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.

Author
Andrzej Oleś, Gregoire Pau, Mike Smith, Oleg Sklyar, Wolfgang Huber, with contributions from Joseph Barry and Philip A. Marais
Date of publication
None
Maintainer
Andrzej Oleś <andrzej.oles@embl.de>
License
LGPL
Version
4.16.0
URLs

View on Bioconductor

Man pages

bwlabel
Binary segmentation
channel
Color and image color mode conversions
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

Files in this package

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