Patching of the BCNB dataset

[hathawayxxh]

Hi Authors,

I am trying to reproduce the experiments on BCNB (Table2 of the manuscript). As you suggested, I tried to use the following codes to segment the WSIs into patches. However, I found the code does not support the .jpg format in the BCNB dataset. Could you please give some hints on how to revise the codes for patching of the BCNB dataset? Thanks!
https://github.com/mahmoodlab/MADELEINE/blob/main/bin/extract_patch_embeddings.py

[guillaumejaume]

All WSIs need to be converted from JPG to a pyramidal format (typically tiff). You can do that using the function provided in https://github.com/mahmoodlab/HEST/blob/main/src/hest/utils.py#L861