program, which has been rendered obsolete by more recent advances in computer software and hardware. APT exploits advances associated with widespread use of the Internet, multiplatform visual development software tools, and overall increases in the power of desktop computer hardware, all in such a way as to make the preparation and submission of proposals more intuitive and make observatory operations less cumbersome. APT provides documentation and help that are friendly, up to date, and easily accessible to users of varying levels of expertise, while defining an extensible framework that is responsive to changes in both technology and observatory operations. APT consists of two major components: (1) a set of software tools that are intuitive, visual, and responsive and (2) an integrated software environment that unifies all the tools and makes them interoperable. The APT tools include the Visual Target Tuner, Proposal Editor, Exposure Planner, Bright Object Checker, and Visit Planner.

Krueger, Tony

Scientific Visualization and Computational Science: Natural Partners

Scientific visualization is developing rapidly, stimulated by computational science, which is gaining acceptance as a third alternative to theory and experiment. Computational science is based on numerical simulations of mathematical models derived from theory. But each individual simulation is like a hypothetical experiment; initial conditions are specified, and the result is a record of the observed conditions. Experiments can be simulated for situations that can not really be created or controlled. Results impossible to measure can be computed.. Even for observable values, computed samples are typically much denser. Numerical simulations also extend scientific exploration where the mathematics is analytically intractable. Numerical simulations are used to study phenomena from subatomic to intergalactic scales and from abstract mathematical structures to pragmatic engineering of everyday objects. But computational science methods would be almost useless without visualization. The obvious reason is that the huge amounts of data produced require the high bandwidth of the human visual system, and interactivity adds to the power. Visualization systems also provide a single context for all the activities involved from debugging the simulations, to exploring the data, to communicating the results. Most of the presentations today have their roots in image processing, where the fundamental task is: Given an image, extract information about the scene. Visualization has developed from computer graphics, and the inverse task: Given a scene description, make an image. Visualization extends the graphics paradigm by expanding the possible input. The goal is still to produce images; the difficulty is that the input is not a scene description displayable by standard graphics methods. Visualization techniques must either transform the data into a scene description or extend graphics techniques to display this odd input. Computational science is a fertile field for visualization research because the results vary so widely and include things that have no known appearance. The amount of data creates additional challenges for both hardware and software systems. Evaluations of visualization should ultimately reflect the insight gained into the scientific phenomena. So making good visualizations requires consideration of characteristics of the user and the purpose of the visualization. Knowledge about human perception and graphic design is also relevant. It is this breadth of knowledge that stimulates proposals for multidisciplinary visualization teams and intelligent visualization assistant software. Visualization is an immature field, but computational science is stimulating research on a broad front.

Uselton, Samuel P.

Beyond the Renderer: Software Architecture for Parallel Graphics and Visualization

As numerous implementations have demonstrated, software-based parallel rendering is an effective way to obtain the needed computational power for a variety of challenging applications in computer graphics and scientific visualization. To fully realize their potential, however, parallel renderers need to be integrated into a complete environment for generating, manipulating, and delivering visual data. We examine the structure and components of such an environment, including the programming and user interfaces, rendering engines, and image delivery systems. We consider some of the constraints imposed by real-world applications and discuss the problems and issues involved in bringing parallel rendering out of the lab and into production.

Crockett, Thomas W.

Component-Based Visualization System

A software system has been developed that gives engineers and operations personnel with no "formal" programming expertise, but who are familiar with the Microsoft Windows operating system, the ability to create visualization displays to monitor the health and performance of aircraft/spacecraft. This software system is currently supporting the X38 V201 spacecraft component/system testing and is intended to give users the ability to create, test, deploy, and certify their subsystem displays in a fraction of the time that it would take to do so using previous software and programming methods. Within the visualization system there are three major components: the developer, the deployer, and the widget set. The developer is a blank canvas with widget menu items that give users the ability to easily create displays. The deployer is an application that allows for the deployment of the displays created using the developer application. The deployer has additional functionality that the developer does not have, such as printing of displays, screen captures to files, windowing of displays, and also serves as the interface into the documentation archive and help system. The third major component is the widget set. The widgets are the visual representation of the items that will make up the display (i.e., meters, dials, buttons, numerical indicators, string indicators, and the like). This software was developed using Visual C++ and uses COTS (commercial off-the-shelf) software where possible.

Delgado, Francisco

Global Precipitation Mission Visualization Tool

The Global Precipitation Mission (GPM) software provides graphic visualization tools that enable easy comparison of ground- and space-based radar observations. It was initially designed to compare ground radar reflectivity from operational, ground-based, S- and C-band meteorological radars with comparable measurements from the Tropical Rainfall Measuring Mission (TRMM) satellite's precipitation radar instrument. This design is also applicable to other groundbased and space-based radars, and allows both ground- and space-based radar data to be compared for validation purposes. The tool creates an operational system that routinely performs several steps. It ingests satellite radar data (precipitation radar data from TRMM) and groundbased meteorological radar data from a number of sources. Principally, the ground radar data comes from national networks of weather radars (see figure). The data ingested by the visualization tool must conform to the data formats used in GPM Validation Network Geometry-matched data product generation. The software also performs match-ups of the radar volume data for the ground- and space-based data, as well as statistical and graphical analysis (including two-dimensional graphical displays) on the match-up data. The visualization tool software is written in IDL, and can be operated either in the IDL development environment or as a stand-alone executable function.

Schwaller, Mathew

Scientific Visualization Using the Flow Analysis Software Toolkit (FAST)

Over the past few years the Flow Analysis Software Toolkit (FAST) has matured into a useful tool for visualizing and analyzing scientific data on high-performance graphics workstations. Originally designed for visualizing the results of fluid dynamics research, FAST has demonstrated its flexibility by being used in several other areas of scientific research. These research areas include earth and space sciences, acid rain and ozone modelling, and automotive design, just to name a few. This paper describes the current status of FAST, including the basic concepts, architecture, existing functionality and features, and some of the known applications for which FAST is being used. A few of the applications, by both NASA and non-NASA agencies, are outlined in more detail. Described in the Outlines are the goals of each visualization project, the techniques or 'tricks' used lo produce the desired results, and custom modifications to FAST, if any, done to further enhance the analysis. Some of the future directions for FAST are also described.

Bancroft, Gordon V.

Automated Code Standard Checker 2002

Coding standards are typically levied on flight software in order to help ensure that the code is testable, maintainable, and modifiable. Visually checking software source against a set of coding standards is time consuming and may be prone to error. Software inspection is typically costly and may require large amounts of highly skilled labor. The objective of this center initiative is to develop an automated method to ensure that mission critical software follows the required coding practices and standards.

Trevino, Luis

Representation of the Physiological Factors Contributing to Postflight Changes in Functional Performance Using Motion Analysis Software

Astronauts experience changes in multiple physiological systems due to exposure to the microgravity conditions of space flight. To understand how changes in physiological function influence functional performance, a testing procedure has been developed that evaluates both astronaut postflight functional performance and related physiological changes. Astronauts complete seven functional and physiological tests. The objective of this project is to use motion tracking and digitizing software to visually display the postflight decrement in the functional performance of the astronauts. The motion analysis software will be used to digitize astronaut data videos into stick figure videos to represent the astronauts as they perform the Functional Tasks Tests. This project will benefit NASA by allowing NASA scientists to present data of their neurological studies without revealing the identities of the astronauts.

Parks, Kelsey

AirShow 1.0 CFD Software Users' Guide

AirShow is visualization post-processing software for Computational Fluid Dynamics (CFD). Upon reading binary PLOT3D grid and solution files into AirShow, the engineer can quickly see how hundreds of complex 3-D structured blocks are arranged and numbered. Additionally, chosen grid planes can be displayed and colored according to various aerodynamic flow quantities such as Mach number and pressure. The user may interactively rotate and translate the graphical objects using the mouse. The software source code was written in cross-platform Java, C++, and OpenGL, and runs on Unix, Linux, and Windows. The graphical user interface (GUI) was written using Java Swing. Java also provides multiple synchronized threads. The Java Native Interface (JNI) provides a bridge between the Java code and the C++ code where the PLOT3D files are read, the OpenGL graphics are rendered, and numerical calculations are performed. AirShow is easy to learn and simple to use. The source code is available for free from the NASA Technology Transfer and Partnership Office.

Mohler, Stanley R., Jr.

Vegetation classification map and covariates associated with NEON AOP survey, East River, CO 2018

This package includes geospatial data layers developed to investigate how environmental gradients—specifically topography and near-surface soil properties—drive the spatial arrangement of dominant plant communities in mountainous watersheds. The geospatial products, which support the analysis of these ecological relationships, are derived from airborne hyperspectral and LiDAR datasets acquired by the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP), in conjunction with an extensive ground field campaign conducted in summer 2018. This work is part of the DOE Watershed Function Science Focus Area (SFA) and features geospatial datasets developed based on observations and ground data collected at East River, Colorado, in collaboration with the National Ecological Observatory Network (NEON) Airborne Observation Platform (AOP) survey in June 2018. Classification Map: - Classification Map (PNG, GeoTIFF): Derived from hyperspectral and LiDAR airborne data using a machine learning approach. - Class Code Mapper (CSV): Associates pixel values with corresponding vegetation/non-vegetation classes. - Classification Reference Data (CSV): Reference data used in the machine learning procedure. LiDAR-Derived Products: - Topographical Metrics (GeoTIFFs): Elevation, slope, curvature, TWI, TPI, solar insolation, and canopy height model (CHM), smoothed with a 5x5 pixel window. Vegetation Indices: - GeoTIFFs of NDVI, NDNI, NDWI: Vegetation indices derived from hyperspectral data. Urban Masks: - Urban Mask (GeoTIFF): Applied to the mapping to convert bare soil classes to urban classes. Software Compatibility: GeoTIFFs: Can be visualized with GIS software or libraries that support GeoTIFF images. CSV Files: Can be opened with any software that handles comma-separated values. The FLMD file provides details and links to the source datasets used to derive the products. The manuscript (in the Method session) provides details on how each product was derived. This work was supported by the Watershed Function Science Focus Area at Lawrence Berkeley National Laboratory funded by the US Department of Energy, Office of Science, Biological and Environmental Research under Contract No. DE-AC02-05CH11231. Update on 2026-03-25: Since the original dataset publication date of 02/28/2020, this package has a new classification map derived by an improved methodology. This update also includes additional ground data that improved the representation of some of the communities. See the methods for further details on what has changed between versions.

2018 NEON and 2025 CHESS Campaigns

Using Visual Programming to Simulate, Test, and Display a Telemetry Stream

Advantages of using visual programming to create, modify, test and display a telemetry stream are presented. Commercial visual programming software is being used to test new algorithms as part of the ground support for the Galileo spacecraft Test Bed.

visual programming real-time data display text-bas

GRIDVIEW: Recent Improvements in Research and Education Software for Exploring Mars Topography

GRIDVIEW is being developed by the GEODYNAMICS Branch at NASA's Goddard Space Flight Center and can be downloaded on the web at http://geodynamics.gsfc.nasa.gov/gridview/. The program is very mature and has been successfully used for more than four years, but is still under development as we add new features for data analysis and visualization. The software can run on any computer supported by the IDL virtual machine application supplied by RSI. The virtual machine application is currently available for recent versions of MS Windows, MacOS X, Red Hat Linux and UNIX. Minimum system memory requirement is 32 MB, however loading large data sets may require larger amounts of RAM to function adequately.

Roark, J. H.

Head-Up Auditory Displays for Traffic Collision Avoidance System Advisories: A Preliminary Investigation

The advantage of a head-up auditory display was evaluated in a preliminary experiment designed to measure and compare the acquisition time for capturing visual targets under two auditory conditions: standard one-earpiece presentation and two-earpiece three-dimensional (3D) audio presentation. Twelve commercial airline crews were tested under full mission simulation conditions at the NASA-Ames Man-Vehicle Systems Research Facility advanced concepts flight simulator. Scenario software generated visual targets corresponding to aircraft that would activate a traffic collision avoidance system (TCAS) aural advisory; the spatial auditory position was linked to the visual position with 3D audio presentation. Results showed that crew members using a 3D auditory display acquired targets approximately 2.2 s faster than did crew members who used one-earpiece head- sets, but there was no significant difference in the number of targets acquired.

Begault, Durand R.