cytoviewer

DOI: 10.18129/B9.bioc.cytoviewer  

An interactive multi-channel image viewer for R

Bioconductor version: Release (3.17)

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>

Installation

To install this package, start R (version "4.3") and enter:

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

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")

 

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

Details

biocViews	DataImport, ImmunoOncology, MultiChannel, OneChannel, SingleCell, Software, Spatial, TwoChannel
Version	1.0.1
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	GPL-3
Depends
Imports	shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, SingleCellExperiment, S4Vectors, SummarizedExperiment
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, markdown, testthat
SystemRequirements
Enhances
URL	https://github.com/BodenmillerGroup/cytoviewer
BugReports	https://github.com/BodenmillerGroup/cytoviewer/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	cytoviewer_1.0.1.tar.gz
Windows Binary	cytoviewer_1.0.1.zip
macOS Binary (x86_64)	cytoviewer_1.0.1.tgz
macOS Binary (arm64)	cytoviewer_1.0.1.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
Old Source Packages for BioC 3.17	Source Archive