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EBImage specifications


Unique identifier OMICS_06485
Name EBImage
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 4.22.1
Stability Stable
methods, stats, graphics, utils, BiocStyle, grDevices, locfit, rmarkdown, knitr, RCurl, digest, abind, htmlwidgets, shiny, png, BiocGenerics(>=0.7.1), tiff, jpeg, fftwtools(>=0.9-7), htmltools
Maintained Yes


No version available



  • person_outline Andrzej Oleś

Publication for EBImage

EBImage citations


Activation of human macrophages by human corneal allogen in vitro

PLoS One
PMCID: 5884541
PMID: 29617399
DOI: 10.1371/journal.pone.0194855

[…] For the morphological cell analysis we used custom made in-house software based on the “R”-Platform (package “EBImage”) []. The data were plotted as box and whiskers plots for descriptive assessment (package “ggplot2”). Tukey's post hoc test was used to compare inter-individual differences in morphology (, pa […]


Identification of the fungal ligand triggering cytotoxic PRR mediated NK cell killing of Cryptococcus and Candida

Nat Commun
PMCID: 5821813
PMID: 29467448
DOI: 10.1038/s41467-018-03014-4
call_split See protocol

[…] mentary Fig.  showing an angle α <45° or β, greater than 45° between these two lines was determined for each pixel. For the analysis, a program written in R language using RStudio with libraries from EBImage was used to identify each fluorescent pixel in each image. The number of the pixels above a set threshold was plotted against their respective angles from the IS (histograms). NKp30 clustering […]


RNA Interference (RNAi) Screening in Drosophila

PMCID: 5844339
PMID: 29487145
DOI: 10.1534/genetics.117.300077

[…] sts as its unique features. Software for image-based screening analysis include CellProfiler, EBImage, CellProfiler analyst, imageHTS, StratomineR, and cytominr (; ; ; ). From these, CellProfiler and EBImage can be used to derive quantitative features from acquired fluorescent images by performing all operations needed for normalizing images, reducing noise, segmenting cells, and extracting numeri […]


Direct cell–cell contact between mature osteoblasts and osteoclasts dynamically controls their functions in vivo

Nat Commun
PMCID: 5775424
PMID: 29352112
DOI: 10.1038/s41467-017-02541-w

[…] alyzing an MIP image of mOBs and mOCs visualized simultaneously by intravital two-photon microscopy. This method was implemented in R language (ver. 3.2.2), with the image processing aspect using the EBImage (ver. 4.10.1) package and the visualization component using the rgl (ver. 0.95.1367) package.Step 1. Image binarization and resizing: As the first step in image analysis, both cyan and red cel […]


Diversity of fruit feeding butterflies in a mountaintop archipelago of rainforest

PLoS One
PMCID: 5493353
PMID: 28666003
DOI: 10.1371/journal.pone.0180007

[…] the photos []. The average of the values of the photos taken at each measurement were used as a value for the understory cover for each island. The images were processed using the R software package “EBImage” []. […]


rosettR: protocol and software for seedling area and growth analysis

Plant Methods
PMCID: 5353781
PMID: 28331535
DOI: 10.1186/s13007-017-0163-9

[…] ackage for R [] as that enabled fast development, easy automation, and access to the huge library of other packages for graphics and statistical analysis.For the image analysis steps, we opted to use EBImage [] which is a general purpose image analysis package for R. Using EBImage, we developed algorithms to estimate the areas of 32 individual seedlings growing together on a tissue culture plate, […]


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EBImage institution(s)
EMBL—European Bioinformatics Institute, Cambridge, UK
EBImage funding source(s)
CancerPathways project (EU FP7, grant HEALTH-F2-2008-201666); Research Grant, Human Frontier Sciences Program

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