New cosmx reader with stitching #339
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This is the cosmx reader from Sopa, which includes:
The code is relatively complex to understand, I'm sorry. This is partly due to the CosMx files being poorly documented and with many breaking changes between different versions. The problem is that we can't read the AtomX version from the input files, so we have to infer multiple things based on the data, which makes it unnecessarily complex...
Not everything is using the CosmxKeys for now, but I can add this later, since there is already quite a lot to review.