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Collection of publicly available imaging mass cytometry (IMC) datasets

Bioconductor version: Release (3.19)

The imcdatasets package provides access to publicly available IMC datasets. IMC is a technology that enables measurement of > 40 proteins from tissue sections. The generated images can be segmented to extract single cell data. Datasets typically consist of three elements: a SingleCellExperiment object containing single cell data, a CytoImageList object containing multichannel images and a CytoImageList object containing the cell masks that were used to extract the single cell data from the images.

Author: Nicolas Damond [aut, cre] , Nils Eling [ctb] , Fischer Jana [ctb]

Maintainer: Nicolas Damond <nicolas.damond at>

Citation (from within R, enter citation("imcdatasets")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

Accessing IMC datasets HTML R Script
Contributing guidelines and datasets format HTML R Script
Reference Manual PDF


biocViews ExperimentData, ExperimentHub, Homo_sapiens_Data, ImmunoOncologyData, PackageTypeData, ReproducibleResearch, SingleCellData, SpatialData, TechnologyData, Tissue
Version 1.12.0
License GPL-3 + file LICENSE
Depends R (>= 4.4.0), SingleCellExperiment, SpatialExperiment, cytomapper
Imports methods, utils, ExperimentHub, S4Vectors, DelayedArray, HDF5Array
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Follow Installation instructions to use this package in your R session.

Source Package imcdatasets_1.12.0.tar.gz
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