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meastybehnazelhaminiaAbdol AAbdolcarljparker
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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 <[email protected]> Co-authored-by: Abdol A <[email protected]> Co-authored-by: Abdol <[email protected]> Co-authored-by: Carl Parker <[email protected]>
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‎README.md‎

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@@ -14,7 +14,7 @@ If you have a question about a tutorial, post in https://dev-discuss.pytorch.org
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You can submit the following types of issues:
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* Feature request - request a new tutorial to be added. Please explain why this tutorial is needed and how it demonstrates PyTorch value.
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* 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.
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* 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.
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# Contributing
2020

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

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‎_static/img/tiatoolbox_tutorial/read_bounds_tissue.webp‎

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‎_static/img/tiatoolbox_tutorial/tiatoolbox_tutorial_001.png‎

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‎_static/img/tiatoolbox_tutorial/tiatoolbox_tutorial_002.png‎

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‎_static/img/tiatoolbox_tutorial/tiatoolbox_tutorial_003.png‎

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‎_static/img/tiatoolbox_tutorial/tiatoolbox_tutorial_004.png‎

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‎_static/img/tiatoolbox_tutorial/tiatoolbox_tutorial_005.png‎

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‎_static/tiatoolbox_tutorial.ipynb‎

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‎en-wordlist.txt‎

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

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