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This is the development version of imcRtools; for the stable release version, see imcRtools.

Methods for imaging mass cytometry data analysis

Bioconductor version: Development (3.20)

This R package supports the handling and analysis of imaging mass cytometry and other highly multiplexed imaging data. The main functionality includes reading in single-cell data after image segmentation and measurement, data formatting to perform channel spillover correction and a number of spatial analysis approaches. First, cell-cell interactions are detected via spatial graph construction; these graphs can be visualized with cells representing nodes and interactions representing edges. Furthermore, per cell, its direct neighbours are summarized to allow spatial clustering. Per image/grouping level, interactions between types of cells are counted, averaged and compared against random permutations. In that way, types of cells that interact more (attraction) or less (avoidance) frequently than expected by chance are detected.

Author: Nils Eling [aut], Tobias Hoch [ctb], Vito Zanotelli [ctb], Jana Fischer [ctb], Daniel Schulz [ctb, cre] , Lasse Meyer [ctb]

Maintainer: Daniel Schulz <daniel.schulz at>

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


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

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

# The following initializes usage of Bioc devel


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:

Tools for IMC data analysis HTML R Script
Reference Manual PDF


biocViews Clustering, DataImport, ImmunoOncology, SingleCell, Software, Spatial
Version 1.11.0
In Bioconductor since BioC 3.14 (R-4.1) (2.5 years)
License GPL-3
Depends R (>= 4.1), SpatialExperiment
Imports S4Vectors, stats, utils, SummarizedExperiment, methods, pheatmap, scuttle, stringr, readr, EBImage, cytomapper, abind, BiocParallel, viridis, dplyr, magrittr, DT, igraph, SingleCellExperiment, vroom, BiocNeighbors, RTriangle, ggraph, tidygraph, ggplot2, data.table, sf, concaveman, tidyselect, distances, MatrixGenerics, rlang, grDevices
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Suggests CATALYST, grid, tidyr, BiocStyle, knitr, rmarkdown, markdown, testthat
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Source Package imcRtools_1.11.0.tar.gz
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macOS Binary (x86_64) imcRtools_1.11.0.tgz
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