Retrieve MPP from WSIs #432
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nkaenzig
reviewed
May 8, 2024
nkaenzig
reviewed
May 8, 2024
roman807
merged commit 1211e5a
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360-aggregated-feature-support-wsi-level-tasks
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roman807
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Jun 24, 2024
* Add base class for WSIs & `openslide` implementation (#365) * Add WSI dataset classes (#368) * Add baseline `panda` workflow (#373) * add panda config * adjust batch size * addressed comments * addressed comments * addressed comments * Add support for grid sampling to `WsiDataset` (#377) * Replaced cached_property in WsiDataset by LRU cache (#388) * Updated `EmbeddingsWriter` to support multi-embedding file outputs (#384) * Simple baseline sampler for foreground patches (#394) * add foreground kaggle * added random foreground sampler kaggle * refactored sampler * moved get_mask * typo * refactor sampler * refactor sampler * addressed comments * addressed comments * Fixed linting in WSI feature branch (#407) * added openslide-python to all dependencies * Fix input batch class name (#414) * Add lower bound for wsi resolution level during mask generation (#412) * Move sampler logic to `samplers` module and add unit tests (#420) * Add `WsiClassificationDataset` (#429) * Retrieve MPP from WSIs (#432) * add mpp conversion * formatting * addressed comments * addressed comments * addressed comments * formatting * formatting * formatting * updated panda config (#437) * update WSI foreground segmentation algorithm (#456) * Add `PANDA` dataset class (#430) * fixed panda (#463) * Update `EmbeddingsWriter` to store tensors as lists (#465) * add tiffslide backend (#468) * added panda cli unit tests (#470) * move wsi initialization to setup method of `MultiWsiDataset` (#472) * 459 add camelyon16 slide level task (#476) * added panda dataset class * clean up * remove samples with noisy labels * clean up table in dataset readme * added function for stratified splits * added unit tests * cleanup * addressed comments * fixed issue with resource download * validation fix * updated readme * added to mkdocs * added image_dir to exception print * updated root path in yaml config * added panda to datasets overview table in docs * added md5 hash for downloaded resources * update init * added camelyon16 * added camelyon16 * updated camelyon16 class * added tests and config * formatting * formatting * formatting * formatting * added test files * formatting * lint * added target transforms * formatting * fixed dataset * addressed comments * addressed comments * fix test * fix test * fixed test * addressed comments * updated loss * fix annotations * lint --------- Co-authored-by: Nicolas Kaenzig <[email protected]> * 475 define slide level evaluation protocol (#511) * updated configs * adjust patience * addressed comments * fixed typo * remove prefetch factor * update 360-aggregated-feature before PR to main (#527) * Updated developer guide (#418) * Update `TotalSegmentator2D` dataset to fetch all the slices (#416) * Move metrics to CPU when using single device (#446) * Remove total segmentator classification dataset (#450) * updated eva logo (#454) * updated eva logo * renamed files * Update actions/checkout digest to a5ac7e5 (#458) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Add configuration logger (#466) * Update `README` with paper citation (#474) * update docs (#482) * Update img shields of README (#480) * Fix `torch` and `jsonargparse` versions (#483) * update depedencies * update * bump micro version (#486) * update config links (#487) * Update paper citation format (#489) * Update the vision dataset return types to `tv_tensors` (#478) * Refactor embeddings writer (#461) * fixed phikon configs (#493) * Refactor embeddings datasets (#495) * Add doc tests and minor fixes (#492) * support setting download as env-variable (#514) * updated confis and doc * typo * update datasets * fixed types * src/eva/core/callbacks/writers/embeddings/base.py * formatting * types --------- Co-authored-by: Nicolas Känzig <[email protected]> Co-authored-by: ioangatop <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Updated documentation with new datasets and leaderboard (#531) * updated layout * updated layout * addressed comment * 532 update leaderboard results with slide level tasks (#538) * updated docs * update leaderboard * update docs and links * updated configs (#539) * updated leaderboard (#543) --------- Co-authored-by: Nicolas Känzig <[email protected]> Co-authored-by: Nicolas Kaenzig <[email protected]> Co-authored-by: ioangatop <[email protected]> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com>
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closes #426