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Collection of public MERFISH datasets

Bioconductor version: Release (3.19)

MerfishData is an ExperimentHub package that serves publicly available datasets obtained with Multiplexed Error-Robust Fluorescence in situ Hybridization (MERFISH). MERFISH is a massively multiplexed single-molecule imaging technology capable of simultaneously measuring the copy number and spatial distribution of hundreds to tens of thousands of RNA species in individual cells. The scope of the package is to provide MERFISH data for benchmarking and analysis.

Author: Ludwig Geistlinger [aut, cre] , Tyrone Lee [ctb], Helena Crowell [ctb] , Jeffrey Moffitt [aut], Robert Gentleman [aut]

Maintainer: Ludwig Geistlinger <ludwig_geistlinger at>

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


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:

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Reference Manual PDF


biocViews ExperimentData, ExperimentHub, ExpressionData, HighThroughputImagingData, Mus_musculus_Data, SingleCellData, SpatialData
Version 1.6.0
License Artistic-2.0
Depends R (>= 4.2.0), EBImage, SpatialExperiment
Imports grDevices, AnnotationHub, BumpyMatrix, ExperimentHub, S4Vectors, SingleCellExperiment, SummarizedExperiment
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Suggests grid, ggplot2, ggpubr, knitr, rmarkdown, testthat, BiocStyle, DropletUtils
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Follow Installation instructions to use this package in your R session.

Source Package MerfishData_1.6.0.tar.gz
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