extractFeatures {imageHTS} | R Documentation |
Extract features from segmented images.
extractFeatures(x, uname, featurePar, access='cache')
x |
An imageHTS object. |
uname |
a character vector, containing the well names to
segment. See |
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 |
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)