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base repository: scverse/spatialdata-notebooks
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compare: add_cells_tutorial
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  • 9 commits
  • 3 files changed
  • 2 contributors

Commits on May 16, 2026

  1. mvp

    @timtreis
    timtreis committed May 16, 2026
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  2. bump

    @timtreis
    timtreis committed May 16, 2026
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Commits on May 18, 2026

  1. bump

    @timtreis
    timtreis committed May 18, 2026
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Commits on Jun 4, 2026

  1. finalised notebook

    @timtreis
    timtreis committed Jun 4, 2026
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  2. Anonymise paths and drop non-notebook files from PR 

    Remove local cluster/home paths from cell outputs, drop the
warnings.filterwarnings cell, and untrack pixi.toml so the PR
contains only the create_cells_dataset notebook.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
    @timtreis @claude
    timtreis and claude committed Jun 4, 2026
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Commits on Jun 5, 2026

  1. Add cells tutorial to gallery and sanitize notebook 

    - Register create_cells_dataset.ipynb in the Intermediate gallery section
  (fixes the RTD orphan-toctree warning under fail_on_warning)
- Add 3:2 thumbnail for the gallery card
- Localize paths in outputs, dedupe markdown, fix zarr write/read cell

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
    @timtreis @claude
    timtreis and claude committed Jun 5, 2026
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  2. removed warnings block

    @timtreis
    timtreis committed Jun 5, 2026
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Commits on Jun 14, 2026

  1. Address review: align crop box, fix typo/casing, clearer wording 

    - Derive red Rectangle from shared bbox_min/bbox_max so it matches the
  bounding_box crop (Luca's comment)
- Fix swallowed <Delayed> tag / stray space in dataset summary
- SpatialData.datasets -> spatialdata.datasets (correct casing)
- Replace unclear 'baked' wording with explicit rasterize phrasing

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
    @timtreis @claude
    timtreis and claude committed Jun 14, 2026
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Commits on Jun 15, 2026

  1. Clean up cells tutorial: paths, warnings, channel names 

    - Preserve H&E channel names (r/g/b) on he_aligned via c_coords
- Anonymise local zarr-store paths in outputs (-> ./cells.zarr)
- Remove blanket warnings.filterwarnings and unused ski/np imports
- Correct table<->region wording (labels via region/instance, cell_id bridge to shapes)
- Revert overview rectangle to the larger context box

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
    @timtreis @claude
    timtreis and claude committed Jun 15, 2026
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