Brilliant! This small, trivial breakthrough has just saved me a ton of time. There are instructions on the CellProfiler Wiki for how to run CP from the command line:
For a full list of command-line options, run CellProfiler like this:python CellProfiler.py --help
To run CellProfiler 2.0 without the graphical user interface, use this:python CellProfiler.py -c -r -i ~/my_image_directory -o ~/my_output_directory -p ~/my_pipe.mat
Which is all well and good except, despite my downloading and installing all the dozen or so libraries and things needed for CellProfiler, I still can’t actually get it to compile. But! The small, trivial breakthrough is just that you can just run the compiled version in command line mode too:
CellProfiler.exe -c -r -i ~/my_image_directory -o ~/my_output_directory -p ~/my_pipe.mat
Which is awesome, since my compiled version works, and since (related breakthrough) you can edit the pipeline (.cp) files in a text editor (or, say, programmatically in Python). So without actually doing anything to the source code (though it’s still nice to have to understand it) you can, say, loop through the different thresholding methods and see which one works for your project.