cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data
Nils Eling1,2, Nicolas Damond1,2, Tobias Hoch1,2
1Department of Quantitative Biomedicine, University of Zurich, 8057 Zurich, Switzerland.
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 visualization 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 visualization 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.
More Related Videos
08:18Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples
Published on: April 7, 2023
05:12ExCYT: A Graphical User Interface for Streamlining Analysis of High-Dimensional Cytometry Data
Published on: January 16, 2019