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Lotfollahi-lab / nichecompass

End-to-end analysis of spatial multi-omics data
https://nichecompass.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
35 stars 6 forks source link

Compatibility with Visium HD data (8 micron) #69

Closed Rafael-Silva-Oliveira closed 3 months ago

Rafael-Silva-Oliveira commented 3 months ago

Hello! Just wanted to quickly ask if this tool is compatible with Visium HD data (8 microns, over 500k bins/spots) and if not, do you plan on expanding NicheCompass to be compatible with such data resolution?

Thanks!

sebastianbirk commented 3 months ago

Hi @Rafael-Silva-Oliveira, Yes our tool is compatible with Visium HD data. Hope that helps :)

Rafael-Silva-Oliveira commented 3 months ago

Hi @Rafael-Silva-Oliveira, Yes our tool is compatible with Visium HD data. Hope that helps :)

Super! Is it possible to share the GP and the other csv files used in the single sample tutorial? Would be quite neat if this data could be fetched directly from the API as well, while also letting the user define their own GPs.

Thanks

sebastianbirk commented 3 months ago

The GP data can be fetched directly via the "extract_gp_dict" functions by setting the "load_from_disk" parameter to False as described in the tutorial ;) Or are you facing any issue with that?

Rafael-Silva-Oliveira commented 3 months ago

The GP data can be fetched directly via the "extract_gp_dict" functions by setting the "load_from_disk" parameter to False as described in the tutorial ;) Or are you facing any issue with that?

Completely missed that, Sebastian! Thank you very much once again :)