Create spatialdata object

[dpshepherd]

The SpatialData documentation updated with how to create the object, found here. This should be easy to add a function to the datastore to collect the polyDT image, decoded RNA, polygons from Baysor, and make the object.

I don't know that we (qi2lab) will internally use this object, but other labs might want it.

[pr4deepr]

Would be very useful for bioinformaticians or computational biologists who will use the data for downstream analysis.

It is possible they may want a SpatialExperiment object for analysis in R, however there are converters for this.

[dpshepherd]

hi @pr4deepr !

One blocker for us is the on-going uncertainty around spatial transforms and OME-NGFF/OME-Zarr. That actually motivated the internal datastore we use to store these large nD experiments, because it is quite slow going with the OME specification update.

Once this issue is solved, I think we will be more comfortable moving forward with creating a SpatialData object. If you have a clear use case for immediate conversion, we can put together a script that does the conversion instead of adding it to the API.

[pr4deepr]

Thanks @dpshepherd.
I do not have a use case yet, but have been using spatialdata objects for 2D spatial omics experiments.
I didn't really follow the ome specification for it, but it was just convenient to have it all in one datastore organized a spatialdata object.