I have been trying for a while to get CellProfiler to identify cells in my images using ilastik + ClassifyPixels but I cannot get it to work.
I am using ilastik 0.5 and have tried both CellProfiler 2.1.1 and 2.1.2 but nothing works.
I am able to make the classifier in ilastik, but when I try to run the CellProfiler ClassifyPixels module I always get the error message of “CellProfiler.exe has stopped working” or “analysis_worker.exe has stopped working”.
I am also using the exact same image in CellProfiler as I used to train the classifier in ilastik, which I attached. I tried to attach my classifier file as well but it does not seem to let me attach an h5 file.
Any help would be much appreciated,