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]

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.

BioMesh3D Client is a light weight application that guides the user through the process of building a tetrahedral mesh based on a labelmap that the user has to provide. As the recipe for building a quality mesh requires a lot of computation, this application allows the user to connect to the Scientific Computing and Imaging Institutes' servers for doing the meshing. Hence this package only contains an interface to connect to this remote server.

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.

ShapeWorksRemote wraps the functionality of ShapeWorks into an easy-to-use UI and allows computation to be performed in a Client/Server setting.

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]