Two improvements to the Xenium notebook

scverse / squidpy_notebooks

Tutorials for Squidpy

https://squidpy.readthedocs.io/en/stable/

MIT License

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Two improvements to the Xenium notebook #128

Open LucaMarconato opened 1 month ago

LucaMarconato commented 1 month ago

CC @giovp @LLehner

The 10x team reviewed the Xenium notebook and found it very useful! (Btw, it's ready to merge https://github.com/scverse/squidpy_notebooks/pull/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 commented 1 month ago

[ ] 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: https://github.com/scverse/spatialdata-notebooks/issues/110).

LucaMarconato commented 1 month ago

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.

giovp commented 6 days ago

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

LucaMarconato commented 4 hours ago

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.