EBImage: Image processing and analysis toolbox for R
Version 4.18.0

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.

AuthorAndrzej Oleś, Gregoire Pau, Mike Smith, Oleg Sklyar, Wolfgang Huber, with contributions from Joseph Barry and Philip A. Marais
Bioconductor views Visualization
Date of publicationNone
MaintainerAndrzej Oleś <andrzej.oles@embl.de>
LicenseLGPL
Version4.18.0
URL https://github.com/aoles/EBImage
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("EBImage")

Getting started

README.md
Introduction to *EBImage*

Popular man pages

channel: Color and image color mode conversions
combine: Combining images
computeFeatures: Compute object features
display: Image Display
filter2: 2D Convolution Filter
io: Image I/O
thresh: Adaptive thresholding
See all...

All man pages Function index File listing

Man pages

bwlabel: Binary segmentation
channel: Color and image color mode conversions
clahe: Contrast Limited Adaptive Histogram Equalization
colorLabels: Color Code Labels
colormap: Map a Greyscale Image to Color
combine: Combining images
computeFeatures: Compute object features
display: Image Display
distmap: Distance map transform
drawCircle: Draw a circle on an image.
EBImage: Package overview
EBImage-defunct: Defunct functions in package 'EBImage'
equalize: Histogram Equalization
fillHull: Fill holes in objects
filter2: 2D Convolution Filter
floodFill: Region filling
gblur: Low-pass Gaussian filter
Image: Image class
io: Image I/O
localCurvature: Local Curvature
medianFilter: 2D constant time median filtering
morphology: Perform morphological operations on images
normalize: Intensity values linear scaling
ocontour: Oriented contours
otsu: Calculate Otsu's threshold
paintObjects: Mark objects in images
propagate: Voronoi-based segmentation on image manifolds
rmObjects: Object removal and re-indexation
spatial: Spatial linear transformations
stackObjects: Places detected objects into an image stack
thresh: Adaptive thresholding
tile: Tiling/untiling images
transpose: Image Transposition
watershed: Watershed transformation and watershed based object detection

Functions

Color Man page
EBImage Man page
EBImage-defunct Man page
Grayscale Man page
Image Man page Source code
Image-class Man page
Math2,Image-method Man page
Ops,Image,Image-method Man page
Ops,Image,numeric-method Man page
Ops,numeric,Image-method Man page
[,Image,ANY,ANY,ANY-method Man page
[,Image-method Man page
affine Man page Source code
animate Man page
as.Image Man page Source code
as.Image.Image Source code
as.Image.default Source code
as.array.Image Man page Source code
as.nativeRaster Source code
as.raster.Image Man page Source code
blackTopHat Man page Source code
blackTopHatGreyScale Man page
blur Man page
bwlabel Man page Source code
castImage Source code
channel Man page Source code
channelLayout Source code
checkCompatibleImages Source code
checkx Source code
clahe Man page Source code
clipImage Source code
closing Man page Source code
closingGreyScale Man page
cmoments Man page
colorLabels Man page Source code
colorMode Man page Source code
colorMode<- Man page
colormap Man page Source code
colormode Man page
combine Man page
combine,ANY,NULL-method Man page
combine,Image,Image-method Man page
combine,NULL,ANY-method Man page
combine,NULL,NULL-method Man page
combine,array,array-method Man page
combine,list,missing-method Man page
combine,matrix,matrix-method Man page
combineImages Source code
computeFeatures Man page Source code
computeFeatures.basic Man page Source code
computeFeatures.haralick Man page Source code
computeFeatures.moment Man page Source code
computeFeatures.shape Man page Source code
convertRef Source code
determineFileType Source code
dilate Man page Source code
dilateGreyScale Man page
display Man page Source code
displayInBrowser Source code
displayRaster Source code
distmap Man page Source code
drawCircle Man page Source code
drawfont Man page
drawtext Man page
edgeFeatures Man page
edgeProfile Man page
equalize Man page Source code
erode Man page Source code
erodeGreyScale Man page
fillHull Man page Source code
filter2 Man page Source code
flip Man page Source code
floodFill Man page Source code
flop Man page Source code
gblob Man page Source code
gblur Man page Source code
getFeatures Man page
getFrame Man page Source code
getFrames Man page Source code
getNumberOfFrames Man page
haralickFeatures Man page Source code
haralickMatrix Man page Source code
hist,Image-method Man page
hullFeatures Man page
image,Image-method Man page
imageData Man page Source code
imageData<- Man page
is.Image Man page Source code
isXbitImage Source code
localCurvature Man page Source code
log,Image-method Man page
makeBrush Man page Source code
median.Image Man page Source code
medianFilter Man page Source code
moments Man page
normalize Man page
normalize,Image-method Man page
normalize,array-method Man page
normalize,matrix-method Man page
normalizeImage Source code
numberOfFrames Man page Source code
ocontour Man page Source code
opening Man page Source code
openingGreyScale Man page
otsu Man page Source code
paintObjects Man page Source code
parseColorMode Source code
plot.Image Man page Source code
print.Image Man page Source code
propagate Man page Source code
quantile.Image Man page Source code
readImage Man page Source code
reenumerate Man page Source code
resize Man page Source code
rgbImage Man page Source code
rmObjects Man page Source code
rmoments Man page
rotate Man page Source code
selectChannel Source code
selfComplementaryTopHat Man page Source code
selfcomplementaryTopHatGreyScale Man page
show,Image-method Man page
showImage Source code
smoments Man page
splitObjects Source code
stackObjects Man page Source code
standardExpandRef Man page Source code
tests Source code
thresh Man page Source code
tile Man page Source code
toRGB Man page Source code
translate Man page Source code
transpose Man page Source code
untile Man page Source code
validImage Source code
validImageObject Source code
watershed Man page Source code
whiteTopHat Man page Source code
whiteTopHatGreyScale Man page
writeImage Man page Source code
zernikeMoments Man page

Files

CHANGES
DESCRIPTION
NAMESPACE
R
R/AllGenerics.R
R/Image.R
R/colormap.R
R/computeFeatures.R
R/display.R
R/drawCircle.R
R/equalize.R
R/filter2.R
R/floodFill.R
R/gblur.R
R/localCurvature.R
R/medianFilter.R
R/morphology.R
R/normalize.R
R/objects.R
R/otsu.R
R/segment.R
R/spatial.R
R/tile.R
R/tools.R
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS.Rd
inst/doc
inst/doc/EBImage-introduction.R
inst/doc/EBImage-introduction.Rmd
inst/doc/EBImage-introduction.html
inst/images
inst/images/cells.tif
inst/images/nuclei.tif
inst/images/sample-color.png
inst/images/sample.png
inst/images/shapes.png
inst/scripts
inst/scripts/figDistanceMapDemo.R
inst/scripts/readWriteTest.R
inst/scripts/readWriteTest.Rout.save
inst/viewer
inst/viewer/display.css
inst/viewer/display.template
inst/viewer/viewer.js
man
man/EBImage-defunct.Rd
man/EBImage.Rd
man/Image.Rd
man/bwlabel.Rd
man/channel.Rd
man/clahe.Rd
man/colorLabels.Rd
man/colormap.Rd
man/combine.Rd
man/computeFeatures.Rd
man/display.Rd
man/distmap.Rd
man/drawCircle.Rd
man/equalize.Rd
man/fillHull.Rd
man/filter2.Rd
man/floodFill.Rd
man/gblur.Rd
man/io.Rd
man/localCurvature.Rd
man/medianFilter.Rd
man/morphology.Rd
man/normalize.Rd
man/ocontour.Rd
man/otsu.Rd
man/paintObjects.Rd
man/propagate.Rd
man/rmObjects.Rd
man/spatial.Rd
man/stackObjects.Rd
man/thresh.Rd
man/tile.Rd
man/transpose.Rd
man/watershed.Rd
src
src/EBImage.c
src/clahe.c
src/clahe.h
src/distmap.cpp
src/distmap.h
src/drawCircle.c
src/drawCircle.h
src/floodFill.cpp
src/floodFill.h
src/getFrames.c
src/getFrames.h
src/haralick.c
src/haralick.h
src/medianFilter.c
src/medianFilter.h
src/morphology.cpp
src/morphology.h
src/nativeRaster.c
src/nativeRaster.h
src/normalize.c
src/normalize.h
src/objects.c
src/objects.h
src/ocontour.c
src/ocontour.h
src/propagate.cpp
src/propagate.h
src/spatial.c
src/spatial.h
src/thresh.cpp
src/thresh.h
src/tile.cpp
src/tile.h
src/tools.c
src/tools.h
src/transpose.cpp
src/transpose.h
src/watershed.cpp
src/watershed.h
tests
tests/test.R
tests/test.Rout.save
vignettes
vignettes/EBImage-introduction.Rmd
vignettes/logo.png
EBImage documentation built on May 20, 2017, 10:37 p.m.

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