Positive Cell Detection with more nuclear conditions

Hello everyone,

I am pretty new to QuPath but it seems like a marvellous tool with a lot of potential!

I performed DAB nuclear staining on liver sections (Ki67 and gammaH2AX) and I am know trying to count positive cells, to assess in particular the hepatocyte proliferation index.

For that purpose, I’d like to use QuPath and the ‘Positive Cell Detection’ tool. It works pretty good but maybe too good: not only hepatocytes are recognised but also the tons of immune cells that are infiltrating the liver and are sometimes DAB positive.

So my question is, is it possible to put conditions in the recognition process ? I am thinking of nuclear area and nuclear circularity. It appears that I can’t set a minimal nuclear circularity in the parameter box in Analyse > Positive Cell Detection.

I tried to write a short script using the runPlugin(‘qupath.imagej.detect.nuclei.PositiveCellDetection’) command in order to add ‘circularity” : 0.8’ but it didn’t work.

Any ideas guys?
Thank you for your help!

Pierre,
Veterinary student

I would start by looking at the links at the top of this thread on classification. There are a lot of options, positive cell detection is only for the simplest projects.

Some further information/discussion here and in the comments.

Thank you for your quick response! I found pretty interesting things and could write a small script which works quite well!

Pierre

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