Loading VisiumHD dataset
0
0
Entering edit mode
29 days ago
bio_info • 0

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!

Spatial transcriptomics Seurat VisiumHD • 572 views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
0
Entering edit mode

Maybe the error message is giving a hint :

file is not in PNG format

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
1
Entering edit mode

That is exactly what the issue is stating

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

ADD REPLY

Login before adding your answer.

Traffic: 1651 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6