convert seurat object to spaCET object

[alipirani88]

Hi @beibeiru

I get this error while converting seurat V5 object to SpaCET object. I reinstalled the most recent version of SpaCET.

object_primary_16um_238687_SpaCET_obj <- convert.Seurat(object_primary_16um_238687) Error in data.frame(pxl_row = slice@coordinates$imagerow * slice@scale.factors$lowres, : no slot of name "coordinates" for this object of class "VisiumV2"
Any idea how I can fix this?

Thanks,

[beibeiru]

Hi, @alipirani88

Would you please share the Seurat object with me?

Best,
Beibei

[wurucheng123]

Hi, @beibeiru

I also get the same error, and this is because after Seurat 5.1.0, all images the Visium and Visium HD data are created as Visium V2. It seems that Visium V2 has less information about coordinates than V1 since V1 has 4 columns named row, col, imagerow and imagecol while V2 only has 2 columns as following.

> head(GetTissueCoordinates(RCC))
                                  x     y                          cell
GSM5924030_AAACAACGAATAGTTC-1 13502  1165 GSM5924030_AAACAACGAATAGTTC-1
GSM5924030_AAACAAGTATCTCCCA-1  4079 10698 GSM5924030_AAACAAGTATCTCCCA-1
GSM5924030_AAACAATCTACTAGCA-1 10544  1737 GSM5924030_AAACAATCTACTAGCA-1
GSM5924030_AAACACCAATAACTGC-1 13174 12414 GSM5924030_AAACACCAATAACTGC-1
GSM5924030_AAACAGAGCGACTCCT-1  4955  3834 GSM5924030_AAACAGAGCGACTCCT-1
GSM5924030_AAACAGCTTTCAGAAG-1 14270  9363 GSM5924030_AAACAGCTTTCAGAAG-1

Seurat official provided the method to convert V2 to V1, but it has to read the coordinates from the original path of data.

So could you fix the convert.Seurat function that can only use Seurat object with V2 images to the SpaCET object? By the way, could you add a parameter "image" to convert.Seurat for Seurat object with multiple images? Thanks!

[beibeiru]

Hi, @wurucheng123

Thank you very much for your explanation!

Would you mind sharing your Seurat object with me (beibei.ru@nih.gov)?

I also have two questions.

1. May I know whether you have the original output from Space Ranger? If yes, you can use create.SpaCET.object.10X to create a SpaCET object directly. Just like V2 has less information, to fix the convert.Seurat function for V2 might also need the coordinates from the original path of data.

2. Currently, convert.Seurat will generate a list if the Seurat object has multiple images. I am wondering what the parameter "image" stands for.

Best,
Beibei

[wurucheng123]

Hi, @beibeiru

1. Yes, I have the original output from Space Ranger. However, it takes a long time to run the upstream analysis, especially integration and batch correction. Since Seurat can visualize the spatial plot as usual using Visium V2 object, I wonder if SpaCET can also visualize only using the information in V2.

2. I'm sorry, I ignored the if structure and only saw the Seurat_obj@images[[1]] and inferred SpaCET only used the first image by default.

I'll send you my Seurat object by email. Thanks!

[beibeiru]

Hi @wurucheng123,

When using convert.Seurat to generate a SpaCET object, the function extracts all counts and images directly from the Seurat object, rather than using batch-corrected data. Therefore, it is equivalent to creating a SpaCET object from the original Space Ranger output.

Since you already have the Space Ranger output, I recommend creating the SpaCET object directly from that. SpaCET offers many visualization options, which should be consistent with V2.

In the meantime, I’ll work on updating convert.Seurat to ensure compatibility with V2.

Best,
Beibei

[wurucheng123]

Hi @wurucheng123,

When using convert.Seurat to generate a SpaCET object, the function extracts all counts and images directly from the Seurat object, rather than using batch-corrected data. Therefore, it is equivalent to creating a SpaCET object from the original Space Ranger output.

Since you already have the Space Ranger output, I recommend creating the SpaCET object directly from that. SpaCET offers many visualization options, which should be consistent with V2.

In the meantime, I’ll work on updating convert.Seurat to ensure compatibility with V2.

Best, Beibei

Thanks, I'll try creating SpaCET object using original output of Space Ranger.