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Related Experiment Video

Updated: May 8, 2026

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data
12:08

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

Published on: August 13, 2014

CellSegm - a MATLAB toolbox for high-throughput 3D cell segmentation.

Erlend Hodneland1, Tanja Kögel, Dominik Michael Frei

  • 1Department of Biomedicine, University of Bergen, Bergen, Norway. erlend.hodneland@biomed.uib.no.

Source Code for Biology and Medicine
|August 14, 2013
PubMed
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Automated whole cell segmentation using CellSegm software enhances cell biology research by enabling reproducible analysis of large fluorescence microscopy datasets. This tool facilitates high-throughput screening and quantitative analysis of cellular structures.

Area of Science:

  • Cell Biology
  • Bioimaging
  • Computational Biology

Background:

  • Fluorescence microscopy generates vast imaging data, making manual cell segmentation time-consuming and less reproducible.
  • Automated segmentation is crucial for efficient and reliable analysis of cellular structures in large datasets.

Purpose of the Study:

  • To present CellSegm, a MATLAB-based command-line software for automated whole cell segmentation.
  • To provide a flexible and scriptable tool for analyzing surface-stained cells in 2D and 3D fluorescence microscopy images.

Main Methods:

  • CellSegm employs a pipeline including smoothing, Hessian-based ridge enhancement, marker-controlled watershed segmentation, and feature-based classification.
  • The software offers both fully automated and semi-automated segmentation options.

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Last Updated: May 8, 2026

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data
12:08

From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

Published on: August 13, 2014

Analysis of Multidimensional Microscopy Data Using Cell-ACDC
06:17

Analysis of Multidimensional Microscopy Data Using Cell-ACDC

Published on: November 7, 2025

  • Its command-line interface supports scripting for tailored workflows and integration with other analysis tools.

    • Main Results:

    • CellSegm successfully detects and outlines various types of surface-stained cells in 3D fluorescence microscopy images.
    • The software demonstrates capability in segmenting tissue samples with suitable characteristics.
    • Its modularity and scripting enable automated workflows for quantitative analysis and high-throughput screening.

    Conclusions:

    • CellSegm provides a robust and flexible solution for automated whole cell segmentation in fluorescence microscopy.
    • The tool enhances reproducibility and efficiency in cell biology research, supporting quantitative analysis and high-throughput screening applications.