SBU-BMI / wsinfer

🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images
https://wsinfer.readthedocs.io
Apache License 2.0
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Add segmentation options to wsinfer run #217

Closed kaczmarj closed 7 months ago

kaczmarj commented 7 months ago

in some cases, it is desirable to customize the tissue segmentation parameters. the defaults may under- or over-estimate tissue.

related to #213 -- in that issue, the entire image was interpreted as tissue using the defaults. changing the binary threshold to 12 resulted in a good segmentation.