simpleSeg
A package to perform simple cell segmentation
Bioconductor version: 3.24 · Package version: 1.15.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("simpleSeg")Details
| Maintainer | Ellis Patrick <ellis.patrick@sydney.edu.au> |
| Author | Nicolas Canete [aut], Alexander Nicholls [aut], Ellis Patrick [aut, cre] |
| License | GPL-3 |
| URL | https://sydneybiox.github.io/simpleSeg/ https://github.com/SydneyBioX/simpleSeg |
| Bug Reports | https://github.com/SydneyBioX/simpleSeg/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | Classification, Normalization, SingleCell, Software, Spatial, Survival |
| Package Short Url | https://bioconductor.org/packages/simpleSeg/ |
Citation
From within R, enter citation("simpleSeg"):
Nicolas Canete, Alexander Nicholls, Ellis Patrick. simpleSeg: A package to perform simple cell segmentation. doi:10.18129/B9.bioc.simpleSeg, R package version 1.15.0, https://bioconductor.org/packages/simpleSeg.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | simpleSeg_1.15.0.tar.gz |
| Windows binary (x86_64) | simpleSeg_1.15.0.zip |
| macOS binary (arm64) | simpleSeg_1.15.0.tgz |
| macOS binary (x86_64) | simpleSeg_1.15.0.tgz |
Dependencies
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