Cell segmentation and quantification with CellX

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Workflow Author: 

Christian Mayer, Sotiris Dimopoulos, Fabian Rudolf, and Jorg Stelling

Workflow Language: 
2D time series
Comment / Instructions: 

CellX is an open-source software package for cell segmentation, intensity quantification, and cell tracking on a variety of microscopy images with distinguishable cell boundary. Installation and a step-by-step usage details are described in [1]. It can be downloaded from here. After users provide a few annotations of cell sizes and cell boundary profiles, it tries to match boundary profile pattern on cells thus provide segmentation and further tracking. It works the best on cells without extreme shapes and with rather homogeneous boundary pattern. It may not work well on images with cells of sizes only a few pixels. Its output comprises control images for visual validation, text files for post-processing statistics, and MATLAB objects for advanced subsequent analysis.


  1. [2446] Mayer C, Dimopoulos S, Rudolf F, Stelling J
    2013.  Using CellX to quantify intracellular events.. Curr Protoc Mol Biol. Chapter 14:Unit14.22..
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