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mahmoodlab / UNI

Towards a general-purpose foundation model for computational pathology - Nature Medicine
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Does 20x magnification correspond to 0.5 microns per pixel? #5

Closed GeorgeBatch closed 7 months ago

GeorgeBatch commented 8 months ago

Hello,

Does the 20x magnification correspond to the resolution of 0.5 microns per pixel (mupp)? I am asking because magnification is not standardised, and I have encountered slides from different scanners with 20x magnification, corresponding to a resolution from 0.23 mupp to 0.55 mupp.

Many thanks, George

GeorgeBatch commented 8 months ago

CLAM's patch extraction script allows to specify these things as arguments if you know the levels/magnification/resolution information about the slides. I want to use tiatoolbox functionality to set the resolution to 0.5 mupp to extract patches without parsing the slide metadata first.

guillaumejaume commented 7 months ago

20x usually maps to 0.5 um/px. Indeed, variations exist from one scanner to another. Thanks to UNI diverse training dataset, these variations should not have a large downstream impact.

GeorgeBatch commented 6 months ago

@guillaumejaume, thank you for your explanation!