DOI: 10.18129/B9.bioc.SPIAT  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see SPIAT.

Spatial Image Analysis of Tissues

Bioconductor version: 3.17

SPIAT (**Sp**atial **I**mage **A**nalysis of **T**issues) is an R package with a suite of data processing, quality control, visualization and data analysis tools. SPIAT is compatible with data generated from single-cell spatial proteomics platforms (e.g. OPAL, CODEX, MIBI, cellprofiler). SPIAT reads spatial data in the form of X and Y coordinates of cells, marker intensities and cell phenotypes. SPIAT includes six analysis modules that allow visualization, calculation of cell colocalization, categorization of the immune microenvironment relative to tumor areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.

Author: Anna Trigos [aut] , Yuzhou Feng [aut, cre] , Tianpei Yang [aut], Mabel Li [aut], John Zhu [aut], Volkan Ozcoban [aut], Maria Doyle [aut]

Maintainer: Yuzhou Feng <yuzhou.feng at petermac.org>

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


To install this package, start R (version "4.3") 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:



HTML R Script Basic analyses with SPIAT
HTML R Script Characterising tissue structure with SPIAT
HTML R Script Identifying cellular neighborhood with SPIAT
HTML R Script Overview of the SPIAT package
HTML R Script Quality control and visualisation with SPIAT
HTML R Script Quantifying cell colocalisation with SPIAT
HTML R Script Reading in data and data formatting in SPIAT
HTML R Script Spatial heterogeneity with SPIAT
PDF   Reference Manual
Text   NEWS


biocViews BiomedicalInformatics, CellBiology, Clustering, DataImport, ImmunoOncology, QualityControl, SingleCell, Software, Spatial, Visualization
Version 1.2.3
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
License Artistic-2.0
Depends R (>= 4.2.0), SpatialExperiment(>= 1.8.0)
Imports apcluster (>= 1.4.7), ggplot2 (>= 3.2.1), gridExtra (>= 2.3), gtools (>= 3.8.1), reshape2 (>= 1.4.3), dplyr (>= 0.8.3), RANN (>= 2.6.1), pracma (>= 2.2.5), dbscan (>= 1.1-5), mmand (>= 1.5.4), tibble (>= 2.1.3), grDevices, stats, utils, vroom, dittoSeq, spatstat.geom, methods, spatstat.explore, raster, sp, SummarizedExperiment, rlang
Suggests BiocStyle, plotly (>= 4.9.0), knitr, rmarkdown, pkgdown, testthat, graphics, alphahull, Rtsne, umap, ComplexHeatmap, elsa
URL https://trigosteam.github.io/SPIAT/
BugReports https://github.com/trigosteam/SPIAT/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package SPIAT_1.2.3.tar.gz
Windows Binary SPIAT_1.2.3.zip
macOS Binary (x86_64) SPIAT_1.2.3.tgz
macOS Binary (arm64) SPIAT_1.2.3.tgz
Source Repository git clone https://git.bioconductor.org/packages/SPIAT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/SPIAT
Bioc Package Browser https://code.bioconductor.org/browse/SPIAT/
Package Short Url https://bioconductor.org/packages/SPIAT/
Package Downloads Report Download Stats

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: