nucMask | R Documentation |
Generate an integer Image
mask from a fluorescent DNA image.
nucMask(
dna,
width = 36,
offset = 0.05,
size = 2,
sigma = 2,
radius = NULL,
gamma = 1
)
dna |
Fluorescent DNA |
width |
Maximum nuclear diameter (in pixels) to be used as
the |
offset |
Offset parameter for |
size |
Radius (in pixels) for |
sigma |
Standard deviation for |
radius |
Radius for |
gamma |
Exponent used for |
Generate an integer object mask (or list of masks) representing
segmented nuclei. The argument nuc
must be a grayscale nuclear image
of one or more dimensions or a list of such images.
Optimal conditions for detecting and segmented nuclei may require empirically
adjusting the arguments, especially width
and offset
.
The image or images will be processed sequentially by (1) an optional gamma
transformation, (2) normalization, (3) a medianFilter
with argument
size
if size
is non-zero, (4) the gblur
filter with
arguments sigma
and radius
, (5) thresholding with thresh2
with arguments width
and offset
, (6) fillHull
,
(7) distmap
, and (8) watershed
.
An integer Image
mask or list of integer Image
masks.
f.ex <- system.file("extdata", "by_folder/b2/file003.tif",package = "virustiter")
nuc.ex <- readImage(f.ex) # single nuclear image
xm0 <- nucMask(nuc.ex)
plot(colorLabels(xm0))
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