Operator for analyzing image sequences from scratch assay/ gap closure/ wound healing experiments
Input can be single images or image stacks from brigthfield as well as fluorescence microscopy
Results are given as segmented images and a table containing scratch areas as well as area differences
input image
scratch assay image (stack)
if an image stack is given, it is assumed, that it represents one scratch assay experiment with the frames being ordered chronologically
detection channel
channel to segment scratch (only available in multichannel images)
scratch orientation
horizontally or
vertically
σ (sigma)
standard deviation of Gaussian filter
increase leads to more image smoothing (noise reduction) but scratch area tends to decrease
entropy filter size
size of entropy filter mask used for emphasizing cell areas
increase let the scratch area decrease
maximum iterations [Advanced View]
maximum number of iterations for level set segmentation
method for checking for scratch absence
method used to check, if there is a scratch/ gap in the single frames
none: no check for scratch absence
INCREASING_AREA: if detected scratch/ gap area increases from one frame to the next about more than defined by maximum area increase then it is assumed the gap is closed already and detected gap is an artifact
all subsequent images are considered to contain an already closed gap
SVM: a previously trained SVM model is used to recognize images without gaps
the path to the SVM model has to be given by path to svm file
a new SVM model can be trained using the ScratchAssaySVMTrainer operator, cf. Scratch Assay SVM Trainer
maximum area increase
maximum increase of gap area between consecutive frames that is not considered to indicate a segmentation artifact due to an already closed gap(only available, if method for checking for scratch absence is set to INCREASING_AREA)
path to svm file
absolute path to an external svm model file (only available, if method for checking for scratch absence is set to SVM)
pixel length, x-direction
physical length of a pixel in x-direction (without unit)
pixel length, y-direction (without unit)
physical length of a pixel in y-direction
unit space
unit of spatial pixel dimensions
Verbose
output some additional information