CellSegmentation3D specifications


Unique identifier OMICS_10248
Name CellSegmentation3D
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data CellSegmentation3D loads the 3D Analyze format image (the suffix ".img" or ".hdr" is not needed in the input image name), and the segmentation result is also saved as the Analyze format.
Output data For each 3D input image, the program will output two results: 1) the segmentation result, in which all voxels belonging to the same cell are labelled with the same unique intensity, 2) the boundary map that separates segmented cells.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes



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  • person_outline Stephen T.C. Wong <>

Publication for CellSegmentation3D

CellSegmentation3D institution(s)
Center for Bioinformatics, Harvard Center for Neurodegeneration and Repair, Harvard Medical School, Boston, MA, USA; School of Automation, Northwestern Polytechnic University, XI'an, China; Functional and Molecular Imaging Center, Department of Radiology, Brigham and Women's Hospital, Boston, MA, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
CellSegmentation3D funding source(s)
This work is funded by a Bioinformatics Research Center Program Grant from Harvard Center for Neurodegeneration and Repair, Harvard Medical School.

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