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New docs section: how to integrate `spatialdata` in your tool

Open LucaMarconato opened this issue 1 year ago • 1 comments

Aim: adding a page in the docs to help methods developers that want to use SpatialData in their tools.

The page could cover the following, showing how SpatialData could be used at various levels:

  • Only downstream. E.g. visualization: one could handle everything outside SpatialData and just export to SpatialData to access napari-spatialdata, spatialdata-plot and soon vitessce
  • Only upstream. E.g. data ingestion: one could use spatialdata-io to read the raw data from common techs into xarray/geopandas/anndata objects and forget about SpatialData objects
  • Fully integrated. E.g. SOPA, bento-tools, squidpy: SpatialData is used as a core data structure for internal representation and (to different degrees) object manipulation.

LucaMarconato avatar Nov 01 '24 06:11 LucaMarconato

Regarding the fully integrated section: We want to add small demos of tools that are using SpatialData as a backend: bento (@ckmah), Sopa, squidpy, ...

quentinblampey avatar Nov 13 '24 09:11 quentinblampey