cytoviewer
An interactive multi-channel image viewer for R
Bioconductor version: 3.24 · Package version: 1.13.3
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cytoviewer")Details
| Maintainer | Lasse Meyer <lasse.meyer@dqbm.uzh.ch> |
| Author | Lasse Meyer [aut, cre] (ORCID: <https://orcid.org/0000-0002-1660-1199>), Nils Eling [aut] (ORCID: <https://orcid.org/0000-0002-4711-1176>) |
| License | GPL-3 |
| URL | https://github.com/BodenmillerGroup/cytoviewer |
| Bug Reports | https://github.com/BodenmillerGroup/cytoviewer/issues |
| Downloads rank | 432 |
| Source branch | devel |
| biocViews | DataImport, ImmunoOncology, MultiChannel, OneChannel, SingleCell, Software, Spatial, TwoChannel |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | cytoviewer_1.13.3.tar.gz |
| Windows binary (x86_64) | cytoviewer_1.13.3.zip |
| macOS binary (arm64) | cytoviewer_1.13.3.tgz |
| macOS binary (x86_64) | cytoviewer_1.13.3.tgz |
Dependencies
Depends: R (>= 4.1.0)
Imports: shiny, shinydashboard, utils, colourpicker, shinycssloaders, svgPanZoom, htmlwidgets, viridis, archive, grDevices, RColorBrewer, svglite, EBImage, methods, cytomapper, ggplot2, ggraph, tidygraph, rlang, SingleCellExperiment, SpatialExperiment, S4Vectors, SummarizedExperiment