DOI: 10.18129/B9.bioc.simpleSeg  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see simpleSeg.

A package to perform simple cell segmentation

Bioconductor version: 3.17

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")):


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biocViews Classification, Normalization, SingleCell, Software, Spatial, Survival
Version 1.2.5
In Bioconductor since BioC 3.16 (R-4.2) (1 year)
License GPL-3
Depends R (>= 3.5.0)
Imports BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper
Suggests BiocStyle, testthat (>= 3.0.0), knitr, ggplot2
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