sosta (spatial omics structure analysis) is a framework to reconstruct, characterize and compare spatial structures from spatial omics data.

sosta builds on existing R packages for spatial analysis such as spatstat, sf and the Bioconductor environment by integrating with packages SpatialExperiment and SpatialFeatureExperiment, which facilitates the implementation of additional custom metrics that fit the needs of users.

Installation of the latest Bioconductor version can be done as follows:

if (!requireNamespace("BiocManager")) {
    install.packages("BiocManager")
}
BiocManager::install("sosta")

You can install the development version of sosta from GitHub with:

# install.packages("devtools")
devtools::install_github("sgunz/sosta")

We are happy to get your feedback. Please send it via email to Samuel Gunz or open a issue on GitHub.

If you use sosta please consider citing:

Gunz, Samuel, Helena Lucia Crowell, and Mark D. Robinson. “Analysis of Anatomical Multi-Cellular Structures from Spatial Omics Data Using Sosta”, p. 2025.10.13.682065. bioRxiv, 14 Oct. 2025, https://doi.org/10.1101/2025.10.13.682065.