Hello! Thank you for offering this awesome software to the public!
I am analyzing the cell shape and density of H&E stained tendon sections. I am able to separate the stains in some of my images with the UnmixColors module. Other images have fatty/scar tissue that does not allow me to unmix (example below). Because of this, I successfully isolated nuclei in two ways: by unmixing, and by thresholding for hematoxylin. I will analyze one of the two output images based on the section and the resulting image.
I am having a problem with segmenting the nuclei. I get both over and under segmentation, and I am unsure how to tackle this problem. This occurs mostly with the fatty samples, in which the UnmixColors isn’t used/effective. These samples are more cellular, with the nuclei clumped closer together.
What are the best strategies for optimizing segmentation? I have tried both the Morph module and the declumping techniques within the IdentifyPrimaryObjects module, but neither of these led to the desired results.
Thank you for your time!
H&E.cpproj (426.8 KB)