simpleSeg
This is the development version of simpleSeg; for the stable release version, see simpleSeg.
A package to perform simple cell segmentation
Bioconductor version: Development (3.21)
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("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.
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 | ||
| NEWS | Text |
Details
| biocViews | Classification, Normalization, SingleCell, Software, Spatial, Survival |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (2 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 | lisaClust, spicyR |
| Suggests Me | spicyWorkflow |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | simpleSeg_1.9.0.tar.gz |
| Windows Binary (x86_64) | simpleSeg_1.9.0.zip (64-bit only) |
| macOS Binary (x86_64) | simpleSeg_1.9.0.tgz |
| macOS Binary (arm64) | simpleSeg_1.9.0.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 |