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simpleSeg

A package to perform simple cell segmentation


Bioconductor version: Release (3.18)

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, enter citation("simpleSeg")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("simpleSeg")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("simpleSeg")
Introduction to simpleSeg HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Classification, Normalization, SingleCell, Software, Spatial, Survival
Version 1.4.1
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
System Requirements
URL https://sydneybiox.github.io/simpleSeg/ https://github.com/SydneyBioX/simpleSeg
Bug Reports https://github.com/SydneyBioX/simpleSeg/issues
See More
Suggests BiocStyle, testthat (>= 3.0.0), knitr, ggplot2
Linking To
Enhances
Depends On Me
Imports Me
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Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package simpleSeg_1.4.1.tar.gz
Windows Binary simpleSeg_1.4.1.zip
macOS Binary (x86_64) simpleSeg_1.4.1.tgz
macOS Binary (arm64) simpleSeg_1.4.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/simpleSeg
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/simpleSeg
Bioc Package Browser https://code.bioconductor.org/browse/simpleSeg/
Package Short Url https://bioconductor.org/packages/simpleSeg/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.18 Source Archive