segmentYeastBF {imageHTS} | R Documentation

## 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.

### 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

### 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.

### Author(s)

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

### 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)

[Package imageHTS version 1.36.0 Index]