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docs(space): add SPATA2-inspired AnnData utilities tutorial#84

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hurry060215-tech wants to merge 15 commits into
omicverse:mainfrom
hurry060215-tech:feat/spata2py-tutorial
Open

docs(space): add SPATA2-inspired AnnData utilities tutorial#84
hurry060215-tech wants to merge 15 commits into
omicverse:mainfrom
hurry060215-tech:feat/spata2py-tutorial

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@hurry060215-tech hurry060215-tech commented Jun 20, 2026

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Summary

Adds rendered English and Chinese notebooks for the SPATA2-inspired AnnData spatial utilities introduced in omicverse/omicverse#847.

The tutorial is scoped as an initial AnnData helper workflow, not as full SPATA2 parity documentation.

Tutorial flow

  1. Build a deterministic Visium-like AnnData fixture with a tissue grid, smooth gene-like variables, and isolated artifact spots.
  2. Extract coordinate tables with ov.space.spata2_get_coords.
  3. Join coordinates with observation metadata and molecular variables via ov.space.spata2_join_variables.
  4. Render spatial gene-like gradients.
  5. Identify and render a convex-hull tissue outline with ov.space.spata2_tissue_outline.
  6. Detect isolated observations with ov.space.spata2_identify_outliers.
  7. Remove flagged observations with ov.space.spata2_remove_outliers.
  8. Demonstrate explicit pixel-to-unit and unit-to-pixel conversion.
  9. Include a notebook-local benchmark and a parity-context section so readers do not mistake this helper layer for complete SPATA2 parity.

Changes

  • Updates English navigation pages.
  • Updates Chinese navigation pages.
  • Adds/refreshes executed notebooks:
    • docs/Tutorials-space/t_spata2py.ipynb
    • docs_zh/Tutorials-space/t_spata2py.ipynb
  • Fixes corrupted Chinese markdown in the notebook and new Chinese SPATA2 index page.
  • Rewords the tutorial from "SPATA2 reconstruction/parity" to "SPATA2-inspired AnnData spatial utilities".

Validation

  • Executed English notebook with PYTHONPATH=D:\scop-dev\omicverse-pr847 against the updated #847 worktree.
  • Executed Chinese notebook with PYTHONPATH=D:\scop-dev\omicverse-pr847 against the updated #847 worktree.
  • nbformat.validate() passed for both notebooks.
  • Checked both notebooks have 26 cells and no corrupted ??? markdown text.
  • git diff --check

Merge note

Merge this tutorial after omicverse/omicverse#847, because it imports the new ov.space.spata2_* APIs.

@hurry060215-tech hurry060215-tech marked this pull request as draft June 20, 2026 04:19
@hurry060215-tech hurry060215-tech changed the title Add SPATA2-style spatial utilities tutorial Draft: add initial SPATA2-style spatial utilities tutorial Jun 20, 2026
@hurry060215-tech hurry060215-tech marked this pull request as ready for review June 20, 2026 08:51
@hurry060215-tech hurry060215-tech changed the title Draft: add initial SPATA2-style spatial utilities tutorial feat(space): add initial SPATA2-style spatial utilities tutorial Jun 20, 2026
@hurry060215-tech hurry060215-tech changed the title feat(space): add initial SPATA2-style spatial utilities tutorial docs(space): add initial SPATA2-style spatial utilities tutorial Jun 20, 2026
@hurry060215-tech hurry060215-tech marked this pull request as draft June 20, 2026 09:02
@hurry060215-tech hurry060215-tech changed the title docs(space): add initial SPATA2-style spatial utilities tutorial docs(space): add SPATA2-style AnnData utilities tutorial Jun 20, 2026
@hurry060215-tech hurry060215-tech marked this pull request as ready for review June 20, 2026 10:15
@hurry060215-tech hurry060215-tech changed the title docs(space): add SPATA2-style AnnData utilities tutorial docs(space): add SPATA2-inspired AnnData utilities tutorial Jul 2, 2026
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