Positive cell detection, DAB detection, Cell expansion, Cell morphology, qupath

Usage & Issues
#1

Hello everyone,

I’m trying to detect DAB in H-DAB staining and in my case the protein is expressed and diffused in the cytoplasm. When I run the positive cell detection command, I see the software smartly segment the cells somehow which is not super accurate, sometimes it consider one big cell as some small ones and the other way round. How can I make sure what value for cell expansion I need to choose to be accurate. I excluded the cell nucleus by the way and I’m detecting Cell: DAB OD mean.

Thanks in advance

#2

I speak a lot about the meaning of cell detection parameters and how to adjust them in this tutorial: https://www.youtube.com/playlist?list=PL4ta8RxZklWk_O_Z7K0bZlhmHtaH73vlh

However, it will depend a lot on your images/staining – cell detection in some images is very challenging and it’s not certain that any combination of parameters will work well.

#4

Hello again,
Thanks for your fast reply. they are really helpful.

2 Likes
#5

I wanted to clarify that “Cell:” measurements include the nucleus. Cytoplasm measurements exclude it. Might also be covered in the YouTube videos, I forget :slight_smile: