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CellX is a tool for segmentation, fluorescence quantification, and tracking of cells on microscopy images. Installation and usage is explained in [1].

CellX MATLAB Image Segmentation Package

CellX is also available as a MATLAB package for segmentation of cells in microscopy images with membrane patterns. For an explanation of the algorithm see [2]. The MATLAB source including examples can be downloaded here:


Redistribution and use in source and binary forms, with or without modification, are permitted provided agreeing to the Simplified BSD Style License (TXT, 2 KB).


  1. Mayer C, Dimopoulos S, Rudolf F, Stelling J (2013)
    Using CellX to quantify intracellular events
    Curr Protoc Mol Biol Chapter 14: Unit 14 22.
  2. Dimopoulos S, Mayer CE, Rudolf F, Stelling J (2014)
    Accurate cell segmentation in microscopy images using membrane patterns.
    Bioinformatics 30: 2644-2651.


CellX makes use of the following libraries/plugins:

Page URL: http://www.csb.ethz.ch/tools/software/cellx.html
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