how to create spateo object using gef from SAW? or adata converted from stereopy object?

aristoteleo / spateo-release

Spatiotemporal modeling of spatial transcriptomics

https://spateo-release.readthedocs.io/

BSD 2-Clause "Simplified" License

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how to create spateo object using gef from SAW? or adata converted from stereopy object? #281

Open xwangda opened 3 weeks ago

xwangda commented 3 weeks ago

Thank you so much for developing this brilliant tool. I briefly went through the tutorial and found there is no guide for creating a spateo object using .gef data from saw output. I tried to use spateo.pl.space while the object converted from stereopy does not have the _type record, and reported me the error below. KeyError: '__type' Could you provide a solution for creating a spateo compatible object using either .gef file or converted stereopy object? Thank you so much!

Best, xwangda

melop commented 3 weeks ago

I have the same question, is there any documentation about importing data from SAW version 8.1.1? I don't seem to find any *_all_bin1.txt.gz from the output of SAW. Perhaps the output format changed between SAW versions?