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A package to perform simple cell segmentation

Bioconductor version: Release (3.19)

Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. This allows for the features of cells such as marker expression and morphology to be extracted, stored and analysed. simpleSeg provides functionality for user friendly, watershed based segmentation on multiplexed cellular images in R based on the intensity of user specified protein marker channels. simpleSeg can also be used for the normalization of single cell data obtained from multiple images.

Author: Nicolas Canete [aut], Alexander Nicholls [aut], Ellis Patrick [aut, cre]

Maintainer: Ellis Patrick <ellis.patrick at>

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


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:

Introduction to simpleSeg HTML R Script
Reference Manual PDF


biocViews Classification, Normalization, SingleCell, Software, Spatial, Survival
Version 1.6.1
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License GPL-3
Depends R (>= 3.5.0)
Imports BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper
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Suggests BiocStyle, testthat (>= 3.0.0), knitr, ggplot2
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Follow Installation instructions to use this package in your R session.

Source Package simpleSeg_1.6.1.tar.gz
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macOS Binary (x86_64) simpleSeg_1.6.1.tgz
macOS Binary (arm64) simpleSeg_1.6.1.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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