Scientific Software Environments
Software at the SCI Institute is developed in close collaboration with application users to satisfy real needs within their research communities. We use a robust, yet agile software process that is fully open-source to produce software environments that integrate leading-edge algorithms in image processing, scientific visualization, and scientific computing. Software products include the SCIRun scientific software problem solving environment for geometric modeling, simulation, and visualization; BioPSE for biomedical computing and visualization; Uintah, designed for combustion, computational fluid dynamics, and mechanical modeling which is implemented on large-scale and distributed with shared memory architectures, map3d, an application to display and edit complex, three-dimensional surface models and associated scalar, time-dependent data; and VisTrails, providing data and process management support for exploratory computational tasks. Recently, the SCI Institute has been developing powerful, stand-alone applications. These software applications include ImageVis3d (formerly BioImage), a high performance volume rendering tool for image and other scalar volume data, BioTensor, a program that processes and visualizes diffusion tensor images, Seg3d, for volume segmentation and image processing, BioMesh3D, for creating tetrahedral and hexahedral meshes; and FusionViewer, for visualizing 3D scalar and vector magnetic fusion data.
 |
SCIRun is a Problem Solving Environment (PSE), for modeling, simulation and visualization of scientific problems. SCIRun now includes the biomedical components formally released as BioPSE, as well as BioMesh3D.
SCIRun is available for free and is open source.
Acknowledgement: SCIRun is an Open Source software project that is principally funded through the SCI Institute's NIH/NCRR CIBC Center. Please use the following acknowledgment and send us references to any publications, presentations, or successful funding applications that make use of NIH/NCRR CIBC software or data sets.
"This work was made possible in part by software from the NIH/NCRR Center for Integrative Biomedical Computing, 2P41 RR0112553-12."
• SCIRun Citation: [bibtex citation] [Endnote citation]
|
|
|
Read more...
 |
BioMesh3D is a tetrahedral mesh generator, that is capable of generating multi-material quality meshes out of segmented biomedical image data. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh. BioMesh3D is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results.
Acknowledgement: BioMesh3D is an Open Source software project that is principally funded through the SCI Institute's NIH/NCRR CIBC Center. Please use the following acknowledgment and send us references to any publications, presentations, or successful funding applications that make use of NIH/NCRR CIBC software or data sets.
"This work was made possible in part by software from the NIH/NCRR Center for Integrative Biomedical Computing, 2P41 RR0112553-12."
• BioMesh3D Citation: [bibtex citation] [Endnote citation]
|
|
|
Read more...
 |
Seg3D is a free volume segmentation and processing tool developed by the NIH Center for Integrative Biomedical Computing at the University of Utah Scientific Computing and Imaging (SCI) Institute. Seg3D combines a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit. Users can explore and label image volumes using volume rendering and orthogonal slice view windows.
Acknowledgement: Seg3D is an Open Source software project that is principally funded through the SCI Institute's NIH/NCRR CIBC Center. Please use the following acknowledgment and send us references to any publications, presentations, or successful funding applications that make use of NIH/NCRR CIBC software or data sets.
"This work was made possible in part by software from the NIH/NCRR Center for Integrative Biomedical Computing, 2P41 RR0112553-12."
• Seg3D Citation: [bibtex citation] [Endnote citation]
|
|
|
Read more...
|
ImageVis3D is a new volume rendering program developed by the NIH/NCRR Center for Integrative Biomedical Computing (CIBC). The main design goals of ImageVis3D are: simplicity, scalability, and interactivity. Simplicity is achieved with a new user interface that gives an unprecedented level of flexibility (as shown in the images). Scalability and interactivity for ImageVis3D mean that both on a notebook computer as well as on a high end graphics workstation, the user can interactively explore terabyte sized data sets. Finally, the open source nature as well as the strict component-by-component design allow developers not only to extend ImageVis3D itself but also reuse parts of it, such as the rendering core. This rendering core for instance is planned to replace the volume rendering subsystems in many applications at the SCI Institute and with our collaborators.
 ImageVis3D Mobile for the iPhone is now available from Apple iTunes App store! |
Acknowledgement: ImageVis3D is an Open Source software project that is principally funded through the SCI Institute's NIH/NCRR CIBC Center and the DOE VACET. Please use the following acknowledgment and send us references to any publications, presentations, or successful funding applications that make use of ImageVis3D software or accompanying data sets.
"This work was made possible in part by software funded by the NIH/NCRR Center for Integrative Biomedical Computing, 2P41 RR0112553-12 and the DOE SciDAC Visualization and Analytics Center for Enabling Technologies, DEFC0206ER25781."
• ImageVis3D Citation: [bibtex citation] [Endnote citation]
Read more...
 |
Uintah is a set of software components and libraries that facilitate the solution of partial differential equations on structured adaptive mesh refinement grids using hundreds to thousands of processors. Uintah is the product of a ten year partnership with the Department of Energy's ASC program through the University of Utah's Center for the Simulation of Accidental Fires and Explosions.
|
|
|
 |
The ShapeWorks software is an open-source distribution of a new method for constructing compact statistical point-based models of ensembles of similar shapes that does not rely on any specific surface parameterization. The method requires very little preprocessing or parameter tuning, and is applicable to a wide range of shape analysis problems, including nonmanifold surfaces and objects of arbitrary topology. The proposed correspondence point optimization uses an entropy-based minimization that balances the simplicity of the model (compactness) with the accuracy of the surface representations. The ShapeWorks software includes tools for preprocessing data, computing point-based shape models, and visualizing the results.
|
|
|
 |
ShapeWorks is a program for computing shape statistics over sample data to capture axes of variation. Inputs are volumetric labelmaps which describe the geometry of structures of interest. ShapeWorks uses a particle system-based approach to resample the sample geometries based on intersample feature correspondences and a minimum intrasample sampling distance.
ShapeWorksRemote wraps the functionality of ShapeWorks into an easy-to-use UI and allows computation to be performed in a Client/Server setting.
|
|
|
Read more...
 |
map3d is a scientific visualization application written to display and edit complex, three-dimensional geometric models and scalar, time-based data associated with those models. [map3d License] (Linux, Mac OSX, SGI, Windows)
Acknowledgment: Map3d, and the data sets provided on this web site are Open Source software projects that are principally funded through the SCI Institute's NIH/NCRR CIBC. [map3d license] For us to secure the funding that allows us to continue providing this software, we must have evidence of its utility. Thus we ask users of our software and data to acknowledge us in their publications and inform us of these publications. Please use one of the following acknowledgments and send us references to any publications, presentations, or successful funding applications that make use of the NIH/NCRR CIBC software or data sets we provide:
"This work was made possible in part by software from the NIH/NCRR Center for Integrative Biomedical Computing, 2P41 RR0112553-12."
• map3d Citation: [bibtex citation] [Endnote citation] Data set Citation: [bibtex citation] [Endnote citation]
|
|
|
Read more...
 |
3D Slicer (www.na-mic.org) is an comprehensive, integrated, open-source environment for medical image visualization and analysis developed as part of the national alliance for medical image computing (NA-MIC) funded as a national center for biomedical computing (NCBC) through the NIH Roadmap for Medical Research. Slicer includes modules for segmentation, registration, diffusion tensor image (DTI) analysis, and many other features. In particular, the SCI institute has contributed modules for DTI analysis including regularization and smoothing. DTI analysis software from the NeuroLib library for neuroimage processing (www.ia.unc.edu/dev) such as FiberViewer has been made compatible with Slicer in order to allow an integrated analysis process. Clinical users are able to load diffusion weighted images into Slicer to perform preprocessing, tensor estimation, and fiber tracking. Data exported from Slicer can then be loaded into the FiberViewer tool to enable the study of diffusion statistics along fiber bundles of interest. This provides a complete environment for end users to process DTI data for clinical studies. |
|
|
|
AtlasWerks is an open-source (BSD license) software package for medical image atlas generation. Such atlases are a widely-used tool for image segmentation, and deformations generated using these techniques are used for statistical analysis of brain shape to identify patterns of change related to disease progression. The AtlasWerks software package provides efficient CPU and GPU implementations of nonlinear deformation algorithms based on the Large Deformation Diffeomorphic Metric Mapping (LDMM) framework for single machines and clusters, command line frontends for atlas and deformation generation, and a number of utility programs for handling 3D medical image data.
Acknowledgement: AtlasWerks is an Open Source software project that is principally funded through NIH/NIBIB Grant 5R01EB007688 and NIH/NCRR Grant 2P41 RR0112553-12. Please use the following acknowledgment and send us references to any publications, presentations, or successful funding applications that make use of the software.
"This work was made possible in part by NIH/NIBIB Grant 5R01EB007688 and NIH/NCRR Grant 2P41 RR0112553-12."
• AtlasWerks Citation: [bibtex citation] [Endnote citation]
|
|
|
The NCR Toolset is a collection of software tools for the reconstruction and visualization of neural circuitry from electron microscopy data.
Join the ir-users mailing list for software support and updates.
|
Read more...
 |
FluoRender is an interactive rendering tool for confocal microscopy data visualization. It combines the renderings of multi-channel volume data and polygon mesh data, where the properties of each dataset can be adjusted independently and quickly. The tool is designed especially for neurobiologists, and it helps them better visualize the fluorescent-stained confocal samples.
|
|
|
|
Visualization of High Dimensional Scalar Functions
Software for the paper
Acknowledgement: Samuel Gerber, Peer-Timo Bremer, Valerio Pascucci, Ross Whitaker, "Visual Exploration of High Dimensional Scalar Functions", IEEE Transactions on Visualization and Computer Graphics to appear, Proceedings of VIS 2010 [pdf]
|
 |
VisTrails is a new scientific workflow management system developed at the University of Utah that provides support for data exploration and visualization. |
|
|
Read more...
|
|
Afront is a tool for meshing and remeshing surfaces. The main application of Afront is the generation of high-quality meshes from a variety of surface descriptions, from triangle meshes themselves (remeshing) to implicit surfaces to point set surfaces. Afront is distributed through SourceForge. |
 |
FEBio is a nonlinear finite element solver that is specifically designed for biomechanical applications. It offers modeling scenarios, constitutive models and boundary conditions that are relevant to many research areas in biomechanics. All features can be used together seamlessly, giving the user a powerful tool for solving 3D problems in computational biomechanics. The software is open-source, and pre-compiled executables for Windows, OS-X and Linux platforms are available. |
|
|
Read more...
 |
PreView is a Finite Element (FE) preprocessor that has been designed specifically to set up FE problems for FEBio. It allows the user to specify the boundary conditions and material properties in a user-friendly graphical environment.
|
|
|
Read more...
 |
PostView is a finite element post-processor that is designed to post-process the results from FEBio. It offers the user a graphical user interface to visualize and analyze the FE model. |
|
|
Read more...
|
STCR is a matlab-based program to reconstruct undersampled DCE radial data, with Compressed Sensing methods. |
|
|
VISPACK is a C++ library that includes matrix, image, and volume objects. The library has functionality that makes it suitable for surface reconstruction work using the level sets method.
|
Read more...
|
|
Teem is a collection of libraries written by Gordon Kindlmann (in C) in support of his research. It includes his implementation of his Master's Thesis work. Teem is now distributed through SourceForge. |
|
Software
