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Add surface sample data#391

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jo-mueller merged 6 commits intov0.9.0from
add-surface-sample-data
Apr 26, 2025
Merged

Add surface sample data#391
jo-mueller merged 6 commits intov0.9.0from
add-surface-sample-data

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Relevant for #376 - adds cells3d data example from https://github.com/haesleinhuepf/napari-process-points-and-surfaces demo notebooks

Long description

This pull request introduces a new sample data function, cells3d_curvatures, to the napari_clusters_plotter package, along with corresponding updates to the package's exports, tests, and plugin configuration. The changes primarily focus on adding support for loading and visualizing 3D mitotic nucleus surface curvatures in Napari.

New Feature: cells3d_curvatures Sample Data

  • New function implementation: Added the cells3d_curvatures function in _sample_data.py to load 3D mitotic nucleus surface curvatures, including vertices, faces, and nucleus images. The function returns layer data tuples for visualization.
  • Exported in __init__.py: Updated the __all__ list to include cells3d_curvatures, making it accessible as part of the public API.

Plugin Configuration Updates

  • Plugin contributions: Added a new entry for cells3d_curvatures in the contributions section of napari.yaml, enabling it as a sample data loader in the Napari plugin.
  • Menu integration: Added a corresponding menu item for cells3d_curvatures in the napari.yaml file, allowing users to load this dataset via the Napari interface.

Testing Enhancements

  • Parameterized testing: Updated the sample data tests in test_sample_data.py to use pytest.mark.parametrize, ensuring both bbbc_1_dataset and cells3d_curvatures are tested for proper functionality.

@jo-mueller jo-mueller added documentation Improvements or additions to documentation enhancement New feature or request labels Apr 26, 2025
@jo-mueller jo-mueller added this to the v0.9.0 milestone Apr 26, 2025
@jo-mueller jo-mueller mentioned this pull request Apr 24, 2025
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@jo-mueller jo-mueller merged commit 90aba48 into v0.9.0 Apr 26, 2025
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@jo-mueller jo-mueller deleted the add-surface-sample-data branch April 26, 2025 21:57
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