imageHTS (version 1.22.0)

segmentYeastBF: Segmentation of yeast cells and ring-shaped objects.

Description

segmentYeastBF segments yeast cells from bright field microscopy images. segmentRing segments ring-shape objects in images.

Usage

segmentYeastBF(x, uname, p, access)
segmentRing(a, p)

Arguments

x

An imageHTS object.

uname

A character string, containing the well name to segment.

p

A list of character vectors, containing the segmentation parameters. This is the output of parseDCF, given an input segmentation configuration file. See details.

access

A character string indicating how to access the data. Valid values are local, server and cache, the default. See fileHTS for details.

a

An EBImage image object or a matrix containing the image to segment.

Value

segmentYeastBF returns a list containing three EBImage images: cal, the calibrated image; nseg, the nucleus mask and cseg, the cell mask.segmentRing returns a list containing two EBImage images: nseg, the nucleus mask and cseg, the cell mask.

Details

segmentYeastBF is a high-level segmentation function that can be specified in the seg.method field of a segmentation configuration file, called by the higher-level function segmentWells. segmentRing is used by segmentYeastBF and segments an image containing ring-shaped objects. The list of parameters p should contain:

• edge.threshold: a threshold parameter giving the cell edges
• max.membrane.thickness: the maximum membrane thickness, in pixels
• crown.thickness: the membrane thickness, in pixels
• crown.steps: a vector of 3 values, containing the minimum cell diameter, the maximum cell diameter, and the step between all possible diameters
• locmin.threshold.width: the adaptive threshold window width to compute the local minima, to call cell centers
• locmin.threshold.offset: the adaptive threshold window offset
• locmin.erode.size: the size of the erode paramter cleaning up the local minima map
• cell.max.overlap: the maximum cell overlap size, in pixels
• nucleus.radius.offset: the nucleus radius negative offset
• cell.radius.offset: the cell radius negative offset

See Also

segmentWells, segmentATH

Examples

filename = system.file('yeast.jpeg', package='imageHTS')
a = readImage(filename)
if (interactive()) display(a)
p = list(edge.threshold=0.05, max.membrane.thickness=5, crown.thickness=8,
    crown.steps=c(31, 61, 4), locmin.threshold.width=9, locmin.threshold.offset=0.15, 
    locmin.erode.size=3, cell.max.overlap=2, nucleus.radius.offset=10,
    cell.radius.offset=4)
seg = segmentRing(a, p)
hseg = highlightSegmentation(EBImage::channel(a, 'rgb'), cseg=seg$cseg, thick=TRUE)
if (interactive()) display(hseg)