R: Segmentation and quantification of cells stained for DNA,...

segmentATH {imageHTS}

R Documentation

Segmentation and quantification of cells stained for DNA, actin and tubulin.

Description

segmentATH and getCellFtrsATH are segmentation and feature extraction functions designed for cell images stained for DNA, actin and tubulin.

Usage

segmentATH(x, uname, p, access)
getCellFtrsATH(cal, seg)

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.
`access`	A character string indicating how to access the data. Valid values are `local`, `server` and `cache`, the default. See `fileHTS` for details.
`cal`	An EBImage image object containing the calibrated image.
`seg`	A list of two EBImage image objects: `cseg`, the cell segmentation mask and `nseg`, the nucleus segmentation mask.

Details

segmentATH is a segmentation function that can be specified in the seg.method field of a segmentation configuration file, called by the higher-level function segmentWells.

getCellFtrsATH is a feature extraction function that can be specified in the extractfeatures.method field of a feature configuration file, called by the higher-level function extractFeatures.

Value

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

getCellFtrsATH returns a data frame containing the cell features.

Author(s)

Gregoire Pau, gregoire.pau@embl.de, 2010

Examples

## see segmentWells and extractFeatures

[Package imageHTS version 1.36.0 Index]