An interactive multi-channel image viewer for R.

This shiny application allows users to interactively visualize multi-channel images and masks. The cytoviewer package is divided into image-level (Composite and Channels) and cell-level visualization (Masks). It allows users to overlay individual images with masks and integrates well with SingleCellExperiment and SpatialExperiment objects for metadata visualization.

Bioc branch	Checks
Release
Devel

The cytoviewer package requires R version >= 4.0. It builds on data objects and functions contained in the cytomapper package.

The cytoviewer package can be installed from Bioconductor via:

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

BiocManager::install("cytoviewer")

The development version of cytoviewer can be installed from Github via:

if (!requireNamespace("remotes", quietly = TRUE))
    install.packages("remotes")

remotes::install_github("BodenmillerGroup/cytoviewer")

To load the package in your R session, type the following:

library(cytoviewer)

library(cytoviewer)
library(cytomapper)

# Load example datasets 
data("pancreasImages")
data("pancreasMasks")
data("pancreasSCE")

# Use shiny with images, masks and SCE object
app <- cytoviewer(image = pancreasImages, mask = pancreasMasks, object = pancreasSCE, img_id = "ImageNb", cell_id = "CellNb")
shiny::runApp(app, launch.browser = TRUE)

For feature requests, please open an issue here.

Alternatively, feel free to fork the repository, add your changes and issue a pull request.

A manuscript is in preparation.

If you are using cytoviewer in your work, please reach out to inquire how to best cite the tool.

Lasse Meyer lasse.meyer 'at' dqbm.uzh.ch

Nils Eling nils.eling 'at' dqbm.uzh.ch