cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data

Abstract

SummaryHighly multiplexed imaging enables single-cell-resolved detection of numerous biological molecules in their spatial tissue context. Interactive data visualization of multiplexed imaging data is necessary for quality control and hypothesis examination. Here, we describe cytoviewer, an R/Bioconductor package for interactive visualization and exploration of multi-channel images and segmentation masks. The cytoviewer package supports flexible generation of image composites, allows side-by-side visualization of single channels, and facilitates the spatial visualization of single-cell data in the form of segmentation masks. The package operates on SingleCellExperiment, SpatialExperiment and CytoImageList objects and therefore integrates with the Bioconductor framework for single-cell and image analysis. Users of cytoviewer need little coding expertise, and the graphical user interface allows user-friendly navigation. We showcase the functionality of cytoviewer by analysis of an imaging mass cytometry dataset of cancer patients. AvailabilityThe cytoviewer package can be installed from Bioconductor via https://www.bioconductor.org/packages/release/bioc/html/cytoviewer.html. The development version and further instructions can be found on GitHub at https://github.com/BodenmillerGroup/cytoviewer. We provide an R script to exemplify the usage of cytoviewer in the supplementary information. Supplementary informationsSupplementary data are available online.