Pipeline for reading Whole-Slide-Images (WSI) in Tiles

matthiaskoenig / zonation-image-analysis

GNU Lesser General Public License v3.0

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Pipeline for reading Whole-Slide-Images (WSI) in Tiles #1

Open matthiaskoenig opened 1 year ago

matthiaskoenig commented 1 year ago

[ ] implement module which reads WSI in tiles with settings for tile sizes & overlap

See: 266 openslide library for loading whole-slide images https://www.youtube.com/watch?v=QntLBvUZR5c 267 Processing whole-slide images as tiles https://www.youtube.com/watch?v=tNfcvgPKgyU&list=PLZsOBAyNTZwYx-7GylDo3LSYpSompzsqW&index=122

One module with code, one with example and one test module;

matthiaskoenig commented 1 year ago

I really like the following pipeline: https://slideflow.dev/slide_processing/ This looks great and solves many issues, i.e., normalization, background filtering, reports of tile extraction. Also has a nice format for the tiles.