countObjects: Count the number of objects in a segmented image

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

Description

Count the number of objects in a segmented image.

Usage

countObjects(cseg)

Arguments

cseg	An image containing the objects.

Value

An integer indicating the number of objects in the cell mask.

Author(s)

Gregoire Pau, [e-mail], 2010

See Also

segmentWells

Examples

## initialize imageHTS object using the local submorph screen
local = tempdir()
server = system.file('submorph', package='imageHTS')
x = parseImageConf('conf/imageconf.txt', localPath=local, serverURL=server)
x = configure(x, 'conf/description.txt', 'conf/plateconf.txt', 'conf/screenlog.txt')

## segment one well
uname = getUnames(x, content='rluc')[1]
z = segmentWells(x, uname=uname, segmentationPar='conf/segmentationpar.txt', writeData=FALSE)
n = countObjects(z$cseg)
cat('number of cells=', n, '\n')

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