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Enable tiling non-PANDA WSI datasets #621

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merged 16 commits into from
Dec 16, 2021
Merged

Enable tiling non-PANDA WSI datasets #621

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2507b05
Add basic dataset and environment changes
dccastro Dec 14, 2021
861c1e7
Add loading/preproc utils
dccastro Dec 14, 2021
b8e7f52
Back-up PANDA tiling scripts
dccastro Dec 14, 2021
cd7af1b
Refactor and generalise tiling scripts
dccastro Dec 14, 2021
163169a
Remove Azure scripts
dccastro Dec 14, 2021
ad14227
Add test WSI file
dccastro Dec 14, 2021
7c071b9
Add preprocessing tests
dccastro Dec 14, 2021
d1fbfef
Update changelog
dccastro Dec 14, 2021
9ffda4a
Add Linux condition for cuCIM in environment.yml
dccastro Dec 15, 2021
6df3fc6
Merge remote-tracking branch 'origin/main' into dacoelh/tiling
dccastro Dec 15, 2021
7f4cbd9
Merge branch 'main' into dacoelh/tiling
dccastro Dec 16, 2021
fa5ec34
Use PANDA instead of TCGA-PRAD in test
dccastro Dec 16, 2021
f599e61
Leave TcgaPradDataset as an example
dccastro Dec 16, 2021
abe7b4a
Fix skipped InnerEye dataset tests
dccastro Dec 16, 2021
a551a9b
Create and test mock slides dataset
dccastro Dec 16, 2021
a56a599
Remove Tests/ML/datasets from pytest discovery
dccastro Dec 16, 2021
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Update changelog
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@dccastro
dccastro committed Dec 14, 2021
commit d1fbfef533b3d8f0cef9624f75e8ec41debf08ad
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -37,6 +37,7 @@ jobs that run in AzureML.
- ([#614](https://github.com/microsoft/InnerEye-DeepLearning/pull/614)) Checkpoint downloading falls back to looking into AzureML if no checkpoints on disk
- ([#613](https://github.com/microsoft/InnerEye-DeepLearning/pull/613)) Add additional tests for histopathology datasets
- ([#616](https://github.com/microsoft/InnerEye-DeepLearning/pull/616)) Add more histopathology configs and tests
- ([#621](https://github.com/microsoft/InnerEye-DeepLearning/pull/621)) Add WSI preprocessing functions and enable tiling more generic slide datasets

### Changed
- ([#588](https://github.com/microsoft/InnerEye-DeepLearning/pull/588)) Replace SciPy with PIL.PngImagePlugin.PngImageFile to load png files.
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