Loupe Browser label transfer go wrong

[lsudupe]

I have a question regarding the differences between the common seurat object image storage and Staffli one. Once I export the .csv file from Loupe Browser, I upload it to Rstudio and add it to my seurat object metadata. But when doing the same in my seurat object with Staffli image, the spots are messed up. The labels are stored by the spot are not well labeled.

I understand this is because some transformation of the image in the Staffli object, but I can not figure out which one. Is there anything I can do to import labels from Loupe Browser to the Staffli object properly?

Thanks

[ludvigla]

Adding additional columns to the Seurat object should not be an issue as long as you don't modify the spot labels, the number of spots or the order of spots. Is it possible that you have changed this somehow?

Cheers, Ludvig