adata slots for table and point spec in ngff

related to #64 and https://github.com/kevinyamauchi/ome-ngff-tables-prototype , as discussed this morning with @kevinyamauchi this is a description of adata slots and how they are used in https://github.com/theislab/squidpy and other spatial analysis tools of the https://github.com/theislab/scanpy ecosystem.

• adata.X and adata.layers["layer"] store molecular info (gene/protein expression etc.).
• adata.obsm stores various "latent" representations of obs (e.g. PCA/UMAP coordinates) but also:
  • adata.obsm["spatial"] stores obs coordinates in space, with shape (N,2) or (N,3).
  • adata.obsm["molecule_spatial"] will store molecule location in FISH-based data (with awkward arrays).
• adata.varm no real use in spatial data afaik
• adata.obsp stores adjacency matrices of e.g. graphs in spatial coordinates, knn graphs in latent spaces etc.
• adata.varp no real use in spatial data afaik
• adata.uns stores a bunch of image-related data. It is structured as follow:
  • adata.uns["spatial"] contains library_id keys that correspond to unique identifiers of images (e.g. tissue slides). These values are also stored in adata.obs["library_ids"] which can be used to subset anndata based on the tissue slide of interest. Furthermore, inside adata.uns["spatial"][<library_id>] there are 2 more dictionaries:
  • images for small-size tissue images (order of Mbs)
  • scalefactors metadata related to scaling original coordinates in adata.obs["spatial"] as well as other infos

adata.uns also stores intermediate analysis results by several analysis tools in the ecosystem. e.g. trajectory analysis, velocity, various plotting params etc. I would therefore consider to support it for a better integration in the ecosystem.
It would also be ok to store the same type of info in metadata in ngff, and then handle this on the API side (it'd be fine for us at Squidpy, not so sure for others).

@kevinyamauchi next week I'll try out https://github.com/kevinyamauchi/ome-ngff-tables-prototype and report back, thanks again for sharing.

Just want to mention one more time that this is super exciting and am really looking forward to see how it develops!

pinging various people @ivirshup @michalk8 @hspitzer @AnnaChristina @LucaMarconato

Start by reviewing related issue #64 and the ome-ngff-tables-prototype, then compare the listed AnnData slots with the NGFF metadata options. Done means reaching and documenting a decided representation for spatial, molecular, graph, image, and intermediate analysis data, including whether it belongs in metadata or dedicated NGFF slots.