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store probe set for image-based transcriptomics in spatialdata #138

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giovp opened this issue Apr 23, 2024 · 3 comments
Open

store probe set for image-based transcriptomics in spatialdata #138

giovp opened this issue Apr 23, 2024 · 3 comments

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@giovp
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giovp commented Apr 23, 2024

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 giovp transferred this issue from scverse/spatialdata Apr 23, 2024
@giovp
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giovp commented Apr 24, 2024

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

@giovp
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giovp commented Apr 24, 2024

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

@LucaMarconato
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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).

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