Slide-Seq data

In this article, we’ll demonstrate how to load Slide-Seq data with semla. First, we need to load a Seurat object with Slide-Seq data. Here we’ll use a prepared Seurat object that can be install with the SeuratData R package.

See ?ReadSlideSeq for more information on how to load raw data.

library(semla)
library(SeuratData)
InstallData("ssHippo")

slide_seq <- LoadData("ssHippo")

Next, we can convert the Seurat object to make it compatible with semla using the UpdateSeuratForSemla function. Note that the Slide-Seq data doesn’t contain H&E images and therefore, all image related functionality of semla will be inaccessible. This includes the Feature Viewer and image alignment tools which requires H&E images to work.

slide_seq_semla <- UpdateSeuratForSemla(slide_seq)

Now we can use visualization functions from semla on our Slide-Seq data.

MapFeatures(slide_seq_semla, features = "nFeature_Spatial", colors = viridis::magma(n = 11, direction = -1)) & ThemeLegendRight()

Zoom in on Dentate gyrus:

MapFeatures(slide_seq_semla, features = "PROX1", colors = viridis::magma(n = 11, direction = -1),
            crop_area = c(0.35, 0.45, 0.7, 0.7)) & 
  ThemeLegendRight() &
  ggtitle("PROX1 expression in the Dentate Gyrus", subtitle = "")

Package versions

semla: 1.4.0

Session info

sessionInfo()

## R version 4.4.2 (2024-10-31)
## Platform: aarch64-apple-darwin20.0.0
## Running under: macOS Sequoia 15.5
## 
## Matrix products: default
## BLAS/LAPACK: /Users/javierescudero/miniconda3/envs/r-semlaupd/lib/libopenblas.0.dylib;  LAPACK version 3.12.0
## 
## 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: Europe/Stockholm
## tzcode source: system (macOS)
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## loaded via a namespace (and not attached):
##  [1] digest_0.6.37     desc_1.4.3        R6_2.6.1          fastmap_1.2.0    
##  [5] xfun_0.53         cachem_1.1.0      knitr_1.50        htmltools_0.5.8.1
##  [9] rmarkdown_2.29    lifecycle_1.0.4   cli_3.6.4         sass_0.4.9       
## [13] pkgdown_2.1.1     textshaping_0.4.0 jquerylib_0.1.4   systemfonts_1.2.1
## [17] compiler_4.4.2    rstudioapi_0.17.1 tools_4.4.2       ragg_1.3.3       
## [21] bslib_0.9.0       evaluate_1.0.5    yaml_2.3.10       jsonlite_1.9.0   
## [25] rlang_1.1.5       fs_1.6.5          htmlwidgets_1.6.4

Last compiled: 08 September 2025