wrong when spatialCluster(Neighbors were identified for 0 out of 2696 spots)

[PepsiZhu]

Hello,

I can't find 'row' and 'col' in Visium V2 data; the only coordinate data I found is ” STdata@images[["1"]]@boundaries[["centroids"]]@coords “. When I copied those data to colData$row and colData$col and ran spatialCluster(), it told me 'Neighbors were identified for 0 out of 2696 spots.'

I would like to inquire if the tool you mentioned has been developed (at #46), allowing for direct clustering analysis using imagecol and imagerow. Indeed, many of the downloaded spatial transcriptomics data only provide pixel positions. I look forward to your response.

Thank you

I am sorry that my English is not very good. I hope you don't mind.

[edward130603]

In Visium V2, the column names are array_row and array_col. If you copy those columns to row and col respectively in colData, it should work. Let me know if you run into further issues.