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gustaveroussy / sopa

Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells
https://gustaveroussy.github.io/sopa/
BSD 3-Clause "New" or "Revised" License
94 stars 8 forks source link

Adds openslide backend #51

Closed stergioc closed 2 months ago

stergioc commented 2 months ago

This is adding the openslide backend for reading WSIs. It is using a modified version of the OpenSlideStore class from manzt/napari-lazy-openslide/napari_lazy_openslide/store.py to do so.

The issue related to stergioc/sopa#3 has been solved. At the moment, the feature extraction excecution time is x3 faster with the openslide backend (related to stergioc/sopa#2).

I let you @quentinblampey do the final checks :)

quentinblampey commented 2 months ago

Looks good to me @stergioc, merging!