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Add tiatoolbox tutorial #2675

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merged 70 commits into from
Dec 19, 2023
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@measty measty commented Nov 12, 2023

Fixes #2669

Description

Adds a tutorial for using TIAToolbox, a python/pytorch library for working with whole slide images (large medical images).

Checklist

  • [x ] The issue that is being fixed is referred in the description (see above "Fixes #ISSUE_NUMBER")
  • [x ] Only one issue is addressed in this pull request
  • [x ] Labels from the issue that this PR is fixing are added to this pull request
  • [ x] No unnecessary issues are included into this pull request.

cc @datumbox @nairbv @fmassa @NicolasHug @YosuaMichael @sekyondaMeta @svekars @carljparker @kit1980 @subramen

@measty measty marked this pull request as ready for review November 15, 2023 19:07
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If one can not autogenerate .ipynb from the .py file, please check it into the tutorials repo and reference it rather than https://colab.research.google.com/drive/1qkTBbMrECLjVAWwg9SJHKFgmSUyv3djE?usp=sharing (because if/when author decided to stop sharing it it will not be accessible to the reader)

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measty commented Dec 7, 2023

If one can not autogenerate .ipynb from the .py file, please check it into the tutorials repo and reference it rather than https://colab.research.google.com/drive/1qkTBbMrECLjVAWwg9SJHKFgmSUyv3djE?usp=sharing (because if/when author decided to stop sharing it it will not be accessible to the reader)

Should this be done by making a PR against the gh-pages branch, or in some other way?

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@malfet Could you respond to the question from @measty about where to commit the Python notebook (.ipynb) file.

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malfet commented Dec 12, 2023

Should this be done by making a PR against the gh-pages branch, or in some other way?

No, just add one to this PR in a folder where it will be published

@carljparker carljparker requested a review from malfet December 14, 2023 22:59
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@malfet: Are we good to merge (provided CI is clean)? @measty added the notebook to an _static subdirectory.

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measty commented Dec 15, 2023

@malfet: Are we good to merge (provided CI is clean)? @measty added the notebook to an _static subdirectory.

Sorry, I noticed I forgot to change the link to point to the new location when I added the notebook to this PR. Should be all set now from my end.

@carljparker carljparker merged commit e77fc43 into pytorch:main Dec 19, 2023
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💡 [REQUEST] - A Tutorial on Whole Slide Image Classification using PyTorch and TIAToolbox
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