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 (3.21)

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] (ORCID: ), Nils Eling [aut] (ORCID: )

Maintainer: Lasse Meyer <lasse.meyer at dqbm.uzh.ch>

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DataImport, ImmunoOncology, MultiChannel, OneChannel, SingleCell, Software, Spatial, TwoChannel
Version	1.7.0
In Bioconductor since	BioC 3.17 (R-4.3) (1.5 years)
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

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_1.7.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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