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manuel-munoz-aguirre / PyHIST

A pipeline to segment tissue from the background in histological images
GNU General Public License v3.0
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normalization #30

Open swvanderlaan opened 2 years ago

swvanderlaan commented 2 years ago

Hi,

Do you apply normalization prior to masking, tiling, etc? I was quickly scanning the code but couldn't immediately find such a step - but I may have overlooked it.

Thanks

Sander

manuel-munoz-aguirre commented 2 years ago

Hi Sander, When using the (default) graph segmentation method, PyHIST relies on an intermediate canny edge detector to help in the segmentation. As of now, we do not perform any other sort of normalization on the input WSIs, since PyHIST is meant to be a simple tile extraction tool, and there might be many different use cases for performing (or not) normalization, depending on the particular application.