Storing sub-obs (variable length per observation data)

Hi, We have a use case related to https://github.com/theislab/anndata/issues/237 but slightly different.

We would like to store a second obs array (“sub-obs”, where an observation is an individual transcript in a MERFISH experiment), but related to the first obs array (where an observation is an individual cell).

Has your team thought about how to deal with this use case?

I am thinking something like this:

where the transcript ID and cell ID columns in the sub-obs can be like foreign keys into the main obs dataframe.

Is it possible to add a differently-shaped obs and obsm to the same AnnData store?

cc @ilan-gold

[ilan-gold]

Yes @keller-mark! We really want a way to store this spot-level data in AnnData but are just not sure how to go about it. I think this proposal is really solid. We would definitely also be interested in crossover with squidpy if that would be of interest.

[ilan-gold]

@giovp You’re totally right about this, I got a little carried away. And there’s no rush on the email - I need to start coding and stop emailing you all so much 😄 Let me collect my thoughts on this and I’ll post soon!