This is the development version of simpleSeg; for the stable release version, see simpleSeg.
A package to perform simple cell segmentationBioconductor version: Development (3.22)
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 sydney.edu.au>
Citation (from within R, entercitation("simpleSeg")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("simpleSeg")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("simpleSeg")Follow Installation instructions to use this package in your R session.
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