The coordinates don't match with the image after running asSPATA2()

[renyzh5-2]

library(SPATAData) library(tidyverse) library(glmGamPoi) library(ggallin) library(hypeR) library(hdf5r) library(reticulate) library(tensorflow) library(Seurat) library(SeuratData) library(SPATA2)#install.packages("./Downloads/theMILOlab-SPATA2-v3.0.3-41-g6bb867d.tar.gz", repos = NULL, type = "source")

seurat_object An object of class Seurat 36601 features across 3382 samples within 1 assay Active assay: Spatial (36601 features, 2000 variable features) 3 layers present: counts, data, scale.data 2 dimensional reductions calculated: pca, umap 1 image present: image

spata_obj <- asSPATA2( object = seurat_object, sample_name = "P8T_Spatial", platform = "VisiumSmall", img_name = "image",
img_scale_fct = "hires", assay_name = "Spatial", assay_modality = "gene", verbose = TRUE )

spata_obj <- identifyPixelContent(spata_obj) plotImage(spata_obj)

plotSurface(object = spata_obj, color_by = "VEGFA", pt_clrsp = "Greens 3",pt_size=0.2)

The coordinates don't match with the image. And the image isn‘t colored. How to sovle the issue, thx.

[renyzh5-2]

[kueckelj]

Hello. How did you create the Seurat object in the first place? With Load10X_Spatial()?