Pixel Classifier Positive Pixel Count

I am attempting to generate pixel counts for DAB staining with the new version of qupath. Now that the positive pixel count command is deprecated I was going to use pixel classification instead. This may be a naive question but with this method am I able to get the the number of positive pixels as a measurement like previously done? I only see positive percent and positive area measurements but no positive pixel numbers/counts.

Any help would be much appreciated. Thanks!

Iā€™m not sure why you would want the pixel counts specifically, but if you do, you would likely need to either multiply that out (area in um^2 / (pixel size*pixel size)) or remove the pixel size metadata before running the thresholder, so that your results are in pixels. Pixels and area are roughly the same thing, so if you have one (and metadata), you have the other.

Specifically, setting the pixel sizes to 0 or lower when you double click on them in the Image tab removes their sizes.

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Thanks! Just to confirm, my pixels in the image tab are 0.2520um by 0.2520um so I would take my DAB positive area in um2 and divide by 0.2520*0.250?

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Right, microns squared divided by (microns per pixel)^2. Ends up in pixels.