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The software packages below are a sample of the software developed or supported by the SCI Institute.
Please note that this list is not exhaustive.


Seg3D layout-1 Seg3D - A free volume segmentation and processing tool developed by the NIH Center for Integrative Biomedical Computing. SEG3D combines a flexible manual segmentation interface with powerful higher-dimensional image processing and segmentation algorithms from the Insight Toolkit.
iv3d ImageVis3D is a new volume rendering program developed by the NIH/NIGMS Center for Integrative Biomedical Computing (CIBC). The main design goals of ImageVis3D are: simplicity, scalability, and interactivity. For the iPhone and iPad, ImageVis3D Mobile is now available from Apple iTunes App store.
multeesum-screenshot MulteeSum is a visualization system that supports inspection and curation of data sets showing gene expression over time, in conjunction with the spatial location of the cells where the genes are expressed -- it is the first tool to support comparisons across multiple such datasets. 
Mizbee overview MizBee is a multiscale synteny browser for exploring conservation relationships in comparative genomics data. Using side-by-side linked views, MizBee enables efficient data browsing across a range of scales, from the genome to the gene. The design of MizBee is grounded in perceptual principles, and includes several techniques such as edge bundling and layering to enhance visual cues about conservation relationships related to proximity, size, similarity, and orientation.
shapeworks ShapeWorks 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. It includes tools for preprocessing data, computing point-based shape models, and visualizing the results.

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.

ncr NCR Toolset is a collection of software tolls for the reconstruction and visualization of neural circuitry from electron microscopy data.
The NCR Toolset has recently been integrated into Seg3D. You can download Seg3D at
Screenshot itkSNAP screen livers

ITK-SNAP is a free open-source multiplatform (Linux, Mac OS, Windows) software application based on the Insight Toolkit computational environment used to segment structures in 3D (bio)medical images. It provides semiautomatic segmentation using active contour methods, manual delineation and image navigation and a large set of supporting utilities.


3D Slicer is a 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.


XNAT is an open-source imaging informatics software platform dedicated to helping you perform imaging-based research. XNAT's core functions manage importing, archiving, processing and securely distributing imaging and related study data. But its extended uses continue to evolve. 

freesurfer output

Freesurfer is an open-source software suite for the analysis and visualization of structural and functional neuroimaging data from cross-sectional and longitudinal studies. It is developed by the Laboratory for Computational NeuroImaging at the Athinoula A. Martinos Center for Biomedical Imaging.