Description Usage Arguments Details Value Author(s) See Also Examples
View source: R/segmentation-segmentYeastBF.R
segmentYeastBF
segments yeast cells from bright field microscopy
images.
segmentRing
segments ring-shape objects in images.
1 2 | segmentYeastBF(x, uname, p, access)
segmentRing(a, p)
|
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 |
access |
A character string indicating how to access the
data. Valid values are |
a |
An EBImage image object or a matrix containing the image to segment. |
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
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.
Gregoire Pau, gregoire.pau@embl.de, 2010
1 2 3 4 5 6 7 8 9 10 | 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)
|
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