Count double postive cells

Hi
I am a beginner in using QuPath.

I have IHC images stained with hematoxylin nucleus stain combined with a double stain ( a purple for CD45 stain and a yellow for aSMA staning). Under section: Brightness and color I can add colors for hematoxylin, and eg yellow, but i need and additional color option so i also can choose only to see purple (CD45 positive cells). How can this be done ?

Additionaly, the cells iam looking at are CD45 positve in the nucleus and SMA postive in the cytoplasm. Any ideas of how to develop a method for detection of theses cells, that have both purple and yellow.

Thanks in advance for any help.


Double click on the Image Tab, Image Type entry to set it as Brightfield (other). Be aware that once you set the third stain, you are entering dangerous territory, as deconvolution is only intended for 2 colors plus a residual (everything else). Also, if you are looking for double positive, cells, overlaps in stains will not have the same minimum threshold as single positive cells.

In other words, a yellow positive cell will have more yellow in it than a yellow/purple positive cell, even if they both have the same amount of yellow protein. That can make thresholding… difficult in any regions where there is overlap. CD45 is generally a cytoplasmic marker for immune cells, which only looks like a nuclear marker when the tissue slice includes “above” or “below” cytoplasm.

If you want specific help, it always is best to show what you have done, how it hasn’t worked, and how you want it to work.

Thank you very much for your help!

Another simple question: I have on one image in my project library where I have set stain vectors for Stain 1, Stain 2 and Stain 3. I would now like to export these properties to all other images in my project library, how is this done ?


Note the second line in the image of the workflow script, that sets the color vectors.