SUMMARY: Highly multiplexed imaging technologies enable spatial profiling of dozens of biomarkers in situ. Here we describe cytomapper, a computational tool written in R, that enables visualisation of pixel- and cell-level information obtained by multiplexed imaging. To illustrate its utility, we analysed 100 images obtained by imaging mass cytometry from a cohort of type 1 diabetes patients. In addition, cytomapper includes a Shiny application that allows hierarchical gating of cells based on marker expression and visualisation of selected cells in corresponding images.
AVAILABILITY AND IMPLEMENTATION: The cytomapper package can be installed via https://www.bioconductor.org/packages/release/bioc/html/cytomapper.html. Code for analysis and further instructions can be found at https://github.com/BodenmillerGroup/cytomapper_publication.
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.