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ckmah / bento-tools

A Python toolkit for subcellular analysis of spatial transcriptomics data
https://bento-tools.readthedocs.io/en/latest/
BSD 2-Clause "Simplified" License
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make sure metadata from formatting is saved to disk #120

Open ckmah opened 4 months ago

ckmah commented 4 months ago

Metadata such as indexing columns generated as columns in spatialdata shapes are ignored when written to file using SpatialData.write() in version spatialdata==0.0.15. For now bento-tools will also reindex when loading data with bt.io.read_zarr().

Solution may be as simple as upgrading to spatialdata>=0.1.0.

ckmah commented 4 months ago

Looks like this is an open issue https://github.com/scverse/spatialdata/issues/311 that still needs to be addressed https://github.com/scverse/spatialdata/issues/293. Could also migrate all our annotations to Tableelements and retrieve with get_values() instead but will be a significant refactor.

LucaMarconato commented 2 months ago

https://github.com/scverse/spatialdata/pull/542 will solve the issue of columns lost when saving shapes.

LucaMarconato commented 1 month ago

The linked PR is now ready 😊