CRImage: CRImage a package to classify cells and calculate tumour cellularity
Version 1.24.0

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.

Browse man pages Browse package API and functions Browse package files

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>
Bioconductor views CellBiology Classification
Date of publicationNone
MaintainerHenrik Failmezger <failmezger@mpipz.mpg.de>, Yinyin Yuan <Yinyin.Yuan@cancer.org.uk>
LicenseArtistic-2.0
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CRImage")

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

Functions

CRImage Man page
CRImage-package Man page
Phansalkar_threshold Man page Source code
SauvolaThreshold Man page Source code
calculateCellularity Man page Source code
calculateMeanStdTarget Man page Source code
calculateOtsu Man page Source code
classificationAperio Man page Source code
classifyCells Man page Source code
classifyPen Source code
classifyStructures Man page Source code
colorCorrection Man page Source code
convertHSVToRGB Man page Source code
convertLABToRGB Man page Source code
convertRGBToHSV Man page Source code
convertRGBToLAB Man page Source code
correctCopyNumber Man page Source code
createBinaryImage Man page Source code
createClassifier Man page Source code
determineCellularity Man page Source code
findSlices Man page Source code
getCorrected Man page
getImageDistance Source code
hist3d Source code
imageCompression Man page Man page Source code
kernelSmoother Man page Source code
labelCells Man page Source code
localORThreshold Man page Source code
localOtsuThreshold Man page
localThreshold Source code
numberOfNeighbors Man page Source code
oregonThreshold Source code
paintCells Man page Source code
parseFinalScan Man page Source code
plotCorrectedCN Man page Source code
plotImage Source code
plotImages Man page
processAperio Man page Source code
searchStructures Man page Source code
segmentCytoplasma Man page Source code
segmentImage Man page Source code
segmentStructures Man page Source code
writeDensityImage Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/Phansalkar_threshold.R
R/SauvolaThreshold.R
R/calculateCellularity.R
R/calculateMeanStdTarget.R
R/calculateOtsu.R
R/classificationAperio.R
R/classifyCells.R
R/classifyPen.R
R/classifyStructures.R
R/colorCorrection.R
R/convertHSVToRGB.R
R/convertLABToRGB.R
R/convertRGBToHSV.R
R/convertRGBToLAB.R
R/correctCopyNumber.R
R/createBinaryImage.R
R/createClassifier.R
R/determineCellularity.R
R/findSlices.R
R/getImageDistance.R
R/hist3d.R
R/imageCompression.R
R/kernelSmoother.R
R/labelCells.R
R/localORThreshold.R
R/localThreshold.R
R/numberOfNeighbors.R
R/oregonThreshold.R
R/paintCells.R
R/parseFinalScan.R
R/plotCorrectedCN.R
R/plotImage.R
R/processAperio.R
R/searchStructures.R
R/segmentCytoplasma.R
R/segmentImage.R
R/segmentStructures.R
R/writeDensityImage.R
build
build/vignette.rds
inst
inst/doc
inst/doc/CRImage.R
inst/doc/CRImage.Rnw
inst/doc/CRImage.pdf
inst/extdata
inst/extdata/8905
inst/extdata/8905/Da0.jpg
inst/extdata/8905/Da1.jpg
inst/extdata/8905/Da2.jpg
inst/extdata/8905/Da3.jpg
inst/extdata/8905/Da4.jpg
inst/extdata/8905/Da5.jpg
inst/extdata/8905/Da6.jpg
inst/extdata/8905/Da7.jpg
inst/extdata/8905/Da8.jpg
inst/extdata/8905/FinalScan.ini
inst/extdata/8905/FinalScanModified.ini
inst/extdata/8905/PreviewSlide.jpg
inst/extdata/8905/ScanScope.icc
inst/extdata/8905/SlideLabel.jpg
inst/extdata/8905/SlideMacro.jpg
inst/extdata/8905/SlideScan.ini
inst/extdata/8905/SlideThumb.jpg
inst/extdata/8905/Ss1.jpg
inst/extdata/8905/Ss2.jpg
inst/extdata/8905/Ss3.jpg
inst/extdata/8905/Ss4.jpg
inst/extdata/8905/index.cws
inst/extdata/classifier_GU_Da33_0.8
inst/extdata/exImg.jpg
inst/extdata/exImg2.jpg
inst/extdata/exImg3.jpg
inst/extdata/imgCorrected.jpg
inst/extdata/lImg.jpg
inst/extdata/penClassifier
inst/extdata/pixelClassifier
inst/extdata/referenceHist
inst/extdata/testClassifier
inst/extdata/trainingData.txt
man
man/CRImage-internal.Rd
man/CRImage-package.Rd
man/SauvolaThreshold.Rd
man/calculateCellularity.Rd
man/calculateMeanStdTarget.Rd
man/calculateOtsu.Rd
man/classifyCells.Rd
man/colorCorrection.Rd
man/convertHSVToRGB.Rd
man/convertLABToRGB.Rd
man/convertRGBToHSV.Rd
man/convertRGBToLAB.Rd
man/correctCopyNumber.Rd
man/createBinaryImage.Rd
man/createClassifier.Rd
man/labelCells.Rd
man/plotCorrectedCN.Rd
man/processAperio.Rd
man/segmentImage.Rd
vignettes
vignettes/CRImage.Rnw
vignettes/cancerHeatmap.jpg
vignettes/cellularity2.jpg
vignettes/cellularity2.pdf
vignettes/classifiedImage.jpg
vignettes/exImg2.jpg
vignettes/exImg3.jpg
vignettes/imgCorrected.jpg
vignettes/labeledImage.pdf
vignettes/segmentedImage.jpg
vignettes/segmentedImage.pdf
vignettes/segmentedImageRaw.jpg
vignettes/segmentedImageRaw.pdf
CRImage documentation built on May 20, 2017, 10:42 p.m.