how to use iSCALE for my own visium data

[AdotaLover]

Hello! Thank you very much for creating such a useful tool! I'd like to ask, since I have Visium HD data, how should I prepare the input to run your tool? Thank you!

[jackBQ]

I also want to know about it. I expect it so much

[amesch441]

Hello! Thank you very much for your interest in our tool! For Visium HD data, the input preparation would be very similar to how we process Xenium data in the iSCALE-img pipeline. In both cases, the cellular or near-cellular resolution measurements are represented in a superpixel grid structure. For Xenium data, the pipeline internally bins the cell-level measurements into this grid, whereas Visium HD data already comes in this structure natively. Once the data is in the grid format, it can be provided to the pipeline in the same way as in the Xenium example.
I would be happy to share additional details or instructions on setting up the input files if that would be helpful.

[LalicJ]

@amesch441 Thank you very much for your explanation. This is very helpful.

I would be interested in learning more about the overall data processing and analysis workflow of Visium HD data, particularly how the input data are prepared and handled in the pipeline. Any additional details or guidance you could share on this would be greatly appreciated.

Thank you again for your time and help.