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

### See Also

`parseDCF`, `segmentWells`, `extractFeatures`

### Examples

    ## see segmentWells and extractFeatures

[Package imageHTS version 1.30.0 Index]