DOI: 10.18129/B9.bioc.cytomapper    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see cytomapper.

Visualization of highly multiplexed imaging cytometry data in R

Bioconductor version: 3.11

Highly multiplexed imaging cytometry acquires the single-cell expression of selected proteins in a spatially-resolved fashion. These measurements can be visualized across multiple length-scales. First, pixel-level intensities represent the spatial distributions of feature expression with highest resolution. Second, after segmentation, expression values or cell-level metadata (e.g. cell-type information) can be visualized on segmented cell areas. This package contains functions for the visualization of multiplexed read-outs and cell-level information obtained by multiplexed imaging cytometry. The main functions of this package allow 1. the visualization of pixel-level information across multiple channels and 2. the display of cell-level information (expression and/or metadata) on segmentation masks.

Author: Nils Eling [aut, cre] , Nicolas Damond [aut]

Maintainer: Nils Eling <nils.eling at>

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biocViews DataImport, ImmunoOncology, MultipleComparison, Normalization, OneChannel, SingleCell, Software, TwoChannel
Version 1.0.0
In Bioconductor since BioC 3.11 (R-4.0) (0.5 years)
License GPL (>= 2)
Depends R (>= 4.0), EBImage, SingleCellExperiment, methods
Imports S4Vectors, RColorBrewer, viridis, utils, SummarizedExperiment, tools, graphics, raster, grDevices, stats
Suggests BiocStyle, knitr, rmarkdown, testthat
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