Thank you so much for your effort. First of all, I want to quantify the number of brownish pixels excluding the bigger brownish regions, just as you correctly wrote.
I have tried your first two suggestions, but I dont see how the “structure size” make any difference (I have tried going from 3 to 9). What I do is: After changing it I then press “train” (in the “classification” tab) to apply/active the command. Is that correct? Because I dont really see any changes in the model. The same thing applies for the exclusion model, I cant see any changes in the model after changing the the Exclusion Model Level from 1 to two.
I have attached a picture of the model (with decreased opacity)(picture 1). I have successfully excluded some of the big brown area (painted orange at the picture) from the small brown spots (painted blue at the picture) by making two separate classes (green is cells and purple is the background). So far so good. But still there is a blue round ring of cells, seemingly not positive for brown staining but still marked as positive , around the orange objects (picture 1 and 2).
For what I know, the “structure size” actually will change that, but I dont seem to manage how to apply it sufficiently. Maybe there is something wrong with the way I classified the the blue objects (marking what I am looking for) in the first place?
Picture 1: Full picture:
Picture 2: A zoom of the original picture of the blue ring with the orange middle at the top left corner of picture 1 showing that the program incorrectly marks the cells around the brown area as positive, when it should be coloring it green (because its just a cell)
Can you guide me once again?