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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




No version available


  • person_outline Stephen T.C. Wong <>

Publication for CellSegmentation3D

CellSegmentation3D citations


Accurate Automatic Detection of Densely Distributed Cell Nuclei in 3D Space

PMCID: 4894571
PMID: 27271939
DOI: 10.1371/journal.pcbi.1004970

[…] 3d watershed plugin in imagej [] consists of local peak detection and seeded watershed. this method is almost the same as the conventional blob detection method used in our proposed method. cellsegmentation3d [] uses gradient flow tracking techniques and was developed for clump splitting. this method has been used in the study of automated nucleus detection and annotation in 3d images […]


Robust and automated three dimensional segmentation of densely packed cell nuclei in different biological specimens with Lines of Sight decomposition

PMCID: 4458345
PMID: 26049713
DOI: 10.1186/s12859-015-0617-x

[…] open-source segmentation tools []. additionally, we tested several other methods described in the literature, e.g. the method presented in [], a three-dimensional cell nuclei segmentation named “cellsegmentation3d” based on gradient flow tracking and the software mins []. all methods were supplied with the same raw images. a major drawback of many segmentation methods is their incapability […]


A Rapid and Efficient 2D/3D Nuclear Segmentation Method for Analysis of Early Mouse Embryo and Stem Cell Image Data

PMCID: 3964288
PMID: 24672759
DOI: 10.1016/j.stemcr.2014.01.010

[…] by any users., we compared mins against several popular tools in the community, including ilastik (http://www.ilastik.org), farsight (http://www.farsight-toolkit.org/wiki/farsight_toolkit), and cellsegmentation3d (http://www.biomedcentral.com/1471-2121/8/40/additional). we tried multiple parameter sets for farsight and chose the best result. for the machine learning-based ilastik, […]

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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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