Operator for segmenting, tracking and analyzing 2D image sequences of fluorescently labeled cells
input image
image (sequence) to be analyzed
detection channel
channel used for segmentation (whole cells should be stained in this channel)
minimum seed size [advanced view]
minimum size (number of pixels) of seed objects to be considered as cells
median filter radius
radius (pixels) of median filter used for noise reduction
gamma
gamma correction with a value smaller than 1 is used to emphasize faintly fluorescing cells/ cell parts
if background noise is very high the value should be increased
maximum number of iterations [advanced view]
maximum number of iterations for level set segmentation
use mask channel [advanced view]
should an additional fluorescence channel be used for excluding certain cells
mask channel [advanced view]
additional fluorescence channel used for excluding certain cells (use mask channel must be activated)
include bright objects from mask [advanced view]
if activated bright cells are excluded from the analysis, else dark cells are excluded (refered to the mask channel; use mask channel must be activated, too)
average factor [advanced view]
only cells with average intensity above / below average factor times average intensity of the whole frame are excluded/ included(depending on whether include bright objects from mask is activated or not)
remove border touching objects
objects that are connected to the image borders will be discarded, if activated
minimum area (pixels)
minimum area (number of pixels) of objects to be retained
objects with a smaller area will not be analyzed (but they do appear on the resulting label image)
determine gating distance automatically
should the gating distance be determined automatically
if not, the maximum distance (pixels) is used
maximum distance (pixels)
maximum distance (gating distance) a cell is assumed to move between two consecutive frames
if the centroid distance of two regions from subsequent frames exceeds this value, these regions are not considered to belong to the same cell
only used if automatic gating distance determination is deactivated!
maximum area change
maximum relative change in area a cell is assumed to undergo between two consecutive frames
if the fraction of the areas of two regions from subsequent frames differ more than this value, these regions are not considered to belong to the same cell
pixel length, x-direction
physical length of a pixel in x-direction
pixel length, y-direction
physical length of a pixel in y-direction
unit x/y
unit of measurement for pixel size
time between frames
time elapsed between the acqusition of two consecutive frames
unit time
unit of measurement for the time
minimum track length
minimum length (number of consecutive frames) of a track to be considered for analysis
analyze trajectories
should cell trajectories be analyzed
analyze shapes
should cell shapes be analyzed
analyze intensities
should image intensities be analysized
requires an intensity image corresponding to the label image
show trajectory map
should a 2D map of the trajectories be created
show overlay image
should a new image sequence with cells and inpainted trajectories be created
Verbose
output some additional information