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S4 Class for Spatially Resolved -omics Data

Bioconductor version: Release (3.19)

Defines an S4 class for storing data from spatial -omics experiments. The class extends SingleCellExperiment 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.

Author: Dario Righelli [aut, cre], Davide Risso [aut], Helena L. Crowell [aut], Lukas M. Weber [aut], Nicholas J. Eagles [ctb]

Maintainer: Dario Righelli <dario.righelli at>

Citation (from within R, enter citation("SpatialExperiment")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Introduction to the SpatialExperiment class HTML R Script
Reference Manual PDF


biocViews DataImport, DataRepresentation, GeneExpression, ImmunoOncology, Infrastructure, SingleCell, Software, Spatial, Transcriptomics
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends methods, SingleCellExperiment
Imports rjson, grDevices, magick, utils, S4Vectors, SummarizedExperiment, BiocGenerics, BiocFileCache
System Requirements
Bug Reports
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Suggests knitr, rmarkdown, testthat, BiocStyle, BumpyMatrix, DropletUtils
Linking To
Depends On Me alabaster.spatial, ExperimentSubset, imcRtools, SPIAT, tidySpatialExperiment, imcdatasets, MerfishData, MouseGastrulationData, spatialLIBD, STexampleData, TENxVisiumData, VectraPolarisData, WeberDivechaLCdata
Imports Me Banksy, CTSV, cytomapper, DESpace, escheR, ggspavis, GSVA, hoodscanR, lisaClust, MoleculeExperiment, nnSVG, scider, signifinder, smoothclust, spaSim, spatialDE, SpatialFeatureExperiment, spicyR, spoon, SpotClean, SpotSweeper, standR, Statial, stJoincount, tpSVG, VisiumIO, Voyager, HCATonsilData, SingleCellMultiModal, SubcellularSpatialData, TENxXeniumData, SpatialDDLS
Suggests Me GeomxTools, ggsc, SPOTlight
Links To Me
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Follow Installation instructions to use this package in your R session.

Source Package SpatialExperiment_1.14.0.tar.gz
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macOS Binary (x86_64) SpatialExperiment_1.14.0.tgz
macOS Binary (arm64) SpatialExperiment_1.14.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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Old Source Packages for BioC 3.19 Source Archive