Package: cytoviewer 1.13.1

Lasse Meyer

cytoviewer: An interactive multi-channel image viewer for R

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.

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

cytoviewer_1.13.1.tar.gz
cytoviewer_1.13.1.zip(r-4.7)cytoviewer_1.13.1.zip(r-4.6)cytoviewer_1.13.1.zip(r-4.5)
cytoviewer_1.13.1.tgz(r-4.6-any)cytoviewer_1.13.1.tgz(r-4.5-any)
cytoviewer_1.13.1.tar.gz(r-4.7-any)cytoviewer_1.13.1.tar.gz(r-4.6-any)
cytoviewer_1.13.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cytoviewer/json (API)

# Install 'cytoviewer' in R:

install.packages('cytoviewer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bodenmillergroup/cytoviewer/issues

On BioConductor:cytoviewer-1.13.0(bioc 3.24)cytoviewer-1.12.0(bioc 3.23)

immunooncology software singlecell onechannel twochannel multichannel spatial dataimport bioconductor imaging shiny visualization

6.25 score 7 stars 56 scripts 368 downloads 1 exports 146 dependencies

Last updated from:bdebb15c6c. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	WARNING	228
linux-devel-x86_64	OK	605
source / vignettes	OK	387
linux-release-x86_64	OK	609
macos-release-arm64	OK	503
macos-oldrel-arm64	OK	280
windows-devel	OK	485
windows-release	OK	436
windows-oldrel	OK	463
wasm-release	OK	219

Exports:cytoviewer

Dependencies:abind archive askpass base64enc beeswarm BH Biobase BiocFileCache BiocGenerics biocmake BiocParallel bit bit64 bitops blob bslib cachem cli codetools colourpicker commonmark cpp11 curl cytomapper DBI dbplyr DelayedArray digest dir.expiry dplyr EBImage evaluate farver fastmap fftwtools filelock fontawesome formatR fs futile.logger futile.options generics GenomicRanges ggbeeswarm ggforce ggplot2 ggraph ggrepel glue graphlayouts gridExtra gtable h5mread HDF5Array highr htmltools htmlwidgets httpuv httr2 igraph IRanges isoband jpeg jquerylib jsonlite knitr labeling lambda.r later lattice lifecycle locfit magick magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI nnls openssl otel pillar pkgconfig png polyclip promises purrr R6 rappdirs raster RColorBrewer Rcpp RcppArmadillo RCurl rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown RSQLite S4Arrays S4Vectors S7 sass scales Seqinfo shiny shinycssloaders shinydashboard shinyjs SingleCellExperiment snow sourcetools sp SparseArray SpatialExperiment stringi stringr SummarizedExperiment svglite svgPanZoom sys systemfonts terra textshaping tibble tidygraph tidyr tidyselect tiff tinytex tweenr utf8 vctrs vipor viridis viridisLite withr xfun xtable XVector yaml

cytoviewer - Interactive multi-channel image visualization in R

Introduction | Highly multiplexed imaging | Imaging mass cytometry | Highly multiplexed image analysis | Application overview | Data input format | Data input variations | Example workflow | Installation | Example dataset | Function call | Interface | Image-level visualization | Cell-level visualization | Point-level visualization | General controls | Image download | Additional Information | Read in data | Add metadata | Add channel names | Generating the object | Run cytoviewer | Session info | References

Rendered fromcytoviewer.Rmdusingknitr::rmarkdown

Last update: 2026-06-10
Started: 2023-03-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
cytoviewer - Shiny application to interactively browse multi-channel images	cytoviewer

Usage by other packages (reverse dependencies)