scverse / scverse/spatialdata-io
ENHANCEMENT: to_legacy_anndata support with region > 1
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- Python
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Description
Hi all,
I managed to reproduce this notebook you also presented in the 2024 SpatialData paper, regarding Visium slide integration on a prostate from a unique patient. My main intention was to test SpaTrack, a spatially-aware trajectory inference tool, on multiple slides at once instead of on individual slides, since those multiple slides belong to the same tumoral focus and hence a unique trajectory is highly desirable instead of one per Visium dataset.
However, SpaTrack queries the AnnData object, so I tried to use to_legacy_anndata with the integrated coordinate_system, and encountered this (expected) error:
ValueError: The table needs to annotate exactly one element. Found 3.
I think it would be nice to have a full retrocompatibility also for this (IMHO) very interesting use case. What do you think about it?
Contributor guide
First steps
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Research direction
Start by reproducing the linked lundeberg.ipynb workflow and tracing to_legacy_anndata with the integrated coordinate_system until the "exactly one element" error occurs. Clarify the expected legacy AnnData representation for multiple regions, then verify that the proposed behavior remains compatible with the SpaTrack use case.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 42/100