Using SpatialDecon to analyze Visium data

[rocketeer1998]

Hi there! I would like to know whether SpatialDecon can be used directly to analyze the data obtained from Visium?
I've tried to get my annotation result but it seems not quite well. Is it a matter of incorrect data preprocessing? Thanks a lot!

[maddygriz]

Hello,
SpatialDecon does work on Visium data with no extra preprocessing. We have a vignette on it if you haven't gotten a chance to look at it.
We recommend that Visium data be in a Seurat object and to use the runspatialdecon() function. The main difference is the background value the algorithm uses, for Visium data we recommend bg = 0.1. If this value was not changed that could explain your low counts.
Maddy

[rocketeer1998]

Thank you Maddy. I have loaded my Visium data into a Seurat object. And I'll give it a try with bg = 0.1 and see what the result will be.