DAB detection - Cell expansion - QuPath

Hi there @petebankhead,

I’m trying to detect DAB in the cytoplasm, and I watched your videos on how to do that. Now I made a semi-optimized workflow. The only problem is that I have different cell types in my tissue cores, like some giant cells and some smaller ones, including red blood cells and white blood cells. I cannot use the same cell expansion for them; otherwise, it considers red blood cells as giant cells. I can ignore them as I mainly work with tumor cells, but is there any way to apply an automatic cell expansion based on the cell size? So that I can finally classify the expression of the protein in each cell type. As I have different tissue cores in one slide, I guess I cannot apply the detection classifier?

My next question is when I select the tissue microarrays and arrange them in rows and columns, I cannot draw on the tissue or use the wand tool anymore. So I guess the only way is first to classify them and then select the TMAs, am I right?

Not with the built-in cell segmentation.

You can with the (somewhat experimental) StarDist cell segmentation. This is rather more complicated to set up, and requires scripting. The key parameter is cellConstrainScale – see
https://qupath.readthedocs.io/en/latest/docs/advanced/stardist.html#cell-expansion-measurements

The detection classifier will end up being applied to all cells across the image, so I think you’re right and the answer is ‘no’.

I’m not sure I understand – can you just deselect the cores first before drawing (e.g. double-click outside a core with the Move tool active)?

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I don’t know if @sadaffazeli1995 wants to dig into scripting, but I think that you pointed out this was possible in a post here:

Passing the children of a given set of TMA cores (or children of children, or checking “contains”) would allow specific classifiers to be applied to specific cores, perhaps by tissue type.

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And wanted to mention that “cell size” in this case is “size of what StarDist detects as the nucleus.” Probably is what everyone meant, but sometimes expectations can be tricky.

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