Command-line option for data-file

I’m unsuccessfully trying to pass in the –data-file= argument for executing CellProfiler for the command file.
There seem to be two different versions of documentation for this option. The one here seems rather simple. You pass in a replacement imageList.csv from the command line.

However, the auto-generated command line help indicates that to use the --data-file option you need to use a ‘LoadData module that uses the “From command-line option”’.

I can’t find such an option in the parameters of the LoadData module, and when I tried to use any combination of the standard options with a command line --data-file option, I get I/O errors indicating that the pipeline is still trying to use the build in images list rather than the one that I’m passing in as an argument from the command line.

Using CP v2.0 (DateRevision: 20130822)

Thanks and best regards

Sorry Ioannis, that feature is unfortunately broken in the 2.0 version, but working in the master branch. I’ve patched the 2.0 bugfix branch with the fix from 2.1 and it should build and be available in a couple of hours. If you download it after it’s built, it should work for you.


Thanks Lee!
It’s an important feature and I will download the new patched version as soon as it becomes available.
Best regards

This issue has been resolved in CellProfiler 2.1 and later, new releases of which can now be downloaded from