# 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 [preprint](https://www.biorxiv.org/content/10.1101/2021.01.27.428431v3). The following schematic illustrates the `SpatialExperiment` class structure. <img src="vignettes/SPE.png" width="800"/> ## Installation The `SpatialExperiment` package can be installed from Bioconductor. Note that Bioconductor follows a "release" and "development" schedule, where the release version is considered to be stable and updated every 6 months, and the development version contains latest updates (and then becomes the next release version every 6 months). ### Release version To install the stable release version, install the latest release version of R from [CRAN](https://cran.r-project.org/), then install the Bioconductor package installer and the `SpatialExperiment` package as follows. ``` install.packages("BiocManager") BiocManager::install("SpatialExperiment") ``` ### Development version To install the development version, there are two options. (i) Install the development version of the `SpatialExperiment` package from GitHub, using a standard installation of the release version of R from [CRAN](https://cran.r-project.org/): ``` install.packages("remotes") remotes::install_github("drighelli/SpatialExperiment") ``` (ii) Install a complete `devel` version of Bioconductor. This requires first installing the [appropriate version of R (currently R-devel)](http://bioconductor.org/developers/how-to/useDevel/). Then, install the Bioconductor package installer and the development version of the `SpatialExperiment` package: ``` install.packages("BiocManager") BiocManager::install("SpatialExperiment", version = "devel") ``` ### Updates in versions 1.5.2 and 1.5.3 In version 1.5.2 the `spatialData` slot was deprecated and columns previously stored in `spatialData` moved to `colData`, and in version 1.5.3 the internal class `SpatialImage` was renamed to `VirtualSpatialImage` to avoid a clash with the same class name in Seurat. We recommend updating to version 1.5.3 (or later) and rebuilding existing objects to ensure longer-term compatibility with future versions. **To use version 1.5.3 or later (as of March 2022), please follow the installation instructions for the development version above.** (These updates will also be available in the release version from mid-April 2022 onwards, following the Bioconductor release schedule.) ## 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.⁺ (2021), *SpatialExperiment: infrastructure for spatially resolved transcriptomics data in R using Bioconductor*, [bioRxiv](https://www.biorxiv.org/content/10.1101/2021.01.27.428431v3).