extractFeatures: Extract features from segmented images.
In imageHTS: Analysis of high-throughput microscopy-based screens

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

Extract features from segmented images.

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

`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.

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.

None.

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

getCellFtrsATH, fileHTS, collectCellFeatures

## 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)