extractFeatures {imageHTS} | R Documentation

## Extract features from segmented images.

### Description

Extract features from segmented images.

### Usage

    extractFeatures(x, uname, featurePar, access='cache')

### Arguments

`x` | An imageHTS object.
`uname` | a character vector, containing the well names to segment. See `getUnames` for details.
`featurePar` | a character string, indicating the filename containing the feature extraction parameters.
`access` | A character string indicating how to access the data. Valid values are `local`, `server` and `cache`, the default. See `fileHTS` for details.

### Details

`extractFeatures` reads the DCF segmentation parameters file pointed by `featurePar`. The file must contain the field `extractfeatures.method` that indicates which core feature extraction function to use. The function takes two arguments: `cal`, the calibrated image to extract the features from, and `seg`, a list of two images, `cseg` and `nseg`, which contains the cell and nucleus segmentation masks, respectively. The function returns a matrix of features. See `getCellFtrsATH` for example.

For each well, `extractFeatures` writes a `ftrs` segmentation data file that contains the cell features. Use `readHTS` or `collectCellFeatures` to get the cell features after extraction.

### Value

None.

### Author(s)

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

### See Also

`getCellFtrsATH`, `fileHTS`, `collectCellFeatures`

### Examples

    ## initialize imageHTS object using the local submorph screen
    local = tempdir()
    server = system.file('submorph', package='imageHTS')
    x = parseImageConf('conf/imageconf.txt', localPath=local, serverURL=server)
    x = configure(x, 'conf/description.txt', 'conf/plateconf.txt', 'conf/screenlog.txt')

    ## segment one well
    uname = getUnames(x, content='rluc')[1]
    segmentWells(x, uname=uname, segmentationPar='conf/segmentationpar.txt')

    ## extract features from the well
    extractFeatures(x, uname=uname, 'conf/featurepar.txt')

    ## read the feature file using readHTS
    y = readHTS(x, type='ftrs', uname=uname)

    ## get features using collectCellFeatures
    y = collectCellFeatures(x, uname=uname)

[Package imageHTS version 1.34.0 Index]