Ivirshup/census builder spatial

[ivirshup]

• Draft Census schema for support of Visium and Spatial data  #1092

To install from this branch

gh pr checkout 1245
pip install -e tools/cellxgene_census_builder

TODO

• Update source datasets links to ones which use schema v5.1.0
• Update builder
  • Don't include normalized layer
  • Figure out what set of genes to use
  • populate spatial collection
    • Add a scene per ingested dataset
      • Add images
        • Remove alpha channel from datasets that have it, and report the one weird dataset
      • Add obsl["loc"], data frame containing ["soma_joinid", "x", "y"]
        • Add radius
      • Add scene as Scene object once that is available: Add the new Scene collection to the python-spec single-cell-data/SOMA#202
      • Use MultiscaleImage (or whatever it ends up being called) for the images
  • Add obs_scene table
  • Add var_scene table
  • Filter out objects with .uns["spatial"]["is_single"]==False (current filtering code seems to rely only on columns in obs)
• Tests
  • Check equivalence of written data to input anndata
    • loc
    • images