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Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data


Eling, Nils; Damond, Nicolas; Hoch, Tobias; Bodenmiller, Bernd (2021). Cytomapper: an R/bioconductor package for visualisation of highly multiplexed imaging data. Bioinformatics, 36(24):5706-5708.

Abstract

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.

Abstract

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.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Quantitative Biomedicine
Dewey Decimal Classification:610 Medicine & health
Language:English
Date:5 April 2021
Deposited On:15 Jan 2021 10:38
Last Modified:01 May 2021 20:26
Publisher:Oxford University Press
ISSN:1367-4803
OA Status:Hybrid
Free access at:PubMed ID. An embargo period may apply.
Publisher DOI:https://doi.org/10.1093/bioinformatics/btaa1061
PubMed ID:33367748

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