CRImage: CRImage a package to classify cells and calculate tumour cellularity

CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.

AuthorHenrik Failmezger <failmezger@mpipz.mpg.de>, Yinyin Yuan <Yinyin.Yuan@cancer.org.uk>, Oscar Rueda <oscar.rueda@cancer.org.uk>, Florian Markowetz <Florian.Markowetz@cancer.org.uk>
Date of publicationNone
MaintainerHenrik Failmezger <failmezger@mpipz.mpg.de>, Yinyin Yuan <Yinyin.Yuan@cancer.org.uk>
LicenseArtistic-2.0
Version1.22.0

View on Bioconductor

Functions

calculateCellularity Man page
calculateMeanStdTarget Man page
calculateOtsu Man page
classificationAperio Man page
classifyCells Man page
classifyStructures Man page
colorCorrection Man page
convertHSVToRGB Man page
convertLABToRGB Man page
convertRGBToHSV Man page
convertRGBToLAB Man page
correctCopyNumber Man page
createBinaryImage Man page
createClassifier Man page
CRImage Man page
CRImage-package Man page
determineCellularity Man page
findSlices Man page
getCorrected Man page
imageCompression Man page
imageCompression Man page
kernelSmoother Man page
labelCells Man page
localORThreshold Man page
localOtsuThreshold Man page
numberOfNeighbors Man page
paintCells Man page
parseFinalScan Man page
Phansalkar_threshold Man page
plotCorrectedCN Man page
plotImages Man page
processAperio Man page
SauvolaThreshold Man page
searchStructures Man page
segmentCytoplasma Man page
segmentImage Man page
segmentStructures Man page
writeDensityImage Man page

Files

CRImage/DESCRIPTION
CRImage/NAMESPACE
CRImage/R
CRImage/R/Phansalkar_threshold.R CRImage/R/SauvolaThreshold.R CRImage/R/calculateCellularity.R CRImage/R/calculateMeanStdTarget.R CRImage/R/calculateOtsu.R CRImage/R/classificationAperio.R CRImage/R/classifyCells.R CRImage/R/classifyPen.R CRImage/R/classifyStructures.R CRImage/R/colorCorrection.R CRImage/R/convertHSVToRGB.R CRImage/R/convertLABToRGB.R CRImage/R/convertRGBToHSV.R CRImage/R/convertRGBToLAB.R CRImage/R/correctCopyNumber.R CRImage/R/createBinaryImage.R CRImage/R/createClassifier.R CRImage/R/determineCellularity.R CRImage/R/findSlices.R CRImage/R/getImageDistance.R CRImage/R/hist3d.R CRImage/R/imageCompression.R CRImage/R/kernelSmoother.R CRImage/R/labelCells.R CRImage/R/localORThreshold.R CRImage/R/localThreshold.R CRImage/R/numberOfNeighbors.R CRImage/R/oregonThreshold.R CRImage/R/paintCells.R CRImage/R/parseFinalScan.R CRImage/R/plotCorrectedCN.R CRImage/R/plotImage.R CRImage/R/processAperio.R CRImage/R/searchStructures.R CRImage/R/segmentCytoplasma.R CRImage/R/segmentImage.R CRImage/R/segmentStructures.R CRImage/R/writeDensityImage.R
CRImage/build
CRImage/build/vignette.rds
CRImage/inst
CRImage/inst/doc
CRImage/inst/doc/CRImage.R
CRImage/inst/doc/CRImage.Rnw
CRImage/inst/doc/CRImage.pdf
CRImage/inst/extdata
CRImage/inst/extdata/8905
CRImage/inst/extdata/8905/Da0.jpg
CRImage/inst/extdata/8905/Da1.jpg
CRImage/inst/extdata/8905/Da2.jpg
CRImage/inst/extdata/8905/Da3.jpg
CRImage/inst/extdata/8905/Da4.jpg
CRImage/inst/extdata/8905/Da5.jpg
CRImage/inst/extdata/8905/Da6.jpg
CRImage/inst/extdata/8905/Da7.jpg
CRImage/inst/extdata/8905/Da8.jpg
CRImage/inst/extdata/8905/FinalScan.ini
CRImage/inst/extdata/8905/FinalScanModified.ini
CRImage/inst/extdata/8905/PreviewSlide.jpg
CRImage/inst/extdata/8905/ScanScope.icc
CRImage/inst/extdata/8905/SlideLabel.jpg
CRImage/inst/extdata/8905/SlideMacro.jpg
CRImage/inst/extdata/8905/SlideScan.ini
CRImage/inst/extdata/8905/SlideThumb.jpg
CRImage/inst/extdata/8905/Ss1.jpg
CRImage/inst/extdata/8905/Ss2.jpg
CRImage/inst/extdata/8905/Ss3.jpg
CRImage/inst/extdata/8905/Ss4.jpg
CRImage/inst/extdata/8905/index.cws
CRImage/inst/extdata/classifier_GU_Da33_0.8
CRImage/inst/extdata/exImg.jpg
CRImage/inst/extdata/exImg2.jpg
CRImage/inst/extdata/exImg3.jpg
CRImage/inst/extdata/imgCorrected.jpg
CRImage/inst/extdata/lImg.jpg
CRImage/inst/extdata/penClassifier
CRImage/inst/extdata/pixelClassifier
CRImage/inst/extdata/referenceHist
CRImage/inst/extdata/testClassifier
CRImage/inst/extdata/trainingData.txt
CRImage/man
CRImage/man/CRImage-internal.Rd CRImage/man/CRImage-package.Rd CRImage/man/SauvolaThreshold.Rd CRImage/man/calculateCellularity.Rd CRImage/man/calculateMeanStdTarget.Rd CRImage/man/calculateOtsu.Rd CRImage/man/classifyCells.Rd CRImage/man/colorCorrection.Rd CRImage/man/convertHSVToRGB.Rd CRImage/man/convertLABToRGB.Rd CRImage/man/convertRGBToHSV.Rd CRImage/man/convertRGBToLAB.Rd CRImage/man/correctCopyNumber.Rd CRImage/man/createBinaryImage.Rd CRImage/man/createClassifier.Rd CRImage/man/labelCells.Rd CRImage/man/plotCorrectedCN.Rd CRImage/man/processAperio.Rd CRImage/man/segmentImage.Rd
CRImage/vignettes
CRImage/vignettes/CRImage.Rnw
CRImage/vignettes/cancerHeatmap.jpg
CRImage/vignettes/cellularity2.jpg
CRImage/vignettes/cellularity2.pdf
CRImage/vignettes/classifiedImage.jpg
CRImage/vignettes/exImg2.jpg
CRImage/vignettes/exImg3.jpg
CRImage/vignettes/imgCorrected.jpg
CRImage/vignettes/labeledImage.pdf
CRImage/vignettes/segmentedImage.jpg
CRImage/vignettes/segmentedImage.pdf
CRImage/vignettes/segmentedImageRaw.jpg
CRImage/vignettes/segmentedImageRaw.pdf

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

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