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store probe set for image-based transcriptomics in spatialdata

Open giovp opened this issue 1 year ago • 3 comments

after discussion with @LouisK92 and @timtreis we realized it would be useful for spatialdata to also store the probe set used to target mRNA transcripts. Where should that be stored, unclear, maybe uns?

giovp avatar Apr 23 '24 15:04 giovp

additionaly, save also additional info such as add-on panel Supplemental: Add-on Panel (CSV)

giovp avatar Apr 24 '24 11:04 giovp

  • [ ] save json file in either dataframe or just json in table.uns
  • [ ] store additional probe information in table.var

giovp avatar Apr 24 '24 11:04 giovp

As discussed during the community call, we can start with var and see how the format from 10x evolves before adding the json dataframe in uns, as it would be a technology-specific way to add metadata and in general we should keep this to a minimum until we have a system taylored for metadata (@melonora).

LucaMarconato avatar Apr 25 '24 21:04 LucaMarconato