Last updated: 2025-11-27

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Knit directory: 2025_cytoconnect_spatial_workshop/

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Introduction

In this tutorial we will explore some resources for finding publicly available spatial transcriptomics and imaging mass cytometry datasets. Generally, it is much harder to find public IMC datasets compared to spatial transcriptomics datasets. Regardless, we will cover some useful resources for both data types.

For both spatial technologies, it is important to check the “Data availability” section of relevant manuscripts. They often contain links to where the data is stored, typically to public repositories like GEO, Zenodo, or Figshare.

Spatial Transcriptomics Data

10x has a comprehensive list of publicly available data they made available on their website. These data were generated in-house and encompasses a variety of tissues and technologies. Link to website: https://www.10xgenomics.com/datasets.

Version Author Date
d8a5e04 Givanna Putri 2025-11-27

You can also search GEO. It is a public repository used for storing genomics data. You will get data from different omics technologies (RNAseq, DNA, etc.).

Version Author Date
d8a5e04 Givanna Putri 2025-11-27

IMC data

Public data is not easy to get hold of.

Cytoforum: https://cytoforum.stanford.edu/viewforum.php?f=10 List all publications that used IMC or Cytof. Maintained by Mike Leiopold from Stanford. Note, not all papers have made their data publicly available.

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d8a5e04 Givanna Putri 2025-11-27 

sessionInfo()
R version 4.5.1 (2025-06-13)
Platform: aarch64-apple-darwin20
Running under: macOS Sequoia 15.5

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1

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: Australia/Perth
tzcode source: internal

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

other attached packages:
[1] workflowr_1.7.2

loaded via a namespace (and not attached):
 [1] vctrs_0.6.5       httr_1.4.7        cli_3.6.5         knitr_1.50       
 [5] rlang_1.1.6       xfun_0.53         stringi_1.8.7     processx_3.8.6   
 [9] promises_1.3.3    jsonlite_2.0.0    glue_1.8.0        rprojroot_2.1.1  
[13] git2r_0.36.2      htmltools_0.5.8.1 httpuv_1.6.16     ps_1.9.1         
[17] sass_0.4.10       rmarkdown_2.29    jquerylib_0.1.4   tibble_3.3.0     
[21] evaluate_1.0.5    fastmap_1.2.0     yaml_2.3.10       lifecycle_1.0.4  
[25] whisker_0.4.1     stringr_1.5.2     compiler_4.5.1    fs_1.6.6         
[29] pkgconfig_2.0.3   Rcpp_1.1.0        rstudioapi_0.17.1 later_1.4.4      
[33] digest_0.6.37     R6_2.6.1          pillar_1.11.0     callr_3.7.6      
[37] magrittr_2.0.4    bslib_0.9.0       tools_4.5.1       cachem_1.1.0     
[41] getPass_0.2-4