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CellProfiler is open-source cellular image analysis software.
Python Java C++ C Shell Inno Setup
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BatchProfiler Fixes #1517 - BPBatch constructor's signature changed
artwork #1398: Stripped ICCP profiles from PNGs (prep for wxWidgets 3.0)
cellprofiler fix typo in SaveImages
contrib removed tifffile (fixes #1439)
imagej Fixes #1616 - remove reliance on ExampleImages for tests
java Fixes #1573 slf4j-simple excluded from POM
jenkins continue build flail
plugins Avoid annoying 'comparison to None' FutureWarning
tutorial refactored cellprofiler.cpmath into a unique package (fixes #1490)
.gitattributes Developer tutorial
.gitignore Ignore .eggs/ and CellProfiler.egg-info/ (resolves #1541)
.travis.yml refactored cellprofiler.cpmath into a unique package (fixes #1490)
CellProfiler.iss moved ./CellProfilerIcon* into artwork directory (fixes #1444) refactored cellprofiler.cpmath into a unique package (fixes #1490)
CellProfiler64.iss moved ./CellProfilerIcon* into artwork directory (fixes #1444)
CellProfiler_python.bat separate 1.0 and 2.0
CellProfiler_python.command Fixed crlf and file mode issues (hopefully)
LICENSE issue #1290 more copyright notices changed to 2015
Makefile.CP2 \ ljosa -> cellprofiler as the real docker repo Fixes #1573 slf4j-simple excluded from POM Fixed crlf and file mode issues (hopefully) Revert "Retrieve prokaryote-*.*.*.jar during setup" Fixed crlf and file mode issues (hopefully)
requirements.txt refactored cellprofiler.cpmath into a unique package (fixes #1490) Revert "Retrieve prokaryote-*.*.*.jar during setup"
usr-bin-cellprofiler Run under xvfb if $DISPLAY is not set refactored cellprofiler.cpmath into a unique package (fixes #1490)

CellProfiler is free, open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

Our website,, is aimed at non-developer users and has lots of information about CellProfiler and how to use it, as well as a forum for asking questions.

The developer wiki covers topic such as how to build CellProfiler from source, how to set up a development environment with all of CellProfiler's dependencies, and the various resources set up to support CellProfiler development.

Getting started with the Docker image of CellProfiler

The Docker image is for advanced users who want to run CellProfiler for high-throughput processing without a graphical user interface in a Linux cluster environment. This is an alternative to installing CellProfiler from source or using the Linux build that we provide. New users will typically want to download and install CellProfiler on a Mac or Windows machine instead; see the download page.

To use the Docker image, you need to Docker's -v option to mount the input directory (which contains your images, pipeline, and other input files) and the output directory (to which images, measurements, and other output files will be written). Because CellProfiler will be run as the user "cellprofiler", you must ensure that the "cellprofiler" user has permission to write to the output directory.

Example for how to use the Docker image:

mkdir input
cd input
curl -O
curl -O
curl -O
curl -O
for a in *.tif; do echo file:///input/$a; done > filelist.txt
cd ..
mkdir -m 777 output
docker run --rm -v $(pwd)/input:/input -v $(pwd)/output:/output cellprofiler/cellprofiler:master -i /input -o /output -p /input/ExampleHuman.cppipe --file-list=/input/filelist.txt

How to file new issues

If you have a bug or other issue to report, please read the wiki page on how to file new issues to learn the best way to report it. You can also search the forum which may have a report or work-around for the issue.

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