Ilastik/ClassifyPixels Error


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,

Hi Tristan,

First, and easiest, you can attach a zip file, so zip up your h5 file and post. That would let me see if I can run your h5 file here.
Please also attach your CellProfiler pipeline, because the issue could lie in its configuration as well.

Also, what are your classes defined as in ilastik? You have to match the order of the classes from top to bottom in ilastik with class 0, 1,2, etc in CP.

Ahh, now I have a better guess. Your image appears as grayscale, but it is actually an RGB image. Load it into FIJI or ImageJ and you’ll see this as “RGB” at the top (attached).

So you could change your NamesAndTypes to input Color (vs. grayscale), but you might better save the raw image as grayscale and then train in ilastik on the grayscale image. It will be faster and less memory intensive anyway. Then you should be able to load into CP OK I suspect.

Let us know,