CP2.0 won't start from command line

Hi CP-Team

I’m currently experiencing some trouble, after I switched my MATLAB-based image analysis from OSX to Windows. I’m stuck right now with CellProfiler. I call CP from MATLAB via the system() command, so it acts like started from the command line. The command works so far, that CP pops up for a fraction of a second and before the GUI is even loaded, it closes again without doing any measurements. When I open CellProfiler.exe via double-click and load the pipeline manually, everything works just fine. Normally I’m running it in headless mode, but I wanted to see what is wrong about it, so i leave the ‘-c’ away.

My command line prompt looks like this: “<path/CellProfiler.exe>” -r -i -o -p

I also tried to just start CellProfiler from the command line using “<path/CellProfiler.exe>”, which produces the exact same phenotype.

Do you have any suggestion what could be wrong here?


Me again,

I figured out what the problem was. CellProfiler 2.0 won’t start on my Windows machine, if the output folder is not yet present. I worked around this by creating the folder in MATLAB, before starting CellProfiler. On my Mac system, the folder is created by CellProfiler automatically. Is there a reason for this difference?


This issue has been resolved with the 2.1.1 release.