segmentATH: Segmentation and quantification of cells stained for DNA,...
In imageHTS: Analysis of high-throughput microscopy-based screens

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/segmentation-segmentATH.R

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

1 2	segmentATH(x, uname, p, access) getCellFtrsATH(cal, seg)

`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.

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.

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.

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

parseDCF, segmentWells, extractFeatures