labelCells: Interactive Session for cell labeling

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

Description

The functions creates an interactive session in order to label cells with their classes. The labeled cells can be used as training set for the classifier. Note!! This is until now only tested for MacOsX.

Usage

labelCells(img, segmentedImage, classes, classColours, nblocks = 3, labeledPoints = NULL, filename = NULL, filenameImage = NULL,transformCoordinates=FALSE)

Arguments

img	The image.
segmentedImage	The segmented image.
classes	The possible class labels.
classColours	The colors for the class labels.
nblocks	The image can be separated in several blocks, as zooming is not possible.
labeledPoints	Labeled cells from a previous training session.
filename	The table of labeled cells is saved at this location.
filenameImage	The image with the labeled cells is saved at this location.
transformCoordinates	deprecated

Details

Use the keys: a: In order to add a label to a cell. d: In order to delete a label from a cell. c: To switch between classes. q: To quit the interactive session. r: To refresh the session (labeled cells will be shown after refreshing)

Value

A table with columns: index: the index of the cell in the segmented image. x: x-coordinate of the cell y: y-coordinate of the cell classCell: Label of the cell xLocal: Local x coordinate in the subimage(block) yLocal: Local y coordinate in the subimage(block) block: Block number in which the cell arises.

Author(s)

Henrik Failmezger

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as

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

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