How to choose QuPath cell detection parameters


I’m trying to follow the multiplexe tutorial to analyse our imaging mass cytometry data. My question is about how to assign cell detection parameters values. I’m using one of the channels to detect DNA to identify the nuclei. How can I know that I’m using the right parameters? Attached two images of the same sample doubling up the values.


Related to your question here: Opening an ImageJ "Stack" in QuPath not recognizing channels
Units in pixels could mean anything, so there will never be standard values for them.

The image could have been taken at 2.5X, 20X, 63X, and someone reading this would have almost no way of knowing. The advantage of the units being in microns is that tends to be somewhat more standard (though not completely) and is part of the reason QuPath’s default measurements usually work so well.

Once you find out the correct pixel size, you can apply that to the file through FIJI (Image->Properties), or tell QuPath what pixel size to use as a translation (double click on the Pixel size entries in the Image tab with no objects selected, or use a short script).

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Going through the guide here (probably starting at 5 or 6) may help if you have questions about individual measurements.

I also have some information here in non-video format:

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