dcm format support

[XinhengLyu]

Hello, the current code has problems when processing the feature extraction patch features of wsi in dcm format (based on conch1.5), but CLAM did not have this problem before. Why is this? In addition, can I use this library to perform slide feature extraction based on TITAN using the patch features extracted by CLAM?

[XinhengLyu]

[XinhengLyu]

Although the progress is 11%, all previous extractions have not been successful

[guillaumejaume]

DCM should be supported by OpenSlide and is one of the accepted formats of trident, see https://github.com/mahmoodlab/TRIDENT/blob/main/trident/Processor.py#L111.

• Does it fail on all DCM images?
• What version of openslide are you using?

Please check the FAQ, first question for clam compatibility. let me know if that works on your end?

[XinhengLyu]

Does it fail on all DCM images? yes
What version of openslide are you using? openslide-bin 4.0.0.6, openslide-python 1.4.1

[guillaumejaume]

can you share one the slides so I can reproduce on my end. debugging openslide errors can be very challenging. it basically cannot read the tile.

[XinhengLyu]

Thanks for your reply. Sorry, I don't know how to upload it. There is a file size limit. The slides are from CPTAC-BRCA. Maybe you can download one from here https://portal.imaging.datacommons.cancer.gov/explore/

[XinhengLyu]

I found that there is no error if num_workers=0 in "dataloader = DataLoader(dataset, batch_size=batch_limit, num_workers=get_num_workers(batch_limit),pin_memory=True)" in WSI.py

[guillaumejaume]

Interesting. It seems to be a known issue with python libraries that wrap C/C++ code.

• Is it significantly slower? I/O with OpenSlide read_region is not very fast, even if data are stored on SSD.
• We'll soon support cuCIM-powered slide readers, which won't have this issue.
• Just to make sure -- can you try including this snippet at the top of the main

import multiprocessing as mp

try:
   mp.set_start_method('spawn', force=True)
   print("spawned")
except RuntimeError:
   pass