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📝 Update Example Notebook 08-nucleus-instance-segmentation.ipynb#993

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gozdeg wants to merge 106 commits intodev-define-engines-abcfrom
dev-update-notebook-08
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📝 Update Example Notebook 08-nucleus-instance-segmentation.ipynb#993
gozdeg wants to merge 106 commits intodev-define-engines-abcfrom
dev-update-notebook-08

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@gozdeg gozdeg commented Feb 5, 2026

PR summary:

  1. Switched the notebook to the current NucleusInstanceSegmentor.run(...) API for tile and WSI inference, with Zarr outputs.
  2. Updated output loading/visualization to read from Zarr instead of joblib.
  3. Edited markdown parameters/examples to match the new API (model, num_workers, patch_mode, output_type, save_dir, auto_get_mask, input_resolutions).

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# Conflicts:
#	requirements/requirements.txt
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@gozdeg gozdeg marked this pull request as draft February 5, 2026 15:57
@gozdeg gozdeg closed this Feb 5, 2026
@gozdeg gozdeg reopened this Feb 5, 2026
@shaneahmed shaneahmed changed the base branch from develop to dev-define-engines-abc February 5, 2026 16:46
@shaneahmed shaneahmed changed the title Update notebook 08-nucleus-instance-segmentation.ipynb 📝 Update Example Notebook 08-nucleus-instance-segmentation.ipynb Feb 5, 2026
@shaneahmed shaneahmed added the documentation Improvements or additions to documentation label Feb 5, 2026
@shaneahmed shaneahmed added this to the Release v2.0.0 milestone Feb 5, 2026
@gozdeg gozdeg marked this pull request as ready for review February 5, 2026 20:21
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