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📝 Add Example Notebook for Foundation Models #887

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ADD: Add feature extraction notebook
adamshephard Nov 29, 2024
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475 changes: 475 additions & 0 deletions examples/11-import-foundation-models.ipynb

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6 changes: 6 additions & 0 deletions examples/README.md
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Expand Up @@ -97,6 +97,12 @@ In this example, the affine transformation is computed using thumbnails of the f

[![image](../docs/images/wsi-registration.png)](./10-wsi-registration.ipynb)

### 11- Feature extraction with foundation models ([11-feature-extraction](./11-import-foundation-models.ipynb))

This Jupyter notebook in TIAToolbox explains how to extract features from whole slide images (WSI) using pre-trained models from the `timm` library. It guides users through selecting appropriate model architectures, visualizing the extracted features using `UMAP` feature embedding, and verifying the model's performance by checking if different tissue types are correctly identified and separated in the feature map.

[![image](../docs/images/feature_extraction.png)](./11-import-foundation-models.ipynb)

## B) Examples of high-level analysis (pipelines) using TIAToolbox

List of Jupyter notebooks that demonstrate how you can use TIAToolbox to simplify high-level analysis in computational pathology.
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