A questio about LoadVizgen

[zhaomou233123]

hi,
I analyzed s2r1 dataset was produced using the Vizgen MERSCOPE system, but got error
Warning in ReadVizgen(data.dir = data.dir, filter = "^Blank-", type = c("centroids", :
Cannot find hdf5r; unable to load segmentation vertices
Error in UseMethod(generic = "CreateSegmentation", object = coords) :
no applicable method for 'CreateSegmentation' applied to an object of class "NULL"

[zhaomou233123]

I can't find the right way to slove it

[alikhuseynov]

what kind of output do you have from Vizgen?

If it's a new output that has .parquet files for cell segmentations, then your data.dir should contain these files:

detected_transcripts.csv
cell_by_gene.csv
cell_metadata.csv
cell_boundaries.parquet

take a look at this PR #7190 and this posts #7080 #7215

[dfhannum]

By default the function looks for segmentation, so if you do not have any it'll give you that error.

Based on not the screenshot you don't have segmentation data for Seurat to access, so you should pass in the argument type = 'centroids to LoadVizgen. This way it'll take the centroid information from the metadata and not look for segmentation data. I haven't tested this but believe it should work.

[alikhuseynov]

By default the function looks for segmentation, so if you do not have any it'll give you that error.

Based on not the screenshot you don't have segmentation data for Seurat to access, so you should pass in the argument type = 'centroids to LoadVizgen. This way it'll take the centroid information from the metadata and not look for segmentation data. I haven't tested this but believe it should work.

I can confirm that, if segmentation data is not provided, and even if the type = c("segmentations", "centroids") it would still make FOV with "centroids" and "molecules" with current PR #7190

[dcollins15]

Thanks for using Seurat!

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