CellC: Software for quantification of labeled bacteria by automated image analysis

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Download the free CellC software for cell and spot analysis.
Numerous research groups around the world have found this tool to be easy to use, as well as reliable in counting!

If you find CellC useful and use it in your publications, please cite the article below.

The CellC software was originally published as a supplement to for the article:  Software for quantification of labeled bacteria from digital microscope images by automated image analysis, by Jyrki Selinummi, Jenni Seppälä, Olli Yli-Harja, and Jaakko A. Puhakka, BioTechniques, Volume 39, Number 6: pp 859-863.


Automated image analysis software, CellC, was developed and validated for quantification of bacterial cells from digital microscope images. CellC enables automated enumeration of bacterial cells, comparison of total count and specific count images [e.g., 4′,6-diamino-2-phenylindole (DAPI) and fluorescence in situ hybridization (FISH) images], and provides quantitative estimates of cell morphology. The software includes an intuitive graphical user interface that enables easy usage as well as sequential analysis of multiple images without user intervention. Validation of enumeration reveals correlation to be better than 0.98 when total bacterial counts by CellC are compared with manual enumeration, with all validated image types. The software is freely available and modifiable: the executable files and MATLAB® source codes can be obtained at https://sites.google.com/site/cellcsoftware/