EBImage
This is the released version of EBImage; for the devel version, see EBImage.
Image processing and analysis toolbox for R
Bioconductor version: Release (3.23)
EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.
Author: Andrzej Oleś, Gregoire Pau, Mike Smith, Oleg Sklyar, Wolfgang Huber, with contributions from Joseph Barry and Philip A. Marais
Maintainer: Andrzej Oleś <andrzej.oles at gmail.com>
citation("EBImage")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("EBImage")
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("EBImage")| Introduction to EBImage | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Software, Visualization |
| Version | 4.54.0 |
| In Bioconductor since | BioC 1.8 (R-2.3) (20.5 years) |
| License | LGPL |
| Depends | methods |
| Imports | BiocGenerics(>= 0.7.1), graphics, grDevices, stats, abind, tiff, jpeg, png, locfit, fftwtools (>= 0.9-7), utils, htmltools, htmlwidgets, RCurl |
| System Requirements | |
| URL | https://github.com/aoles/EBImage |
| Bug Reports | https://github.com/aoles/EBImage/issues |
See More
| Suggests | BiocStyle, digest, knitr, rmarkdown, shiny |
| Linking To | |
| Enhances | |
| Depends On Me | CRImage, cytomapper, flowcatchR, ImageArray, DonaPLLP2013, furrowSeg, MerfishData, nucim |
| Imports Me | alabaster.sfe, bnbc, CatsCradle, cytoviewer, flowCHIC, heatmaps, imcRtools, MoleculeExperiment, RBioFormats, simpleSeg, sosta, SpatialFeatureExperiment, SpatialOmicsOverlay, synapsis, xenLite, yamss, BioImageDbs, OSTA, AiES, bioimagetools, BioThermR, FastSegmentation, LFApp, LOMAR, ProxReg, RockFab, SAFARI, spatialGE |
| Suggests Me | HilbertVis, Voyager, aroma.core, cooltools, glow, ijtiff, juicr, metagear, pliman |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | EBImage_4.54.0.tar.gz |
| Windows Binary (x86_64) | EBImage_4.54.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | EBImage_4.54.0.tgz |
| macOS Binary (sonoma-arm64) | EBImage_4.54.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/EBImage |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/EBImage |
| Bioc Package Browser | https://code.bioconductor.org/browse/EBImage/ |
| Package Short Url | https://bioconductor.org/packages/EBImage/ |
| Package Downloads Report | Download Stats |