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Fix xenium default instances #179

Merged
merged 3 commits into from
Jul 30, 2024
Merged

Fix xenium default instances #179

merged 3 commits into from
Jul 30, 2024

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LucaMarconato
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This PR closes #123 by implementing the following:

  • cells_as_circles now defaults to False.
  • When cells_as_circles is False, the table annotates the cells labels (and not the cells polygons anymore). When cells_as_circles is True, the table annotates the circles (as before).
  • The circles have centers equal to the cell centroids (as before), but now the radii are computed form the cells areas and not from the nuclei area.
    • This makes the visualization more "crowded" but more correct.
    • Also, this fixes the problem of not being able to compute the cell circles for those datasets that have cells without nuclei (Xenium 2.0.0).
  • Improved docs by adding an example that shows how to change the annotation target of the table.

Comes together with a small fix upstream scverse/spatialdata#648.

@LucaMarconato LucaMarconato merged commit d311f3f into main Jul 30, 2024
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@LucaMarconato LucaMarconato deleted the fix/xenium_radii branch July 30, 2024 14:00
lucas-diedrich pushed a commit to lucas-diedrich/spatialdata-io that referenced this pull request Nov 26, 2024
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Consider using nuclei locations for Xenium data when cells_as_circles is True
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