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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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Problems segmentiong Ventana bif WSI #177

Closed Tato14 closed 1 year ago

Tato14 commented 1 year ago

Thanks for the great tools. I am trying to tile and segment some Ventana bif slides using your create_patches_fp.py script and I am getting a couple of problems:

1) The images can be segmented quite accurately but the thumbnails in the "masks" directory are somehow incorrectly shown. Here is an example: image

Do you know why is this noise in the image?

2) On some bif images (DP200 scanned) openslide throws an error Bad direction attribute "LEFT"

I found in the openslide repor than this problem is actually solved in this PR. Is this something you experienced before?

Thanks

fedshyvana commented 1 year ago

regarding:

  1. please verify that you're using pixman > 0.38 (e.g. 0.40). upgrading to pixman 0.40.0 should solve the issue - this can be done via conda.
  2. I am not sure unfortunately - i have never worked with bif images.
Tato14 commented 1 year ago

It seems that the pixman=0.40.0 is not compatible with the clam.yaml file for setting up the conda env