Ilastik pixel classification/Classify Pixel?


Hi, I have been trying to add the binary mask which I have generated in ilastik 1.2.0 into CP2.2.0 (rev ac0529e). I am wondering should I use ClassifyPixels or ilastik pixel classification as part of the pipeline? When I tried to do via ilastik pixel classification, it has an error saying " ilastikPixelClassifcation cannot run on this platform because the necessary libraries are not available. IlastikPixelClassification is supported on 64-bit versions of Windows Vista etc" My window is a 64-bit and i have downloaded the correct CP so i am a bit puzzled. What does the “necessary libraries” mean? Is there something else I am missing?


Sounds like if you’ve already created binary masks in ilastik you don’t need to worry about using ClassifyPixels within your CellProfiler pipeline. Just load the binary masks and do whatever you need to do in the pipeline.

If in the future you did want to use ilastik and CellProfiler together, you can check the status here, it’s complicated:



Thanks Anne for your reply. Yes I have created the binary masks in ilastik. So do you mean I can just simply load the masks in CP and perform a cell count and calculate intensity? Sorry this may sound bit naïve but i am quite new to CP and also Ilastik.

Thank you in advance!


Hi, please refer to this link Co-culture pipeline/ground truth