seg-level

[zaizaiwa]

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]

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]

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.