EBImage protocols

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EBImage specifications

Information


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
Requirements
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

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Maintainer


  • person_outline Andrzej Oleś <>

Publication for EBImage

EBImage in pipelines

 (2)
2018
PMCID: 5844339
PMID: 29487145
DOI: 10.1534/genetics.117.300077

[…] prior to further feature extraction, and corrected, if needed (). to extract image features describing the cells and connect them to cellular phenotypes, software packages such as cellprofiler or ebimage can be used (; ; ). once features are extracted, they serve as a vector of measurement, which characterizes the phenotype of each cell. multivariate phenotypes acquired this way enable […]

2016
PMCID: 4769224
PMID: 26919712
DOI: 10.1371/journal.pone.0150170

[…] [, ]. briefly, flat binary images of each intestinal section were converted to distance map images, which indicate for each position the euclidean distance to the nearest opposite color, using the ebimage software package []. the average minimum distance to the opposite color measures the mosaic patch size, which was compared to patch sizes from aggregation chimeras ()., some adenomas […]


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EBImage in publications

 (40)
PMCID: 5884541
PMID: 29617399
DOI: 10.1371/journal.pone.0194855

[…] counted by macrophage-like differentiation patterns using the “cell finder” software., 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 (, […]

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

[…] data set, and in case high resolution is not needed, many microscopes offer binning of px to lower resolutions. images are then used as input for image analysis software such as cellprofiler or r/ebimage (; )., data storage and image processing are two important issues to consider in image-based high-throughput screening where large data sets are produced. for example, a single gray-scale […]

PMCID: 5821813
PMID: 29467448
DOI: 10.1038/s41467-018-03014-4

[…] 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 […]

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

[…] 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 […]

PMCID: 5529420
PMID: 28747710
DOI: 10.1038/s41598-017-06544-x

[…] i and j. the actual features are various properties of the co-occurrence matrix such as the energy, entropy, or correlation. a total of 26 such features are readily available and documented in the ebimage r-package. , standardized entropy of all the pixels in the region calculated in the same manner as for the individual windows in the thresholding phase (1 feature), standard deviation […]


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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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