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Issue with LoadVizgen #8597
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I'm not from Seurat dev team.. however, It is related to
Here is an example on how to use that optimized function. Instead of using |
Hm.. do you know how I would use the optimized LoadVizgen instead? |
You didn't install that PR on Vizgen properly. After install restart your R session, then it should work. |
Adding my voice to the choir of users who have run into this issue while testing Seurat's suitability for our spatial transcriptomics experiments. I was able to get data loaded using @alikhuseynov 's PR. Hopefully this is incorporated into Seurat in a future update. |
Yes I was able to make the object but it was unable to read the hdf5 files still. |
did it read any hdf5 files at all or just didn't read some? |
It wasn't able to read any of the hdf5 files.
and this was the session info:
|
you have these versions
could you show the complete output of messages (not a screenshot) when you run:
check FOVs:
show the object and plot of a given gene:
|
This is the full output after running
This is the output after checking FOVs:
and this is the object and plot:
|
ok, it does read some segmentations It seems to be an issue here -> |
@angie-john, did it finally work? |
I'm trying to follow this tutorial: https://satijalab.org/seurat/articles/seurat5_spatial_vignette_2 but I'm unable to properly load the data. I'm having the same issue as #7142 however, I'm unable to fix it like they did. I believe I have the data downloaded and named correctly.
This is the error I get:
This is my session info:
These are what my files look like:
I would greatly appreciate any help with this.
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