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@quentinblampey quentinblampey commented Apr 17, 2024

Adding stitching to the CosMX reader. It's also possible to load one FOV only (if desired), and reading the proteins has also been added.

This is still a very early version of the reader, and it lacks the things below, but I made the PR so that we can start a discussion.

  • Update CHANGELOG
  • Add all constants in CosmxKeys
  • Add labels to the SpatialData object
  • Update the docstrings (this current docstrings were copy-pasted from Sopa)
  • Adding some tests?

@LucaMarconato LucaMarconato marked this pull request as draft May 29, 2024 12:02
@LucaMarconato
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Hi @quentinblampey, I'd like to go through this PR soon. Is there anything outstanding missing or can I review the current state? Thanks for the info.

@quentinblampey
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Hi @LucaMarconato, it should look mostly fine, except that the cell segmentation is not currently read. This is because this reader comes from Sopa, and I don't need the cells labels.

But I imagine you can already check what is there, and maybe then we can work on adding the cells labels?

Btw, it seems some user struggle to export the right files from AtomX. I don't know exactly the reason for it, but it seems that not all users have the same software version, and depending on that they can't always export all the files that are needed for this reader. See this issue: gustaveroussy/sopa#146

@LucaMarconato
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Thanks for the explanation. Btw, some R users also reported problems with the latest formats of CosMx.

But I imagine you can already check what is there, and maybe then we can work on adding the cells labels?

Ok I will have a look at the PR and let you know. Btw @timtreis (or some colleagues from his lab?) is also going to work on CosMx data, so we could even merge a first iteration of this PR and then improve with future PRs.

@quentinblampey
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Sounds good!
Working with CosMX inputs is really painful, I hope we'll find a way to make it nice and easy 😊

@quentinblampey
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Tagging this sopa issue that may help

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