search

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
1.02k stars 340 forks source link

Patch magnification #165

Closed bryanwong17 closed 1 year ago

bryanwong17 commented 1 year ago

May I know to patch at 20x instead of 40x? Is there a value I should change in patch_level?

fedshyvana commented 1 year ago

sorry for the late reply! but you should set the patch-level according to the WSI dataset you're using e.g. in my house, the hospital's scanner produces WSIs for which the level 0 is 40x, level 1 is 20x etc., but you can verify this by opening the slide using viewers such as QuPath or using openslide to read the metadata of the slide.

weiaicunzai commented 8 months ago

May I know to patch at 20x instead of 40x? Is there a value I should change in patch_level?

wsi.properties['aperio.AppMag'] or wsi.properties['openslide.mpp-x']