Add tiatoolbox tutorial (#2675)

* add initial file

* add test tutorial

* rename tutorial

* add notebook

* just test

* just test

* just test

* just test

* just test

* just test

* just test2

* just test3

* add feature extraction

* 🚧 Change tutorial name

* 📝 Update introduction section

* update text

* 🍱 Add WSI pyramid stack image

* just test3

* I tried to Cut down the patch-prediction stuff and shift the focus towards using PyTorch different models. I edited some of the text and made them more concise.

* I tried to Cut down the patch-prediction stuff and shift the focus towards using PyTorch different models. I edited some of the text and made them more concise.

* Focus towards using PyTorch

* update

* Removed sections related to image tile

* clear outputs

* remove output

* update

* ♻️ Update tutorial installation commands

* ♻️ Clean imports and logging

* ♻️ Clean imports and remove imagenet download

* 📝 Add comments to label dict

* 🚸 Rewritten `PatchPredictor` instantiation

* fix wrong text about overview resolution used

* 🐛 Fix model loading and remove patch section

* 📝 Minor text edits

* remove references to the tile image we no longer use

* test compile

* 📝 Address team edits and comments

* address feedback

* update supress cm

* ⏪ Restore patch prediction and add further links

* remove files for submission

* 📝 Minor edits and tweaks

* 🍱 Update tutorial thumbnail

* change tiatoolbox dep to develop

* remake as rst

* remove added reqs

* update link

* ✏️ Add to wordlist and fix typos

* ✏️ Fix more typos

* update index

* fix typo

* fix typo

* add notebook to _static

* update link to where notebook will be when merged

---------

Co-authored-by: Behnaz <behnazelhaminia@yahoo.com>
Co-authored-by: Abdol A <u2271662@live.warwick.ac.uk>
Co-authored-by: Abdol <a@fkrtech.com>
Co-authored-by: Carl Parker <carljparker@meta.com>

Author: 5 people

README.md

@@ -14,7 +14,7 @@ If you have a question about a tutorial, post in https://dev-discuss.pytorch.org
 You can submit the following types of issues:
 
 * Feature request - request a new tutorial to be added. Please explain why this tutorial is needed and how it demonstrates PyTorch value.
-* Bug report - report a failiure or outdated information in an existing tutorial. When submitting a bug report, please run: `python3 -m torch.utils.collect_env` to get information about your environment and add the output to the bug report.
+* Bug report - report a failure or outdated information in an existing tutorial. When submitting a bug report, please run: `python3 -m torch.utils.collect_env` to get information about your environment and add the output to the bug report.
 
 # Contributing
 

_static/img/thumbnails/cropped/TIAToolbox-Tutorial.png

@@ -515,3 +515,41 @@ warmstart
 warmstarted
 warmstarting
 warmup
+wsi
+WSI
+TIAToolbox
+tiatoolbox
+HistoEnc
+HistoEncoder
+histoencoder
+ModelABC
+UMAP
+umap
+WSIs
+wsis
+WSI’s
+TorchVision
+img
+webp
+OpenJpeg
+OpenSlide
+Pixman
+MacOS
+tmp
+Kather
+Colorectal
+LYM
+mucosa
+STR
+stroma
+ADI
+MUC
+PatchPredictor
+Cuda
+mpp
+Joona
+Pohjonen
+pre
+otsu
+rgb
+histologically

_static/img/tiatoolbox_tutorial/read_bounds_tissue.webp

@@ -142,6 +142,13 @@ What's new in PyTorch tutorials?
    :link: intermediate/spatial_transformer_tutorial.html
    :tags: Image/Video
 
+.. customcarditem::
+   :header: Inference on Whole Slide Images with TIAToolbox
+   :card_description: Learn how to use the TIAToolbox to perform inference on whole slide images.
+   :image: _static/img/thumbnails/cropped/TIAToolbox-Tutorial.png
+   :link: intermediate/tiatoolbox_tutorial.html
+   :tags: Image/Video
+
 .. customcarditem::
    :header: Semi-Supervised Learning Tutorial Based on USB
    :card_description: Learn how to train semi-supervised learning algorithms (on custom data) using USB and PyTorch.
@@ -919,6 +926,7 @@ Additional Resources
    beginner/dcgan_faces_tutorial
    intermediate/spatial_transformer_tutorial
    beginner/vt_tutorial
+   intermediate/tiatoolbox_tutorial
 
 .. toctree::
    :maxdepth: 2