8000 seg-level · Issue #292 · mahmoodlab/CLAM · GitHub
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seg-level #292

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zaizaiwa opened this issue Jan 13, 2025 · 2 comments
Open

seg-level #292

zaizaiwa opened this issue Jan 13, 2025 · 2 comments

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@zaizaiwa
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I would like to ask, if I want to utilize 256 at 20X magnifcation on the TCGA dataset, how should I set the seg-level and patch-level?
@his0car
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his0car commented Jan 16, 2025

Seg-level has nothing to do with patch-level.

I don't know what magnification or file format the TCGA slides have. But in general:

When a slide has a pyramidal image format like
Level 0 -> 100.000x100.000 px at 40x magnification
Level 1 -> 50.000x50.000 px at 20x magnification
Level 2 -> 25.000x25.000 px at 10x magnification

then we need to specify the patch-level as 1 with a patch size of 256

@guillaumejaume
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Feel free to refer to our new trident repo for WSI image processing: https://github.com/mahmoodlab/trident

You can directly set the mag and patch size, the rest is handled internally.

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@guillaumejaume @his0car @zaizaiwa
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