Seurat object for stereoseq spatial data

[Carissimo]

I tried to create a Seurat object for Stereoseq spatial data , but I cannot find the information related to the image in it. How can resolve it? Is there any indication about creating a Seurat object from a .gef stereoseq file?

[MathurinD]

Hi, the stereoseq pipeline also produces a .h5ad file under 05.spatialcluster (or the output of singularity exec $sif spatialCluster if you run each step yourself) that can be converted to .h5seurat then loaded with:

library(SeuratDisk)
Convert('data.h5ad','data.h5seurat')
LoadH5Seurat('data.h5seurat')

The .gef file does not contain the image information, it is combined with a .ipr file by spatialCluster. Note that if you have a cell segmentation the output will be in 041.cellcut.

[igrabski]

Hi, please see @8969 for an example!