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Two improvements to the Xenium notebook #128

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LucaMarconato opened this issue Jul 31, 2024 · 4 comments
Open
1 task

Two improvements to the Xenium notebook #128

LucaMarconato opened this issue Jul 31, 2024 · 4 comments
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@LucaMarconato
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CC @giovp @LLehner

The 10x team reviewed the Xenium notebook and found it very useful! (Btw, it's ready to merge #125).

They suggested to consider two improvements.

  • To show an example of how to use the multimodal segmentation as part of the analysis. The information is readily available in the SpatialData object, as shown here.
@LucaMarconato
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  • They suggested also to consider using a different dataset for the example since we are using a preview one. I'd suggest to wait until a 5K Xenium Onboard Analysis 3.0 is available (I'll update the notebook in SpatialData when it's available and put the link here: Update Xenium dataset spatialdata-notebooks#110).

@LucaMarconato
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I'd suggest to make a PR for the first issue and then transfer the second task item in a new issue to address later on.

@LLehner LLehner self-assigned this Aug 3, 2024
@giovp
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giovp commented Sep 2, 2024

update: #125 merged. I understand we want to keep this open for the 5k tutorial as well?

@LucaMarconato
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LucaMarconato commented Sep 9, 2024

Very nice! Yes, I'd keep this to track the usage on the 5k dataset; but also, as pointed out by 10x, it would be nice to plot/use the new multimodal segmentation.

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