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### Please make sure these conditions are met
- [X] I have checked that this issue has not already been reported.
- [X] I have confirmed this bug exists on the latest version of anndata.
- [ ] (optio…
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As discussed during the VIB Ghent 2024 hackathon with @giovp and @melonora, removing the legacy `_models.py` from the codebase, and access the data directly form `layer.metadata['sdata']` would improv…
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Hi,
I am receiving the error below when I am loading in Nanostring data. And I found that if I delete the imge folder ("CellComposite", "CellOverlay") and only keep the exprMat, matadata and fo…
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I have a SpatialData with two images, a and b. Each image is mapped to two coordinate system: global and aligned, with the following mapping:
a -> global: identity
b -> global: identity
a -> ali…
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**Is your feature request related to a problem? Please describe.**
When the specification of SpatialData is changed, existing datasets do not have these changes, and under circumstances may even beco…
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`h5py` happily reads file-like objects, and anndata kind of partially supports doing so. However, anndata only accepts `os.PathLike` objects. It first opens them with `h5py.File` in `read_h5ad_backed`…
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Hello,
I have a dataset made of unpaired RNA/ATAC seq data.
I performed PCA / nearest neighbors on each modality using a standard approach and I was going for the joint neighbors embedding.
I…
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Splitting out the discussion on how we do interactivity of the notebooks.
> > There should be some sort of interactivity (i.e. the possibility to execute the notebooks online)
> > – @grst
>
> Y…
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**User story**
User has segmentations that are represented using polygon shapes within a SpatialData object. User wants to visualize these segmentations using Vitessce without converting them to a …
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Cannot plot table annotations for points as it seems that the annotations columns from the table are treated as the annotation column that would be found in the points dataframe.
To reproduce pleas…