Loading VisiumHD dataset
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!
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Arup Ghosh
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bio_info •
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Maybe the error message is giving a hint :
Check here : https://github.com/satijalab/seurat/issues/9533
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
That is exactly what the issue is stating
The
Load10X_Spatialfunction expects the images to be present in a subdirectory calledspatialalongside the H5 file.https://satijalab.org/seurat/reference/load10x_spatial