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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.
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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 the Power Apps: BioTensor, BioFEM, and BioImage. PowerApps are expansion packages for SCIRun that extend its capabilities for specific applications. They are included automatically when you download SCIRun.
SCIRun is available for free and is open source.
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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.
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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! |
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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, P41-RR12553-10 and the DOE SciDAC Visualization and Analytics Center for Enabling Technologies, DEFC0206ER25781."
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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) |
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VisTrails is a new scientific workflow management system developed at the University of Utah that provides support for data exploration and visualization. |
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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. |
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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.
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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.
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3D Slicer and FiberViewer |
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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. |
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FEBio is a software tool that uses the finite element method for solving nonlinear large deformation problems in solid biomechanics. It is specifically aimed at solving problems in the field of biomechanics, by providing appropriate modeling scenarios, constitutive models and boundary conditions. |
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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.
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Software
