Documentation is available at: https://bodenmillergroup.github.io/imcdatasets/index.html
| Bioc branch | Checks |
|---|---|
| Devel | |
| BioC Devel | |
| BioC Release | |
The imcdatasets package is an extensible resource containing a set of publicly
available and curated Imaging Mass Cytometry datasets. Each dataset consists of
three data objects:
SingleCellExperiment or
SpatialExperiment class object.CytoImageList class object.CytoImageList class object.These formats facilitate accession and integration into R/Bioconductor workflows. The data objects are hosted on Bioconductor's ExperimentHub platform.
The release version
of imcdatasets requires R version >= 4.6 and Bioconductor version >= 3.23.
The current release of Bioconductor should be installed:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.23")
Then, imcdatasets can be installed from Bioconductor:
BiocManager::install("imcdatasets")
The development version
of imcdatasets requires R version >= 4.6 and Bioconductor version >= 3.24.
The development version of Bioconductor should be installed:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version='devel')
Then, imcdatasets can be installed from Bioconductor:
BiocManager::install("imcdatasets")
imcdatasets can also be installed from GitHub using devtools:
if (!requireNamespace("devtools", quietly = TRUE))
install.packages("devtools")
devtools::install_github("BodenmillerGroup/imcdatasets", build_vignettes = TRUE)
imcdatasets builds on data objects contained in the
SingleCellExperiment,
SpatialExperiment,
and cytomapper packages.
These packages can be installed as follows:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("SingleCellExperiment", "SpatialExperiment", "cytomapper"))
To load imcdatasets in your R session, use:
library(imcdatasets)
Detailed information on how to access the datasets is available in the imcdatasets vignette.
The vignette can also be viewed directly in R:
vignette("imcdatasets")
The imcdatasets package provides quick and easy access to published and
curated imaging mass cytometry datasets. Each dataset consists of three data
objects that can be retrieved individually:
Single cell data in the form of a SingleCellExperiment or a
SpatialExperiment class object:
This object contains cell-level expression values and metadata. The rowData
entry contain marker information while the colData entry contain cell-level
metadata, including image names and cell numbers. The assays slots contain
marker expression levels per cell: the counts assay contains average ion
counts per cell whereas the other assays contain counts transformations
(details available in the documentation of each dataset).
Multichannel images formatted into a CytoImageList class object.
This object contains multichannel images and metadata, including channel names
and image names.
Cell segmentation masks formatted into a CytoImageList class object.
This object contains single-channel images representing cell segmentation masks
and metadata, including image names. The mask intensity values map to
cell number values in the SingleCellExperiment object so that single cell
data can be associated to segmentation masks.
The three data objects can be mapped using the image names contained in the metadata of each object. Details are available in the vignette (see above).
For more information about the SingleCellExperiment, SpatialExperiment,
and CytoImageList objects, please refer to the
SingleCellExperiment,
SpatialExperiment,
and cytomapper packages,
respectively.
In R, currently available datasets can be viewed with:
imc <- imcdatasets::listDatasets()
imc <- as.data.frame(imc)
imc
Detailed information about each dataset is available in the help pages
(e.g., ?JacksonFischer_2020_BreastCancer).
For more information, please refer to the
ExperimentHub vignette.
Suggestions for new Imaging Mass Cytometry datasets to include in the
imcdatasets package are welcome and can be made by
opening an issue on GitHub.
Guidelines about contributions and dataset formatting are provided in a dedicated vignette.
Damond N, Steenbuck N, Eling N, Fischer J, Hoch T, Meyer L (2026). imcdatasets: Collection of publicly available imaging mass cytometry (IMC) datasets. R package version 1.21.3, https://github.com/BodenmillerGroup/imcdatasets.