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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("EBImage")
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
Version4.16.0
https://github.com/aoles/EBImage

View on Bioconductor

Functions

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

Files

CHANGES
DESCRIPTION
NAMESPACE
R
R/AllGenerics.R R/Image.R R/colormap.R R/computeFeatures.R R/defunct.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/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/distmap.c
src/distmap.h
src/drawCircle.c
src/drawCircle.h
src/floodFill.cpp
src/floodFill.h
src/haralick.c
src/haralick.h
src/medianFilter.c
src/medianFilter.h
src/morphology.c
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.c
src/thresh.h
src/tile.c
src/tile.h
src/tools.c
src/tools.h
src/watershed.cpp
src/watershed.h
tests
tests/test.R
tests/test.Rout.save
vignettes
vignettes/EBImage-introduction.Rmd
vignettes/logo.png

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.