SpatialDimPlot not showing spots

Hello, I have an issue with Seurat plotting the spatial data. I have analyzed the data long time ago, and when I tried to load the saved object and make some plots, it won't show the spots on the image. However, the DimPlot function is working. Same thing happened with SpatialFeaturePlot vs FeaturePlot.

I also tried to adjust the image.alpha and group.by parameters, but still no luck.

I was using Seurat v4, I update it to v5 hoping to solve this issue, but it didn't work.

When I use the LinkedDimPlot and move my mouse over the tissue image, it will show the spots barcode information. have tried several processed spatial objects from different samples, and they all have the same issue.

The figure I generated before:

Here is the sessioninfo

R version 4.3.3 (2024-02-29)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Sonoma 14.6

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.11.0

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

time zone: America/New_York
tzcode source: internal

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] shiny_1.8.1.1         ComplexHeatmap_2.18.0 cowplot_1.1.3         scCustomize_2.1.2     harmony_1.2.0         Rcpp_1.0.12           patchwork_1.2.0      
 [8] dplyr_1.1.4           qs_0.26.3             ggplot2_3.5.1         Seurat_5.1.0          SeuratObject_5.0.2    sp_2.1-4             

loaded via a namespace (and not attached):
  [1] RColorBrewer_1.1-3     rstudioapi_0.16.0      jsonlite_1.8.8         shape_1.4.6.1          magrittr_2.0.3         spatstat.utils_3.0-4   ggbeeswarm_0.7.2      
  [8] farver_2.1.2           ragg_1.3.2             GlobalOptions_0.1.2    vctrs_0.6.5            ROCR_1.0-11            memoise_2.0.1          spatstat.explore_3.2-7
 [15] paletteer_1.6.0        janitor_2.2.0          htmltools_0.5.8.1      forcats_1.0.0          sass_0.4.9             sctransform_0.4.1      parallelly_1.37.1     
 [22] bslib_0.7.0            KernSmooth_2.23-24     htmlwidgets_1.6.4      ica_1.0-3              plyr_1.8.9             cachem_1.1.0           lubridate_1.9.3       
 [29] plotly_4.10.4          zoo_1.8-12             igraph_2.0.3           iterators_1.0.14       mime_0.12              lifecycle_1.0.4        pkgconfig_2.0.3       
 [36] Matrix_1.6-5           R6_2.5.1               fastmap_1.2.0          clue_0.3-65            snakecase_0.11.1       fitdistrplus_1.1-11    future_1.33.2         
 [43] digest_0.6.35          colorspace_2.1-0       rematch2_2.1.2         S4Vectors_0.40.2       tensor_1.5             RSpectra_0.16-1        irlba_2.3.5.1         
 [50] textshaping_0.4.0      labeling_0.4.3         progressr_0.14.0       timechange_0.3.0       fansi_1.0.6            spatstat.sparse_3.0-3  httr_1.4.7            
 [57] polyclip_1.10-6        abind_1.4-5            compiler_4.3.3         doParallel_1.0.17      withr_3.0.0            fastDummies_1.7.3      MASS_7.3-60.0.1       
 [64] rjson_0.2.21           tools_4.3.3            vipor_0.4.7            lmtest_0.9-40          beeswarm_0.4.0         httpuv_1.6.15          future.apply_1.11.2   
 [71] goftest_1.2-3          glue_1.7.0             nlme_3.1-165           promises_1.3.0         Rtsne_0.17             cluster_2.1.6          reshape2_1.4.4        
 [78] generics_0.1.3         gtable_0.3.5           spatstat.data_3.0-4    tidyr_1.3.1            data.table_1.15.4      RApiSerialize_0.1.3    stringfish_0.16.0     
 [85] utf8_1.2.4             BiocGenerics_0.48.1    spatstat.geom_3.2-9    RcppAnnoy_0.0.22       foreach_1.5.2          ggrepel_0.9.5          RANN_2.6.1            
 [92] pillar_1.9.0           stringr_1.5.1          spam_2.10-0            RcppHNSW_0.6.0         ggprism_1.0.5          later_1.3.2            circlize_0.4.16       
 [99] splines_4.3.3          lattice_0.22-6         survival_3.7-0         deldir_2.0-4           tidyselect_1.2.1       miniUI_0.1.1.1         pbapply_1.7-2         
[106] gridExtra_2.3          IRanges_2.36.0         scattermore_1.2        stats4_4.3.3           matrixStats_1.3.0      stringi_1.8.4          lazyeval_0.2.2        
[113] codetools_0.2-20       tibble_3.2.1           cli_3.6.2              uwot_0.2.2             RcppParallel_5.1.7     systemfonts_1.1.0      xtable_1.8-4          
[120] reticulate_1.37.0      jquerylib_0.1.4        munsell_0.5.1          globals_0.16.3         spatstat.random_3.2-3  png_0.1-8              ggrastr_1.0.2         
[127] parallel_4.3.3         dotCall64_1.1-1        listenv_0.9.1          viridisLite_0.4.2      scales_1.3.0           ggridges_0.5.6         crayon_1.5.2          
[134] leiden_0.4.3.1         purrr_1.0.2            GetoptLong_1.0.5       rlang_1.1.4

msraredon / NICHES

SpatialDimPlot not showing spots #44