I want to analyze gonad histologies stained with hematoxylin and eosin using threshold analysis with fiji.
The prodcedure I follow is: image substract background, colour deconvolution HyE2 (the stains separations is better than with HyE) and auto threshold in hematoxylin image (purple).
The problem I have is that the same threshold method does not work for all my images. The three methods that I used for my analysis were: minimun, shanbhag and yen.
I want to know if my analyzes would be comparable if I use a different threshold method for all the images, or I must use the same threshold method for all my images to make comparisons.