Pixel count on immunofluorescence images

Hello! I was wondering if there is a way to count pixels on immunofluorescence images.

Have you tried the thesholding tools?
https://qupath.readthedocs.io/en/latest/docs/tutorials/measuring_areas.html#threshold-stained-areas
You will, by default, get the areas in square microns unless you remove the pixel size metadata, but you can also divide the area by the pixel size to get the pixel count.

square microns/(microns/pixelside*microns/pixelside) = pixels

Alternatively, if you mean the value in the lower right, turn that on or off in the Preferences.
image

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So if I have the area in sq microns of the projections (from another script you helped me run earlier), how would I know the microns and pixel side?Screen Shot 2021-01-13 at 2.13.34 PM

You just need to plug in the annotation area and the pixel width and height, which are slightly different in your case.
area/(pixelwidth*pixelheight)=pixels

Alternatively, you can use a script which will return the area in pixels, I suppose.

getAnnotationObjects().each{
print( it.getROI().getArea())
}

Off the top of my head, but should print how many pixels are in each annotation. You may want to do something other than just print it, but that is how you can access the value.

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