Support for Visium HD 3'

[BioinfSina]

I saw in an issue that there is a plan for supporting Visium HD 3' data in the future. Is there any timeline for when that will be available? I am creating materials for teaching and would really like to include the newest Visium version if possible, but as we are basing it on Seurat analysis that is currently not possible.

[YoukaiFromAccounting]

Hello @BioinfSina,

Thank you for your interest in the Seurat project; we are currently in the process of finalizing a new Load10X_Spatial function and subfunctions to include support for SpaceRanger 4.0 and Visium HD 3' datasets. We estimate that we should have a working prototype branch to allow users to load in these datasets in about a week or so.

Here's a sneak peek at the new Visium HD 3' objects visualized in Seurat:
Plotting with SpatialDimPlot (tissue image overlay with cell segmentations):

Zoomed in look at cell segmentations:

Gene expression image on spatial data:

We are always interested in supporting Seurat as an educational resource; please let us know if there are certain functionalities that are of particular importance to your teaching materials, and we will try to prioritize those functionalities in getting a working prototype out.

[kebbekny]

Commenting for updates.

[YoukaiFromAccounting]

Hello everyone,

A working branch for Seurat and Seurat object have just been released that contain support for reading in, loading, and visualizing Spaceranger 4.0 outputs and Visium HD 3' objects. Please refer to this pull request here, (#10028) which contains instructions on how to use existing Seurat functions with these new datasets.

As this is a branch in development, we anticipate that users may encounter a higher amount of warnings or errors. We appreciate everyone's patience as we continue development on more robust support of Visium HD 3' objects. Please report any issues you may encounter in Seurat's issue board.

We thank everyone for their continued interest in the Seurat project.