Package: EBImage 4.49.0
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_4.49.0.tar.gz
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EBImage.pdf |EBImage.html✨
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-4.49.0(bioc 3.21)EBImage-4.48.0(bioc 3.20)
visualizationbioinformaticsimage-analysisimage-processingcpp
Last updated 2 months agofrom:ad8004f5d6. Checks:OK: 5 NOTE: 1 WARNING: 3. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-win-x86_64 | WARNING | Dec 18 2024 |
| R-4.5-linux-x86_64 | NOTE | Dec 18 2024 |
| R-4.4-win-x86_64 | WARNING | Dec 18 2024 |
| R-4.4-mac-x86_64 | OK | Dec 18 2024 |
| R-4.4-mac-aarch64 | OK | Dec 18 2024 |
| R-4.3-win-x86_64 | WARNING | Dec 18 2024 |
| R-4.3-mac-x86_64 | OK | Dec 18 2024 |
| R-4.3-mac-aarch64 | OK | Dec 18 2024 |
Exports:abindaffineas.ImageblackTopHatbwlabelchannelclaheclosingColorcolorLabelscolormapcolorModecolorMode<-combinecomputeFeaturescomputeFeatures.basiccomputeFeatures.haralickcomputeFeatures.momentcomputeFeatures.shapedilatedisplaydisplayOutputdistmapdrawCircleequalizeerodefillHullfilter2flipfloodFillflopgblobgblurgetFramegetFramesGrayscalehistimageImageimageDataimageData<-is.ImagelocalCurvaturemakeBrushMath2medianFilternormalizenumberOfFramesocontouropeningOpsotsupaintObjectspropagatereadImagereenumeraterenderDisplayresizergbImagermObjectsrotateselfComplementaryTopHatshowstackObjectsstandardExpandRefthreshtiletoRGBtranslatetransposeuntilewatershedwhiteTopHatwriteImage
Dependencies:abindbase64encBiocGenericsbitopsbslibcachemclidigestevaluatefastmapfftwtoolsfontawesomefsgenericsgluehighrhtmltoolshtmlwidgetsjpegjquerylibjsonliteknitrlatticelifecyclelocfitmemoisemimepngR6rappdirsRCurlrlangrmarkdownsasstifftinytexxfunyaml
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 |
