Reading in CosMx data failed

[StudyingAnt]

Hello, I'm trying to read in CosMx flat files into Seurat and do analysis but I immediately bumped into error just reading in files.

library(Seurat)
library(future)
plan("multisession", workers = 10)
library(ggplot2)

base_path = "C:/Cx/"
nano.obj <- LoadNanostring(data.dir = paste(base_path, "B01f/V22659", sep = ""), fov = "V22659")

Resulted in

> nano.obj <- LoadNanostring(data.dir = paste(base_path, "B01f/V22659", sep = ""), fov = "V22659")
|--------------------------------------------------|
|==================================================|
Error in base::colSums(x, na.rm = na.rm, dims = dims, ...) : 
  'x' must be numeric

Is this some kind of bug?
I'm also attaching the session info.

Session info()

> sessionInfo()
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8    LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

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

other attached packages:
[1] ggplot2_3.4.4      future_1.33.0      Seurat_5.0.1       SeuratObject_5.0.1 sp_2.1-1          

loaded via a namespace (and not attached):
  [1] Rtsne_0.16             colorspace_2.1-0       deldir_1.0-9           ellipsis_0.3.2         ggridges_0.5.4         RcppHNSW_0.5.0         rstudioapi_0.15.0      spatstat.data_3.0-3   
  [9] leiden_0.4.3.1         listenv_0.9.0          ggrepel_0.9.4          RSpectra_0.16-1        fansi_1.0.6            codetools_0.2-19       splines_4.2.3          R.methodsS3_1.8.2     
 [17] polyclip_1.10-6        spam_2.9-1             jsonlite_1.8.7         ica_1.0-3              cluster_2.1.4          png_0.1-8              R.oo_1.25.0            uwot_0.1.16           
 [25] shiny_1.8.0            sctransform_0.4.1      spatstat.sparse_3.0-2  compiler_4.2.3         httr_1.4.7             Matrix_1.6-4           fastmap_1.1.1          lazyeval_0.2.2        
 [33] cli_3.6.1              later_1.3.1            htmltools_0.5.6.1      tools_4.2.3            igraph_1.5.1           dotCall64_1.1-0        gtable_0.3.4           glue_1.6.2            
 [41] RANN_2.6.1             reshape2_1.4.4         dplyr_1.1.3            Rcpp_1.0.11            scattermore_1.2        vctrs_0.6.4            spatstat.explore_3.2-3 nlme_3.1-163          
 [49] progressr_0.14.0       lmtest_0.9-40          spatstat.random_3.1-6  stringr_1.5.1          globals_0.16.2         mime_0.12              miniUI_0.1.1.1         lifecycle_1.0.4       
 [57] irlba_2.3.5.1          goftest_1.2-3          MASS_7.3-60            zoo_1.8-12             scales_1.3.0           promises_1.2.1         spatstat.utils_3.0-3   parallel_4.2.3        
 [65] RColorBrewer_1.1-3     reticulate_1.34.0      pbapply_1.7-2          gridExtra_2.3          stringi_1.7.12         fastDummies_1.7.3      rlang_1.1.1            pkgconfig_2.0.3       
 [73] matrixStats_1.0.0      lattice_0.21-9         ROCR_1.0-11            purrr_1.0.2            tensor_1.5             patchwork_1.1.3        htmlwidgets_1.6.2      cowplot_1.1.1         
 [81] tidyselect_1.2.0       parallelly_1.36.0      RcppAnnoy_0.0.21       plyr_1.8.9             magrittr_2.0.3         R6_2.5.1               generics_0.1.3         pillar_1.9.0          
 [89] withr_2.5.2            fitdistrplus_1.1-11    survival_3.5-7         abind_1.4-5            tibble_3.2.1           future.apply_1.11.0    KernSmooth_2.23-22     utf8_1.2.4            
 [97] spatstat.geom_3.2-5    plotly_4.10.3          grid_4.2.3             data.table_1.14.8      digest_0.6.33          xtable_1.8-4           tidyr_1.3.0            httpuv_1.6.11         
[105] R.utils_2.12.3         munsell_0.5.0          viridisLite_0.4.2     

[corrinenief]

There have been formatting changes with Nanostring data that Seurat has not kept up with (at this time), see details at https://nanostring-biostats.github.io/CosMx-Analysis-Scratch-Space/posts/flat-file-exports/flat-files-compare.html

Removing the new "cell" column in the metadata.csv and the tx_file.csv worked for me. A simple cut could work:

cut -d, -f-2,4- oldfile.csv > newfile.csv

Just remember to rename the files with the ending "_metadata.csv" and "_tx_file.csv" that you want ReadNanostring to load