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KatherLab / STAMP

Solid Tumor Associative Modeling in Pathology
MIT License
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heatmaps #19

Open victor-moreno opened 2 months ago

victor-moreno commented 2 months ago

Hi, Check line 214 of cli.py should be: model_path=Path(c.model_path),

Also, in heatmaps.main line 106 hardcodes 256 as "microns". I had changed it to a different values (112, 224, 448 to test resolutions) and the top tiles showed wrong mappings. I noticed because I got many completely blank tiles as the 8 top. There is other 256 in line 71 but I think this only scales the thumbnail and is ok independently of the microns defined for preprocessing.

For heatmaps, it would be great if asterisk could be expanded to a list of different files or the files listed in a file.

Avic3nna commented 2 months ago

@cornzz could you check out heatmaps.main with the issue above? I assumed only 10x at the time for the protocol and doesn't scale to other options