anndata i.e. Annotated data is a NumFOCUS-supported Python package that handles annotated data matricies on memory and disk, and is between Pandas and Xarray.

Without going into every fancy Python-based data structure, we think that still today no other alternative really exists that:

• Handles sparsity
• Handles unstructured data
• Handles observation- and feature-level metadata
• Is user-friendly

–Getting started guide

It is well integrated with:

• Dask
• PyTorch
• Awkward Arrays
• Zarr
• TileDB?

References

https://anndata.readthedocs.io/en/latest/