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How to cite CellProfiler in publications (the project's survival depends on it!) CellProfiler for cells (feel free to cite the most recent) : Stirling DR, Swain-Bowden MJ, Lucas AM, Carpenter AE, Cimini BA, Goodman A (2021). CellProfiler 4: improvements in speed, utility and usability. BMC...

Our CellProfiler software has yielded discoveries in several translational projects, some of which have had a direct impact on the treatment of disease. For example, CellProfiler has been used to identify several small molecules that are effective in treating particular diseases in mouse models. In...

CellProfiler is free, open-source software for quantitative analysis of biological images. No prior experience in programming or computer vision is required – this page is intended to help you get up and running. The quickest way to get up and running with CellProfiler is to: Download CellProfiler...

Previous Examples Previous examples (prior to 4.0) can be found on the previous examples page, but we discourage their use because they are now outdated.

Software for analyzing CellProfiler-produced data Software Description Interface CellProfiler In addition to performing image analysis to generate measurements, CellProfiler has built-in tools in the Data Tools menu to generate a few types of plots. CellProfiler output files in MATLAB (.mat) and...

You can see talks and read articles about CellProfiler and the group at the Carpenter Lab website [ here]. Anne Carpenter’s public talks ( PDFs of slides)

Version Manual CellProfiler 4.2.8 [ HTML] 4.2.7 [ HTML] 4.2.6 [ HTML] 4.2.5 [ HTML] 4.2.4 [ HTML] 4.2.1 [ HTML] 4.2.0 [ HTML ] 4.1.3 [ HTML ] 4.0.7 [ HTML] 3.1.9 [ HTML ] 3.1.8 [ HTML ] 3.1.5 [ HTML ] 3.0 [ HTML ] 2.1 and 2.2 [ HTML ] 2.0 [ PDF ] 1.0 [ PDF ]