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

Files in this package

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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