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The CellProfiler project team is based in the Cimini Lab at the Broad Institute of MIT and Harvard. The project was started in 2003 by Anne E. Carpenter and Thouis (Ray) Jones in the Sabatini Laboratory (Whitehead Institute for Biomedical Research) and Golland laboratory (MIT’s CSAIL) and is...

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examples (prior to 4.0) can be found on the previous examples page, but we discourage their use because they are now outdated.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