SPIAT (Spatial Image Analysis of Tissues) is an R package with a suite of data processing, quality control, visualisation 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 visualisation, calculation of cell colocalisation, categorisation of the immune microenvironment relative to tumour areas, analysis of cellular neighborhoods, and the quantification of spatial heterogeneity, providing a comprehensive toolkit for spatial data analysis.
An overview of the functions available is shown in the figure below.