Package: EBImage 4.55.0
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:
EBImage_4.55.0.tar.gz
EBImage_4.55.0.zip(r-4.7)EBImage_4.55.0.zip(r-4.6)EBImage_4.55.0.zip(r-4.5)
EBImage_4.55.0.tgz(r-4.6-x86_64)EBImage_4.55.0.tgz(r-4.6-arm64)EBImage_4.55.0.tgz(r-4.5-x86_64)EBImage_4.55.0.tgz(r-4.5-arm64)
EBImage_4.55.0.tar.gz(r-4.7-arm64)EBImage_4.55.0.tar.gz(r-4.7-x86_64)EBImage_4.55.0.tar.gz(r-4.6-arm64)EBImage_4.55.0.tar.gz(r-4.6-x86_64)
EBImage_4.55.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
EBImage/json (API)
NEWS
| # 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
On BioConductor:EBImage-4.55.0(bioc 3.24)EBImage-4.54.0(bioc 3.23)
visualizationbioinformaticsimage-analysisimage-processingcpp
Last updated from:4d9e17ea56. Checks:1 ERROR, 11 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 157 | ||
| linux-devel-arm64 | NOTE | 154 | ||
| linux-devel-x86_64 | NOTE | 222 | ||
| source / vignettes | OK | 188 | ||
| linux-release-arm64 | NOTE | 165 | ||
| linux-release-x86_64 | NOTE | 175 | ||
| macos-release-arm64 | NOTE | 102 | ||
| macos-release-x86_64 | NOTE | 315 | ||
| macos-oldrel-arm64 | NOTE | 122 | ||
| macos-oldrel-x86_64 | NOTE | 447 | ||
| windows-devel | NOTE | 148 | ||
| windows-release | NOTE | 136 | ||
| windows-oldrel | NOTE | 176 | ||
| wasm-release | OK | 121 |
Exports:abindaffineas.ImageblackTopHatbwlabelchannelclaheclosingColorcolorLabelscolormapcolorModecolorMode<-combinecomputeFeaturescomputeFeatures.basiccomputeFeatures.haralickcomputeFeatures.momentcomputeFeatures.shapedilatedisplaydisplayOutputdistmapdrawCircleequalizeerodefillHullfilter2flipfloodFillflopgblobgblurgetFramegetFramesGrayscalehistimageImageimageDataimageData<-is.ImagelocalCurvaturemakeBrushMath2medianFilternormalizenumberOfFramesocontouropeningOpsotsupaintObjectspropagatereadImagereenumeraterenderDisplayresizergbImagermObjectsrotateselfComplementaryTopHatshowstackObjectsstandardExpandRefthreshtiletoRGBtranslatetransposeuntilewatershedwhiteTopHatwriteImage
Dependencies:abindbase64encBiocGenericsbitopsbslibcachemclidigestevaluatefastmapfftwtoolsfontawesomefsgenericshighrhtmltoolshtmlwidgetsjpegjquerylibjsonliteknitrlatticelifecyclelocfitmemoisemimepngR6rappdirsRCurlrlangrmarkdownsasstifftinytexxfunyaml
Readme and manuals
Help Manual
| 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 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 |
