Package: EBImage 4.55.1

Andrzej Oleś

EBImage: Image processing and analysis toolbox for R

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.

Authors:Andrzej Oleś, Gregoire Pau, Mike Smith, Oleg Sklyar, Wolfgang Huber, with contributions from Joseph Barry and Philip A. Marais

EBImage_4.55.1.tar.gz
EBImage_4.55.1.zip(r-4.7)EBImage_4.55.1.zip(r-4.6)EBImage_4.55.1.zip(r-4.5)
EBImage_4.55.1.tgz(r-4.6-x86_64)EBImage_4.55.1.tgz(r-4.6-arm64)EBImage_4.55.1.tgz(r-4.5-x86_64)EBImage_4.55.1.tgz(r-4.5-arm64)
EBImage_4.55.1.tar.gz(r-4.7-arm64)EBImage_4.55.1.tar.gz(r-4.7-x86_64)EBImage_4.55.1.tar.gz(r-4.6-arm64)EBImage_4.55.1.tar.gz(r-4.6-x86_64)
EBImage_4.55.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
EBImage/json (API)

# Install 'EBImage' in R:

install.packages('EBImage', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aoles/ebimage/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:EBImage-4.55.0(bioc 3.24)EBImage-4.54.0(bioc 3.23)

visualization bioinformatics image-analysis image-processing cpp

12.56 score 77 stars 45 packages 2.9k scripts 81 mentions 74 exports 37 dependencies

Last updated from:63e63949be. Checks:1 ERROR, 11 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	176
linux-devel-arm64	WARNING	202
linux-devel-x86_64	WARNING	191
source / vignettes	OK	234
linux-release-arm64	WARNING	199
linux-release-x86_64	WARNING	184
macos-release-arm64	WARNING	168
macos-release-x86_64	WARNING	421
macos-oldrel-arm64	WARNING	126
macos-oldrel-x86_64	WARNING	366
windows-devel	WARNING	127
windows-release	WARNING	148
windows-oldrel	WARNING	155
wasm-release	OK	148

Exports:abind affine as.Image blackTopHat bwlabel channel clahe closing Color colorLabels colormap colorMode colorMode<-combine computeFeatures computeFeatures.basic computeFeatures.haralick computeFeatures.moment computeFeatures.shape dilate display displayOutput distmap drawCircle equalize erode fillHull filter2 flip floodFill flop gblob gblur getFrame getFrames Grayscale hist image Image imageData imageData<-is.Image localCurvature makeBrush Math2 medianFilter normalize numberOfFrames ocontour opening Ops otsu paintObjects propagate readImage reenumerate renderDisplay resize rgbImage rmObjects rotate selfComplementaryTopHat show stackObjects standardExpandRef thresh tile toRGB translate transpose untile watershed whiteTopHat writeImage

Dependencies:abind base64enc BiocGenerics bitops bslib cachem cli digest evaluate fastmap fftwtools fontawesome fs generics highr htmltools htmlwidgets jpeg jquerylib jsonlite knitr lattice lifecycle locfit memoise mime png R6 rappdirs RCurl rlang rmarkdown sass tiff tinytex xfun yaml

Introduction to EBImage

Rendered fromEBImage-introduction.Rmdusingknitr::rmarkdown

Last update: 2020-03-28
Started: 2015-05-27

Help page	Topics
Combine Image Arrays	abind abind,ANY-method abind,Image-method abind,list-method abind-methods
Binary segmentation	bwlabel
Color and image color mode conversions	channel rgbImage toRGB
Contrast Limited Adaptive Histogram Equalization	clahe
Color Code Labels	colorLabels
Map a Greyscale Image to Color	colormap
Combine images	combine combine,ANY,NULL-method combine,array,array-method combine,Image,Image-method combine,list,missing-method combine,matrix,matrix-method combine,NULL,ANY-method combine,NULL,NULL-method
Compute object features	computeFeatures computeFeatures.basic computeFeatures.haralick computeFeatures.moment computeFeatures.shape gblob standardExpandRef
Image Display	display plot.Image
Shiny Bindings for display	display-shiny displayOutput renderDisplay
Distance map transform	distmap
Draw a circle on an image.	drawCircle
Package overview	EBImage
Defunct functions in package 'EBImage'	animate blackTopHatGreyScale blur closingGreyScale cmoments dilateGreyScale drawfont drawtext EBImage-defunct edgeFeatures edgeProfile erodeGreyScale getFeatures getNumberOfFrames haralickFeatures haralickMatrix hullFeatures moments openingGreyScale rmoments selfcomplementaryTopHatGreyScale smoments whiteTopHatGreyScale zernikeMoments
Histogram Equalization	equalize
Fill holes in objects	fillHull
2D Convolution Filter	filter2
Region filling	floodFill
Low-pass Gaussian filter	gblur
Image class	as.array.Image as.Image as.raster.Image Color colorMode colormode colorMode<- getFrame getFrames Grayscale hist,Image-method Image image,Image-method Image-class imageData imageData<- is.Image log,Image-method Math2,Image-method median.Image numberOfFrames Ops,Image,Image-method Ops,Image,numeric-method Ops,numeric,Image-method print.Image quantile.Image show,Image-method [,Image,ANY,ANY,ANY-method [,Image-method
Image I/O	readImage writeImage
Local Curvature	localCurvature
2D constant time median filtering	medianFilter
Perform morphological operations on images	blackTopHat closing dilate erode makeBrush opening selfComplementaryTopHat whiteTopHat
Intensity values linear scaling	normalize normalize,array-method normalize,Image-method normalize,matrix-method
Oriented contours	ocontour
Calculate Otsu's threshold	otsu
Mark objects in images	paintObjects
Voronoi-based segmentation on image manifolds	propagate
Spatial linear transformations	affine flip flop resize rotate rotate,array-method rotate,Image-method translate
Object removal and re-indexation	reenumerate rmObjects
Places detected objects into an image stack	stackObjects
Adaptive thresholding	thresh
Tiling/untiling images	tile untile
Image Transposition	transpose
Watershed transformation and watershed based object detection	watershed

Package: EBImage 4.55.1

EBImage: Image processing and analysis toolbox for R

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Help Manual

Usage by other packages (reverse dependencies)