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Cell detection does not work probably because of high DAB background. Help me please? #305
I have IHC images to analyze and it has high DAB background.
Probably because of the background, 'Cell detection' function does not work at all to detect any cells in the image even after changing the parameters.
Could anybody help how to train Qupath to detect cells in this case?
I attach my script below and an original image as well. Thanks!
I think the main problem is that your TIFF file was saved with incorrect pixel size information. Without that information it is very difficult to find settings that will work, though it is possible. Note that each one of your pixels is expected to be 163 um in size. Your entire image is about 0.2 meters in size.
If you are using the ImageJ server, everything needs to be in pixels instead, though since you have a requestedPixelSize entry, I am guessing that is not the case here.
If you are using a BioFormats server (see Image tab), you can get started with these settings, though I have not optimized them at all.
Note the extremely large values in most measurements. It would be better to fix the pixel sizes in ImageJ, though.
I looked at the image and there are two main problems:
The first of these is the bigger problem. I don't know the source of your image, but ideally you'd be able to go back to it and save the file in a format that preserves the pixel size information properly.
Any follow-up discussion should be at https://forum.image.sc/t/cell-detection-not-working-prob-because/24807