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CellProfiler also supports headless installation with pipenv. For more information about pipenv, see the pipenv documentation. Pipenv can be used once a version is tagged/published to ensure that the dependencies that went into the GUI (scikit-image, numpy, scipy, etc) are the same ones being run on your cluster.
Unfortunately, due to our dependency on wxPython 3 for the GUI, CellProfiler can only run in headless mode at this time.
Once the pipenv environment is built, CellProfiler can be run using
pipenv run cellprofiler, e.g.
pipenv run cellprofiler -r -c -p ExampleHuman/ExampleHuman.cppipe --file-list ExampleHuman/imagelist.csv.
Note that pipenv environments to not behave like regular virtual environment. Pipenv manages the environments itself, pipenv requires being in a specific folder for the virtual environment to be used properly. Pipenv does have a flag to overwrite where the pipenv environment is stored (see