📝 Update Example Notebook 11-import-foundation-models.ipynb

[YijieZhu15]

📘 Summary

This PR updates the 11-import-foundation-models.ipynb example to align with the latest TIAToolbox APIs and modern best practices. The notebook now uses Hugging Face Hub for dataset retrieval, Zarr for feature storage, the updated DeepFeatureExtractor pipeline, and improved IO configuration. Several cells and metadata entries were cleaned up for a more consistent, reproducible, and user-friendly demo.

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🔧 What’s Changed

Data Access

• Replaced deprecated download_data() usage with hf_hub_download() for fetching sample WSIs.
• Automatically creates a local ./tmp directory if missing.

Imports & Dependencies

• Added dask.array and zarr to support lazy, chunked feature loading.
• Updated TIAToolbox imports:
  • DeepFeatureExtractor from engine.deep_feature_extractor
  • IOPatchPredictorConfig from engine.io_config

Model & Pipeline Updates

• Removed explicit TimmBackbone usage; now uses model="UNI" directly in DeepFeatureExtractor.
• Replaced IOSegmentorConfig with the updated IOPatchPredictorConfig.
• Inference call migrated from predict() to run() using the new API.

Output Format Changes

• Switched from storing features as .npy files to a consolidated Zarr store.
• Updated later steps to read features and coordinates using zarr.open() + dask.array.from_zarr().

Notebook Cleanup

• Changed several cell tags from remove-cell to hide-output for cleaner diffs and readability.
• Cleared execution counts and removed unnecessary output noise.
• Added a cleanup cell to delete temporary directories.
• Updated kernel metadata to Python 3.10 and renamed environment to tiatoolbox-dev.

Documentation Edits

• Corrected model-selection guidance for UNI, Prov‑GigaPath, and H‑optimus‑0.
• Updated text to reference the newer model argument and correct IO config naming.

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Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 95.33%. Comparing base (d6ef926) to head (6d1da44).
⚠️ Report is 1 commits behind head on dev-define-engines-abc.

Additional details and impacted files

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##           dev-define-engines-abc     #994   +/-   ##
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  Coverage                   95.33%   95.33%           
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  Files                          79       79           
  Lines                       10001    10001           
  Branches                     1290     1290           
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  Hits                         9534     9534           
  Misses                        431      431           
  Partials                       36       36           

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[shaneahmed]

Thanks @YijieZhu15

Looks good. I have reverted the output to previous image.