DOI: 10.18129/B9.bioc.cytomapper  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see cytomapper.

Visualization of highly multiplexed imaging data in R

Bioconductor version: 3.16

Highly multiplexed imaging acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualised across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualised on segmented cell areas. This package contains functions for the visualisation of multiplexed read-outs and cell-level information obtained by multiplexed imaging technologies. The main functions of this package allow 1. the visualisation of pixel-level information across multiple channels, 2. the display of cell-level information (expression and/or metadata) on segmentation masks and 3. gating and visualisation of single cells.

Author: Nils Eling [aut, cre] , Nicolas Damond [aut] , Tobias Hoch [ctb]

Maintainer: Nils Eling <nils.eling at>

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


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HTML R Script On disk storage of images
HTML R Script Visualization of imaging cytometry data in R
PDF   Reference Manual
Text   NEWS


biocViews DataImport, ImmunoOncology, MultipleComparison, Normalization, OneChannel, SingleCell, Software, TwoChannel
Version 1.10.1
In Bioconductor since BioC 3.11 (R-4.0) (3 years)
License GPL (>= 2)
Depends R (>= 4.0), EBImage, SingleCellExperiment, methods
Imports SpatialExperiment, S4Vectors, BiocParallel, HDF5Array, DelayedArray, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats, ggplot2, ggbeeswarm, svgPanZoom, svglite, shiny, shinydashboard, matrixStats, rhdf5, nnls
Suggests BiocStyle, knitr, rmarkdown, markdown, cowplot, testthat, shinytest
Depends On Me imcdatasets
Imports Me imcRtools, simpleSeg
Suggests Me
Links To Me
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