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.

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.

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.

The NCR Toolset is a collection of software tools for the reconstruction and visualization of neural circuitry from electron microscopy data.

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