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?