Magnification selection not working properly

AICAN-Research / FAST-Pathology

⚡ Open-source software for deep learning-based digital pathology

BSD 2-Clause "Simplified" License

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Closed andreped closed 2 years ago

andreped commented 2 years ago

Tried to run the BACH model on a x40 WSI, and it crashed due to:

Exception caught: Thread stopped because: No level close enough to magnification of 20 was found in the image pyramid.

This image plane exists, so there is something wrong.

andreped commented 2 years ago

Same for the breast cancer segmentation pipeline:

Exception caught: Thread stopped because: No level close enough to magnification of 10 was found in the image pyramid.

andreped commented 2 years ago

Just tested on a WSI stored in the CellSens VSI format and this works, but it fails for the TIFF format.

Perhaps it only works for the CellSens VSI format currently?

WSIs are stored on the sintef server for testing, in the images/ directory where all the other pathology stuff lies.

smistad commented 2 years ago

This was a bug in FAST, conversion of spacing from TIFF was incorrect. Fixed in: https://github.com/smistad/FAST/commit/9d11f1675fecca64335a1b302e63790bfea16103