Loading VisiumHD dataset

Question

[bio_info]

Hi all,

I am trying to load the output of Spaceranger for some VisiumHD datasets I have, but I am encountering an error with the Load10X_Spatial function from Seurat. I would appreciate your help in solving this issue. I have triple checked all the paths and I can't figure out the problem:

sobj <- Load10X_Spatial(
data.dir = localdir,
filename = "filtered_feature_bc_matrix.h5",
bin.size = 8)

Error in png::readPNG(source = file.path(image.dir, image.name)) : 
  file is not in PNG format

Thank you!

[Arup Ghosh]

The Load10X_Spatial function expects the images to be present in a subdirectory called spatial alongside the H5 file.

https://satijalab.org/seurat/reference/load10x_spatial

[Bastien Hervé]

Maybe the error message is giving a hint :

file is not in PNG format

Check here : https://github.com/satijalab/seurat/issues/9533

[bio_info]

Hi! I found that GitHub post but the spaceranger output is present in PNG format, so I am not sure why the error is occurring, maybe because it is a symlink... In this case I am not sure what to do

[Bastien Hervé]

That is exactly what the issue is stating

I fixed the error by copying the full png file to the expected locations