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Lasse Meyer1,2,3, Nils Eling1,2, Bernd Bodenmiller1,2

  • 1Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland.

Biorxiv : the Preprint Server for Biology
|June 9, 2023
PubMed
Summary
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Cytoviewer is a user-friendly R package for interactive visualization of highly multiplexed imaging data. It aids in exploring single-cell spatial biology, facilitating quality control and hypothesis testing for researchers.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Image Analysis

Background:

  • Highly multiplexed imaging generates complex, high-dimensional datasets requiring advanced visualization tools.
  • Interactive exploration is crucial for quality control and hypothesis generation in spatial biology research.
  • Existing tools may lack user-friendliness or seamless integration with single-cell analysis workflows.

Approach:

  • We introduce cytoviewer, an R/Bioconductor package designed for interactive visualization of multiplexed imaging data.
  • The package supports the creation of image composites, side-by-side channel viewing, and spatial visualization of segmentation masks.
  • Cytoviewer integrates with Bioconductor's SingleCellExperiment and SpatialExperiment objects for streamlined analysis.

Key Points:

Related Experiment Videos

  • Cytoviewer offers intuitive navigation through a graphical user interface, requiring minimal coding expertise.
  • It enables flexible generation of image composites and visualization of individual channels.
  • The package facilitates spatial exploration of single-cell data represented by segmentation masks.

Conclusions:

  • Cytoviewer enhances the accessibility and efficiency of analyzing highly multiplexed imaging data.
  • It empowers researchers to perform quality control and explore spatial relationships within tissues.
  • The tool is demonstrated on an imaging mass cytometry dataset, highlighting its utility in cancer research.