`ConstructMetaspots` not compatible with Seurat's `VisiumV2` class

[ppm1337]

Since Seurat v5.1 the default image class (also for non-Visium HD data) is VisiumV2. Unfortunately, the resulting object has a completely different structure and hence no slot anymore called coordinates, which ConstructMetaspots tries to access:

Error in nrow(cur_seurat@images[[x]]@coordinates) : 
  no slot of name "coordinates" for this object of class "VisiumV2"

I came across the error following the described workflow for Visium ST data when calling MetaspotsByGroups.

The SeuratObject I'm using returns 5.0.2 when checking it's version slot.

R session info

R version 4.3.3 (2024-02-29)
Platform: x86_64-conda-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS

Matrix products: default
BLAS/LAPACK: /home/peter/universal_envs/hdwgcna/lib/libopenblasp-r0.3.27.so;  LAPACK version 3.12.0

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Brussels
tzcode source: system (glibc)

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

other attached packages:
 [1] purrr_1.0.2           patchwork_1.2.0       hdWGCNA_0.3.01        igraph_2.0.2         
 [5] WGCNA_1.71            fastcluster_1.2.6     dynamicTreeCut_1.63-1 ggrepel_0.9.5        
 [9] Seurat_5.1.0          SeuratObject_5.0.2    sp_2.1-3              harmony_1.2.0        
[13] Rcpp_1.0.12           ggplot2_3.4.4         GeneOverlap_1.38.0    furrr_0.3.1          
[17] future_1.33.2         enrichR_3.2           dplyr_1.1.4           cowplot_1.1.3        

loaded via a namespace (and not attached):
  [1] RcppAnnoy_0.0.22        splines_4.3.3           later_1.3.2             bitops_1.0-7           
  [5] tibble_3.2.1            polyclip_1.10-6         preprocessCore_1.64.0   rpart_4.1.23           
  [9] fastDummies_1.7.3       lifecycle_1.0.4         doParallel_1.0.17       globals_0.16.3         
 [13] lattice_0.22-6          MASS_7.3-60             backports_1.4.1         magrittr_2.0.3         
 [17] rmarkdown_2.26          Hmisc_5.1-2             plotly_4.10.4           httpuv_1.6.15          
 [21] sctransform_0.4.1       spam_2.10-0             spatstat.sparse_3.0-3   reticulate_1.36.0      
 [25] pbapply_1.7-2           DBI_1.2.2               RColorBrewer_1.1-3      abind_1.4-5            
 [29] zlibbioc_1.48.0         Rtsne_0.17              BiocGenerics_0.48.1     RCurl_1.98-1.14        
 [33] nnet_7.3-19             WriteXLS_6.5.0          GenomeInfoDbData_1.2.11 IRanges_2.36.0         
 [37] S4Vectors_0.40.2        irlba_2.3.5.1           listenv_0.9.1           spatstat.utils_3.0-4   
 [41] goftest_1.2-3           RSpectra_0.16-1         spatstat.random_3.2-3   fitdistrplus_1.1-11    
 [45] parallelly_1.37.1       leiden_0.4.3.1          codetools_0.2-20        tidyselect_1.2.1       
 [49] farver_2.1.1            tester_0.2.0            matrixStats_1.1.0       stats4_4.3.3           
 [53] base64enc_0.1-3         spatstat.explore_3.2-6  jsonlite_1.8.8          progressr_0.14.0       
 [57] Formula_1.2-5           ggridges_0.5.6          survival_3.5-8          iterators_1.0.14       
 [61] foreach_1.5.2           tools_4.3.3             ica_1.0-3               glue_1.7.0             
 [65] gridExtra_2.3           xfun_0.43               GenomeInfoDb_1.38.1     withr_3.0.0            
 [69] fastmap_1.1.1           fansi_1.0.6             caTools_1.18.2          digest_0.6.35          
 [73] R6_2.5.1                mime_0.12               colorspace_2.1-0        scattermore_1.2        
 [77] GO.db_3.18.0            gtools_3.9.5            tensor_1.5              spatstat.data_3.0-4    
 [81] RSQLite_2.3.4           utf8_1.2.4              tidyr_1.3.1             generics_0.1.3         
 [85] data.table_1.15.2       httr_1.4.7              htmlwidgets_1.6.4       uwot_0.1.16            
 [89] pkgconfig_2.0.3         gtable_0.3.4            blob_1.2.4              impute_1.76.0          
 [93] lmtest_0.9-40           XVector_0.42.0          htmltools_0.5.8.1       dotCall64_1.1-1        
 [97] scales_1.3.0            Biobase_2.62.0          png_0.1-8               rstudioapi_0.16.0      
[101] knitr_1.46              reshape2_1.4.4          rjson_0.2.21            checkmate_2.3.0        
[105] nlme_3.1-164            curl_5.1.0              proxy_0.4-27            zoo_1.8-12             
[109] cachem_1.0.8            stringr_1.5.1           KernSmooth_2.23-22      parallel_4.3.3         
[113] miniUI_0.1.1.1          foreign_0.8-86          AnnotationDbi_1.64.1    pillar_1.9.0           
[117] grid_4.3.3              vctrs_0.6.5             RANN_2.6.1              gplots_3.1.3.1         
[121] promises_1.3.0          xtable_1.8-4            cluster_2.1.6           htmlTable_2.4.2        
[125] evaluate_0.23           cli_3.6.2               compiler_4.3.3          rlang_1.1.3            
[129] crayon_1.5.2            future.apply_1.11.2     labeling_0.4.3          plyr_1.8.9             
[133] stringi_1.8.3           viridisLite_0.4.2       deldir_2.0-4            munsell_0.5.1          
[137] Biostrings_2.70.1       lazyeval_0.2.2          spatstat.geom_3.2-9     Matrix_1.6-5           
[141] RcppHNSW_0.6.0          bit64_4.0.5             KEGGREST_1.42.0         shiny_1.8.1.1          
[145] ROCR_1.0-11             memoise_2.0.1           bit_4.0.5

[smorabit]

Thank you for taking the time for writing this issue and for diagnosing the problem regarding the new class structure. FYI, I am currently very busy with some upcoming deadlines over the next couple of weeks, so I will not be able to push a fix for this until late June or early July. For now you might want to just use Seurat 4 if possible.

[ppm1337]

Thanks for considering the support of the VisiumV2 class in the future. I've also opened an issue in the Seurat repository regarding the handling of the different image classes. A Seurat maintainer specifically addressed hdWGCNA in their reply, so you may want to check out the corresponding Seurat issue.

[Lucayao777]

Thank you for taking the time for writing this issue and for diagnosing the problem regarding the new class structure. FYI, I am currently very busy with some upcoming deadlines over the next couple of weeks, so I will not be able to push a fix for this until late June or early July. For now you might want to just use Seurat 4 if possible.

Thank you! I have same problems. Do you find the way to get the row, col, imagerow, and imagecol in Seurat 5.1.0?just like the tutorial https://smorabit.github.io/hdWGCNA/articles/ST_basics.html, I can't find coordinates in this data and I try to run

coords <- GetTissueCoordinates(cur_seurat)
coords <- coords[, 1:2]
colnames(coords) <- c("row", "col")

still lack two cols. And I try to install Seurat V4, it's still not work

[ppm1337]

The easiest workaround without downgrading to Seurat v4 is to use the coordinates directly from the spaceranger output (<space_ranger_dir>/outs/spatial/tissue_positions.csv) and bind them to the meta data of the SeuratObject. To obtain these from the file, you could use the Seurat::Read10X_Coordinates method. Alternatively, you can just use Seurat::GetTissueCoordinates on the SeuratObject with VisiumV2 image(s) and provide different scale parameters to obtain the relevant (scaled/unscaled) coordinates.

However, this will not prevent the error described in this issue because hdWGCNA::ConstructMetaspots will try to access the coordinates slot of the input SeuratObject. A workaround to create a VisiumV1 object manually is described in the linked Seurat issue.

[Lucayao777]

不降级到Seurat v4的最简单解决方法是直接使用spaceranger输出（<space_ranger_dir>/outs/spatial/tissue_positions.csv）的坐标，并将其绑定到SeuratObject的元数据。要从文件中获取这些，您可以使用Seurat::Read10X_Coordinates方法。或者，您只需在带有VisiumV2图像的SeuratObject上使用Seurat::GetTissueCoordinates，并提供不同的scale参数来获得相关的（缩放/未缩放）坐标。

然而，这不会阻止此问题中描述的错误，因为hdWGCNA::ConstructMetaspots将尝试访问输入SeuratObject的coordinates插槽。链接的Seurat问题中描述了手动创建VisiumV1对象的变通方法。

The easiest workaround without downgrading to Seurat v4 is to use the coordinates directly from the spaceranger output (<space_ranger_dir>/outs/spatial/tissue_positions.csv) and bind them to the meta data of the SeuratObject. To obtain these from the file, you could use the Seurat::Read10X_Coordinates method. Alternatively, you can just use Seurat::GetTissueCoordinates on the SeuratObject with VisiumV2 image(s) and provide different scale parameters to obtain the relevant (scaled/unscaled) coordinates.

However, this will not prevent the error described in this issue because hdWGCNA::ConstructMetaspots will try to access the coordinates slot of the input SeuratObject. A workaround to create a VisiumV1 object manually is described in the linked Seurat issue.

so,seurat or hdwgcna must do some changes, and I notice that dcollins15 said he will make a patch soon, so we can wait for him