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

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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.

Author
Henrik 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 publication
None
Maintainer
Henrik Failmezger <failmezger@mpipz.mpg.de>, Yinyin Yuan <Yinyin.Yuan@cancer.org.uk>
License
Artistic-2.0
Version
1.22.0

View on Bioconductor

Man pages

calculateCellularity
Calculation of tumour cellularity
calculateMeanStdTarget
Calculates Mean and Standard deviation of an image
calculateOtsu
Does Otsu thresholding
classifyCells
A function to classify cells
colorCorrection
Color transfer between images.
convertHSVToRGB
Conversion from HSV color space to RGB color space
convertLABToRGB
Conversion of LAB colour space to RGB colour space
convertRGBToHSV
Conversion from RGB color space to HSV color space
convertRGBToLAB
Converts RGB to LAB color space.
correctCopyNumber
Allelic Copy Number correction for cellularity
createBinaryImage
Thresholding
createClassifier
Construction of a classifier
CRImage-internal
Internal CRImage Functions
CRImage-package
CRImage is a package to analyze images and classify cells.
labelCells
Interactive Session for cell labeling
plotCorrectedCN
Plot CN profiles corrected for cellularity
processAperio
Cellularity Calculation of Aperio TX Scanner
SauvolaThreshold
Do Sauvola thresholding
segmentImage
Segmentation of an image

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