simpleSeg

DOI: 10.18129/B9.bioc.simpleSeg    

A package to perform simple cell segmentation

Bioconductor version: Release (3.16)

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 "4.2") 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")

 

HTML R Script Introduction to simpleSeg
PDF   Reference Manual
Text   NEWS

Details

biocViews Classification, Normalization, SingleCell, Software, Survival
Version 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
License GPL-3
Depends R (>= 3.5.0)
Imports BiocParallel, EBImage, terra, stats, spatstat.geom, S4Vectors, grDevices, SummarizedExperiment, methods, cytomapper
LinkingTo
Suggests BiocStyle, testthat (>= 3.0.0), knitr, ggplot2
SystemRequirements
Enhances
URL https://github.com/SydneyBioX/simpleSeg
BugReports https://github.com/SydneyBioX/simpleSeg/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package simpleSeg_1.0.0.tar.gz
Windows Binary simpleSeg_1.0.0.zip (64-bit only)
macOS Binary (x86_64) simpleSeg_1.0.0.tgz
macOS Binary (arm64) simpleSeg_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/simpleSeg
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/simpleSeg
Package Short Url https://bioconductor.org/packages/simpleSeg/
Package Downloads Report Download Stats

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