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mahmoodlab / CLAM

Data-efficient and weakly supervised computational pathology on whole slide images - Nature Biomedical Engineering
http://clam.mahmoodlab.org
GNU General Public License v3.0
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I want to use your tumor segmentation pretrained model #203

Closed AnitaGoro closed 11 months ago

AnitaGoro commented 11 months ago

Hello, I have a bunch of TCGA endometrial svs files and I want to extract their tumoral region without a pathologist´s annotation. Do you think that I can use your normal-tumor model to do this? If this is the case, how do I do it? I have already cloned the github and installed the libraries. I tried running your first command on the readme file and it worked. Thank you very much!!

fedshyvana commented 11 months ago

Hi @AnitaGoro, we do not have a tumor vs. normal model to accomplish your task. The toolbox is currently designed to perform WSI-level classification instead of ROI-level classification. For your task description you may need to find tumor vs. normal classifiers trained on ROIs for endometrial cancers, although I am not aware of any off the top of my head.