From Seurat to Loupe for integrated Visium HD data

[endonutriHUPR]

Hi all!

I have an integrated dataset of four VISIUM HD samples. I've analyzed it in Seurat and now I want to export the results in Loupe.

I'd like to load the Seurat's results into Loupe 9 including high resolution images. How could I do it?

Thank you in advance.
Sincerely.

[esiegel]

This is definitely a request that we get often, but unfortunately we don't currently support importing the images.

[endonutriHUPR]

Thank you so much for this quick answer.

There is another option uploading projections here using other packages (seurat2cloupe function in funcutils):

For UMAP it works perfectly. However, for images the following error is obtained:

In SpaceRanger outputs, as far as I saw, we do not have these type of barcodes. Instead, i've got the ID equivalences for different bin sizes and segmentation (cellid_...). In the spot-based Visium data we could easily upload our experiments into Loupe browser. However, something have changed for Visium HD.

Does any of you know how can we solve this?

Thank you.
Best,

N

[gmjoseph]

Hello,

It's possible you just need to update loupeR to the latest version (1.1.5). cellid handling was just recently added ~3 weeks ago: #103

Take care,