load Xenium clustering into h5ad file

[BioinfoTongLI]

No description provided.

[codecov-commenter]

Codecov Report

Patch coverage has no change and project coverage change: -0.17 ⚠️

Comparison is base (fe507fd) 37.17% compared to head (edd0c02) 37.01%.

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Additional details and impacted files

@@            Coverage Diff             @@
##              dev      #74      +/-   ##
==========================================
- Coverage   37.17%   37.01%   -0.17%     
==========================================
  Files          14       14              
  Lines         694      697       +3     
==========================================
  Hits          258      258              
- Misses        436      439       +3     

Impacted Files	Coverage Δ
bin/build_config.py	0.00% <ø> (ø)
bin/process_xenium.py	32.65% <0.00%> (-2.13%)	⬇️

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[BioinfoTongLI]

looks like an doc action deployment issue?

[davehorsfall]

The reason the deploy action fails is because you're merging from a fork of the repo, not a branch - so you don't have permission to deploy to the docs from your forked repo.

[davehorsfall]

I'm not familiar enough with this Xenium code to approve. Is this a blocker for submission @BioinfoTongLI? Does the cluster need to be reindexed like this? @dannda can you review please?

[BioinfoTongLI]

not really. Especially you said that the 10x Xenium dataset is working well with the current version. We can come back to this after biorXiv submission

[dannda]

Current version was not loading embeddings and clusters so we do need to merge this.
I've dded logic similar to processing spaceranger to load all clusters and embeddings.