I try to analyse some wsi kidney biopsy images made with our Zeiss Axio Scan.Z1.
The goal is to detect and count the positive red stained cells inside and outside the glomerula.
Images are loaded fine by qupath. I set all to HE-DAB (it is AEC staining in red, but I think it should work?)
Now I try to create a thresholder, playing arround with a lot of settings in the tresholder, to detect the tissue for further analysis
Problem is: at the border of my pictures I always get some areas which I dont want to have.
Tried with pixel-classifier is more or less the same result.
Picture3 bigger ones
What can I try to get rid of those unwanted regions?
Is this a bug, or just a settings problem?