segmentATH: 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

An imageHTS object.

uname

A character string, containing the well name to segment.

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.

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.

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.

Examples

Run this code

## see segmentWells and extractFeatures

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