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

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gozdeg wants to merge 164 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 164 commits intodev-define-engines-abcfrom
dev-update-notebook-08

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@gozdeg
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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 commented Feb 11, 2026

Update:

  • Added a TIAviz example with an embedded screenshot.
  • Corrected the setup cell: removed OpenSlide from install steps.
  • Updated the output description to reflect Zarr format instead of the old dict.
  • Standardized paths so outputs/downloads are created under a new tmp folder (mirrors patch prediction notebook).

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codecov bot commented Feb 12, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.07%. Comparing base (d6ef926) to head (bbc9a86).

Additional details and impacted files
@@                    Coverage Diff                     @@
##           dev-define-engines-abc     #993      +/-   ##
==========================================================
+ Coverage                   95.33%   99.07%   +3.74%     
==========================================================
  Files                          79       80       +1     
  Lines                       10001    10341     +340     
  Branches                     1290     1354      +64     
==========================================================
+ Hits                         9534    10245     +711     
+ Misses                        431       64     -367     
+ Partials                       36       32       -4     

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