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CellProfiler Video Tutorials Visit our YouTube playlist for video tutorials on CellProfiler, CellProfiler Analyst, segmentation strategies, how to construct pipelines, and much more. CellProfiler Written Tutorials Technical descriptions of CellProfiler and CellProfiler Analyst software can be found...

Update September 2024: CellProfiler 4.2.8. release New release for MacOS (Intel and ARM) is available here New release for Windows 10 and 11 is available here. After June 28th, 2023, if you try to download CellProfiler from a very old browser, you might not be able to due to updated AWS security...

CellProfiler Analyst (CPA) provides tools for classifying biological images and exploring and visualizing multidimensional data (particularly from high-throughput experiments) that has been extracted from companion image analysis software CellProfiler. CellProfiler Analyst’s primary tools: Image...

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...

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examples (prior to 4.0) can be found on the previous examples page, but we discourage their use because they are now outdated.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