Some WSI cannot be segmented

mahmoodlab / CLAM

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering

http://clam.mahmoodlab.org

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Some WSI cannot be segmented #214

Closed Ysc-shark closed 6 months ago

Ysc-shark commented 10 months ago

I am using the CLAM for segmenting ovarian cancer WSI images, utilizing parameters from the bwh_biopsy.csv file. However, I am encountering issues with two types of WSI images: those with very faint colors and those containing several sections within a single image. How can I resolve these issues? 39872_thumbnail

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scjjb commented 10 months ago

My suggestion would be to try reducing sthresh (the saturation threshold used, lower means less saturation needed to be considered as tissue) until you start to get what you want, if this doesn't work play around with mthresh and use_otsu