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cytoviewer

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 (3.19)

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 dqbm.uzh.ch>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("cytoviewer")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("cytoviewer")
Interactive multi-channel image visualization in R HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataImport, ImmunoOncology, MultiChannel, OneChannel, SingleCell, Software, Spatial, TwoChannel
Version 1.3.2
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3
Depends
Imports shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment
System Requirements
URL https://github.com/BodenmillerGroup/cytoviewer
Bug Reports https://github.com/BodenmillerGroup/cytoviewer/issues
See More
Suggests BiocStyle, knitr, rmarkdown, markdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package cytoviewer_1.3.2.tar.gz
Windows Binary cytoviewer_1.3.2.zip (64-bit only)
macOS Binary (x86_64) cytoviewer_1.3.2.tgz
macOS Binary (arm64) cytoviewer_1.3.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/cytoviewer
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/cytoviewer
Bioc Package Browser https://code.bioconductor.org/browse/cytoviewer/
Package Short Url https://bioconductor.org/packages/cytoviewer/
Package Downloads Report Download Stats