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Teichlab / bin2cell

Join subcellular Visium HD bins into cells
MIT License
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How could we convert cdata into Seurat object? #23

Closed LinAU closed 1 day ago

LinAU commented 3 weeks ago

Thank you very much for the wonderful tools!

I am now working with Visium HD data and would like to use seurat for some of the analysis after cell segmentation. May I ask how you suggest to convert the cdata into a seurat object?

Thank you in advance for your help!

KR, Lin

ktpolanski commented 3 weeks ago

Please look into existing AnnData to Seurat conversion tools, being mindful of the fact they probably don't support image data. Please look into how Seurat stores images when handling spatial data and attempt to insert images R side.

bmateosa commented 1 day ago

@LinAU did you manage to open the Bin2Cell data in R to work with Seurat? I'm trying to do the same but I'm losing the image in the process. Thank you.

bmateosa commented 1 day ago

I just found this package that solved my problem: https://github.com/cellgeni/schard

ktpolanski commented 1 day ago

That's a great catch - I didn't know schard supported image imports!

LinAU commented 1 day ago

@bmateosa Thanks! I will try this as well!