CRImage-package: CRImage is a package to analyze images and classify cells.

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

Description

CRImage allows classification of cells in biological images. It offers methods to segment cells or cell nuclei in biological images for example HE stained images. It offers methods to create a classifier and to classify cells in these images. Furthermore it allows the calculation of tumour cellularity for large microscope images.

CRImage makes use of the image processing package EBImage, which uses the 'ImageMagick' library for image I/O operations and the 'GTK' library to display images.

Details

Package:	CRImage
Type:	Package
Version:	1.0
Date:	2010-04-27
License:	LGPL Version 2 or later
LazyLoad:	yes

Package content

Image processing methods:

• calculateThreshold

• segmentImage

Classification:

• createTrainingSet

• createClassifier

• classifyCells

Tumour cellularity

• calculateCellularity

• processAperio

Author(s)

Henrik Failmezger, <[e-mail]>

Yinyin Yuan, <[e-mail]>

Oscar Rueda, <[e-mail]>

Florian Markowetz, <[e-mail]>

CRI Cambridge

Li Ka Shing Centre

Robinson Way

Cambridge, CB2 0RE, UK

Ludwigs-Maximilians University of Munich

Examples

example(segmentImage)
example(createClassifier)
example(classifyImage)

Example output

Loading required package: EBImage
Loading required package: DNAcopy
Loading required package: aCGH
Loading required package: cluster
Loading required package: survival
Loading required package: multtest
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.


Attaching package: 'Biobase'

The following object is masked from 'package:EBImage':

    channel


Attaching package: 'aCGH'

The following object is masked from 'package:stats':

    heatmap


sgmntI> #segment image
sgmntI> #f = system.file('extdata' ,'exImg.jpg',package='CRImage')
sgmntI> #segmentationValues=segmentImage(f,maxShape=800,minShape=40,failureRegion=2000,threshold="otsu",numWindows=4)
sgmntI> #image=segmentationValues[[1]]
sgmntI> #segmentedImage=segmentationValues[[2]]
sgmntI> #imageFeatures=segmentationValues[[3]]
sgmntI> 
sgmntI> 
sgmntI> 

crtCls> f = system.file("extdata", "trainingData.txt", package="CRImage")

crtCls> #read training data
crtCls> trainingData=read.table(f,header=TRUE)

crtCls> #create classifier
crtCls> classifier=createClassifier(trainingData)[[1]]
Warning message:
In example(classifyImage) : no help found for 'classifyImage'

CRImage documentation built on Nov. 8, 2020, 8:01 p.m.