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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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patching slides with ndpi extension #148

Closed fnurkinali closed 2 years ago

fnurkinali commented 2 years ago

Hello,

I need to patch slides with ndpi extension. create_patches_fp.py is not able to segment tissue with default parameters. There is a --slide_ext parser for feature extraction, but I can't find it for patching.

Can you help me how to patch ndpi slides?

Thank you!

ptomaszewska commented 2 years ago

Hello, @fnurkinali I encountered the same problem. The images with ndpi extension were not properly segmented using create_patches_fp.py. I can see that you closed an issue. Could you share what you changed in the default settings to make it work better?

yuechen9 commented 2 years ago

Use different preset will fix this. bwh_biopsy.csv should work pretty well (basically you need to increase the threshold, e.g. increase sthresh) this is what they reposed to me before. #95

ptomaszewska commented 2 years ago

@Legendddd - Thank you for the valuable hint! It worked :)