SBU-BMI / wsinfer

🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images
https://wsinfer.readthedocs.io
Apache License 2.0
56 stars 9 forks source link

add a choice of slide backend: openslide and tiffslide #136

Closed kaczmarj closed 1 year ago

kaczmarj commented 1 year ago

replace openslide with tiffslide https://github.com/bayer-science-for-a-better-life/tiffslide

tiffslide is implemented in pure python and should make distribution easier.

kaczmarj commented 1 year ago

let's wait to incorporate tiffslide until https://github.com/bayer-science-for-a-better-life/tiffslide/issues/72 is resolved. i have found that tiffslide is slower than openslide when reading patches from a TCGA BRCA slide.

kaczmarj commented 1 year ago

instead of removing openslide, we have included a choice of backend, tiffslide or openslide in https://github.com/SBU-BMI/wsinfer/pull/139

this will require uses to install openslide or tiffslide separately. let's think about how to do this... what should be listed as a required dependency in setup.py?