Bin export for Visium HD

[visanuwan]

Hi,

Thanks for developing a wonderful tool. I'm working with Visium HD data.
I have successfully run the tool and converted the results into Anndata.
However, I am having difficulty finding the 2um bin information for each cell after segmentation.
Do you have a tutorial or guide for accessing this information from the results?

[dcjones]

There isn't a great way to access bin-level data from the proseg output currently. Internally, proseg converts the visium bin data to something that resembles xenium (a table of transcripts). So that's what gets output by by proseg. It's not entirely trivial to convert this back to bin data.

It would make sense though to add an option to output something resembling visium bin data.

[adamdingl2]

Hello,

Just to follow up on the bin-to-cell assignment for Visium HD data. Since Proseg converts bin data into a table of transcripts, can I assume it assigns a fraction of the transcripts (on a per-transcript basis) from a 2um bin to nearby cells?