highlightSegmentation: Highlight segmented objects in an image

In imageHTS: Analysis of high-throughput microscopy-based screens

Description

Highlight segmented objects in an image.

Usage

  highlightSegmentation(cal, nseg=NULL, cseg=NULL, thick=FALSE, opac=1, col=c('#ffff00', '#ff00ff'), border=FALSE, toRGB=TRUE) 

Arguments

cal	An EBImage Image object containing the original image.
nseg	An optional EBImage Image object containing the nucleus mask.
cseg	An optional EBImage Image object containing the cell mask.
thick	A logical indicating whether to use thick borders (useful for print). Default is FALSE.
opac	A numeric of the opacity value for drawing object contours; can be either a single numeric value or a numeric vector containing two opacity values, the first one for nuclei and the second one for cell bodies. Opacity ranges from 0 to 1, with 0 being fully transparent and 1 fully opaque
col	A character vector of two R colors for drawing contours of nuclei and cell bodies. By default, nuclei are highlighted in yellow and cells are highlighted in magenta.
border	A logical indicating whether contours should be closed at borders or not. Default is FALSE.
toRGB	A logical indicating whether Grayscale images should be promoted to Color ones or not. Default is TRUE.

Details

Highlights nuclei and cells by drawing contours of their boundaries. The colors, opacity, and border thicknes can be customized via the col, opacity, and thick arguments, repsectively.

Value

An EBImage image containing the annotated image.

Author(s)

Gregoire Pau, [e-mail], 2010

See Also

segmentWells

Examples

## see segmentWells for an example of highlightSegmentation
## example(segmentWells)

Example output

Loading required package: EBImage
Loading required package: cellHTS2
Loading required package: RColorBrewer
Loading required package: Biobase
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

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

Loading required package: genefilter
Loading required package: splots
Loading required package: vsn
Loading required package: hwriter
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: grid
Warning message:
In read.dcf(con) :
  URL 'http://bioconductor.org/BiocInstaller.dcf': status was 'Couldn't resolve host name'
Warning message:
system call failed: Cannot allocate memory 

imageHTS documentation built on Nov. 8, 2020, 8:29 p.m.