# SpatialExperiment [](https://github.com/drighelli/SpatialExperiment/actions) `SpatialExperiment` is an R/Bioconductor S4 class for storing data from spatial -omics experiments. The class extends the `SingleCellExperiment` class for single-cell data to support storage and retrieval of additional information from spot-based and molecule-based platforms, including spatial coordinates, images, and image metadata. A specialized constructor function is included for data from the 10x Genomics Visium platform. The `SpatialExperiment` package is available from [Bioconductor](https://bioconductor.org/packages/SpatialExperiment). A vignette containing examples and documentation is available from [Bioconductor](https://bioconductor.org/packages/SpatialExperiment), and additional details are provided in our [paper](https://doi.org/10.1093/bioinformatics/btac299). The following schematic illustrates the `SpatialExperiment` class structure. <img src="vignettes/SPE.png" width="800"/> ## Installation The current release version of the `SpatialExperiment` package can be installed from Bioconductor as follows. This is the recommended approach for most users. ``` install.packages("BiocManager") BiocManager::install("SpatialExperiment") ``` The latest development version can be installed from the [development version of Bioconductor](https://contributions.bioconductor.org/use-devel.html) or from GitHub (which may also require some dependency packages to be installed manually). ``` remotes::install_github("drighelli/SpatialExperiment") ``` ## Citation Righell D.\*, Weber L.M.\*, Crowell H.L.\*, Pardo B., Collado-Torres L., Ghazanfar S., Lun A.T.L., Hicks S.C.⁺, and Risso D.⁺ (2022). *SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor.* [Bioinformatics](https://doi.org/10.1093/bioinformatics/btac299), 38(11), 3128-3131.