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

An interactive multi-channel image viewer for R

Bioconductor version: Development (3.20)

This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with segmentation masks, integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization and supports image downloads.

Author: Lasse Meyer [aut, cre] , Nils Eling [aut]

Maintainer: Lasse Meyer <lasse.meyer at>

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


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:

Interactive multi-channel image visualization in R HTML R Script
Reference Manual PDF


biocViews DataImport, ImmunoOncology, MultiChannel, OneChannel, SingleCell, Software, Spatial, TwoChannel
Version 1.5.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Imports shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment
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Suggests BiocStyle, knitr, rmarkdown, markdown, testthat
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Follow Installation instructions to use this package in your R session.

Source Package cytoviewer_1.5.0.tar.gz
Windows Binary
macOS Binary (x86_64) cytoviewer_1.5.0.tgz
macOS Binary (arm64) cytoviewer_1.5.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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