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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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Heatmaps reversed #173

Closed nam1410 closed 1 year ago

nam1410 commented 1 year ago

@fedshyvana

I have been generating some heatmaps, and I see that if I use

cmap = cmap.reversed()

after the following line, I get heatmaps closer to the expectations of a clinical expert.

https://github.com/mahmoodlab/CLAM/blob/9482cbc72df522087cfbaa3e6b52da5207a7980a/wsi_core/WholeSlideImage.py#L624

I'm not sure why this happens. Can you please explain?

nam1410 commented 1 year ago

@fedshyvana

Can you please look into this?

fedshyvana commented 1 year ago

I don't think there's any issue with the heatmap code - this could be a unique phenomenon to the task/dataset you're using. Sorry I am unable to comment on it.