Is Xenium data can be 3D visualization/ can the Stardist do 3D segmentation/ is squidy able to crop image for further analysis

scverse / squidpy

Spatial Single Cell Analysis in Python

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

BSD 3-Clause "New" or "Revised" License

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Is Xenium data can be 3D visualization/ can the Stardist do 3D segmentation/ is squidy able to crop image for further analysis #873

Closed Yifan-debug closed 3 months ago

Yifan-debug commented 3 months ago

Hi developer,

Thank so much for the package. I'm currently looking for a package can do 3D segmentation and visualizarion on xenium dataset. And also can crop the dataset to the region I'm only interested to avoid the large requirement of power.

Yifan-debug commented 3 months ago

I see it could do 3D on merfish. I'm wondering it also could do in Xenium data

giovp commented 3 months ago

you might want to take a look at https://github.com/gustaveroussy/sopa closing this for the moment, feel free to reopen