Please see the following discussion showing an issue with the scale of values in the output of
separate_stains, where I get really high values corresponding to potential artifacts or just high density staining, rendering the other positive values (which are the ones I am interested in capturing) too low.
I used the following strategy but I am not sure if it’s reasonable and would scale well to other images, because I don’t want to determine thresholds per image separately and manually.
Here is the potential culprit rendering the high values. I don’t know if and how to remove these artifacts from the image, or otherwise, should I just set a lower upper threshold on the hema values?
And this is what it looks like in the original image for reference: