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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CRImage")
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
Version1.22.0

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
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

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

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

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.