segmentWells: Segment cells in well images
In imageHTS: Analysis of high-throughput microscopy-based screens

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

Segment cells in well images.

1	segmentWells(x, uname, segmentationPar, access='cache', writeData=TRUE)

`x`	An imageHTS object.
`uname`	A character vector, containing the well names to segment. See `getUnames` for details.
`segmentationPar`	A character string, indicating the filename containing the segmentation parameters.
`access`	A character string indicating how to access the data. Valid values are `local`, `server` and `cache`, the default. See `fileHTS` for details.
`writeData`	A boolean indicating whether the segmentation data should be written to the project directory. Default is `TRUE`.

segmentWells reads the DCF segmentation parameters file pointed by segmentationPar. The file must contain the core segmentation function name indicated in the seg.method field. For each well indicated by uname, segmentWells calls the core segmentation function which returns a list containing a list of three EBImage images: cal, the calibrated image; nseg, the nucleus mask and cseg, the cell mask. See segmentATH for an example of a core segmentation function.

If writeData is TRUE, segmentWells writes for each well indicated by uname: the calibrated image data cal, the segmentation data seg, a calibrated JPEG image viewfull, untiled JPEG images viewunmonted, a calibrated JPEG image with segmentation annotation viewseg, a thumbnail JPEG image viewthumb and Javascript segmentation contour information contour. See fileHTS for details about these files.

If uname is of length 1, returns an invisible list containing: cal, the calibrated image; nseg, the nucleus mask and cseg, the cell mask.

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

segmentATH, getUnames, fileHTS

## 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]
z = segmentWells(x, uname=uname, segmentationPar='conf/segmentationpar.txt', writeData=FALSE)
if (interactive()) {
  seg = highlightSegmentation(z$cal, z$nseg, z$cseg)
  display(seg)
}