operator for segmentation of the cytoplasm of cells, i.e. cell boundaries
based on snakes
iteratively expands cytoplasm area from initial nuclei regions
Input image
the single-channel image to be analyzed
if the image contains multiple channels, only the first one is processed
Initial snakes
initial snake contours, i.e. segmented nuclei regions, can be loaded from the ImageJ ROI Manager, edited manually or read from XML files
Snake optimizer
active contour snake operator to be used for segmentation, see Snake Segmentation for details
Operation mode
mode to be used for segmentation:
iterativeVoronoiExpansion: default mode
meanVarEnergies: without functionality at the moment
Max. level count
maximal number of iterations done in iterative expansion
most likely a single iteration will be ok
Max. distance in voronoi expansion
in Voronoi expansion mode cell regions are expanded by dilation at the beginning of each iteration
this parameter specifies how far they are expanded
unit is pixels
Min. area growth
area expansion stops if region growth becomes too small between two iterations
this parameter relates to the threshold for minimal region growth
Min. intensity variance
region expansion also stops if the intensity variance in the region fraction added during the most recent iteration is too small
regions with low variance are deemed to belong to the background
this parameter specifies the minimum admissible intensity variance in cytoplasm regions
note that the threshold needs to be adapted to the bit-depth per pixel of the image to be analyzed
Show intermediate results
disables/enables display of intermediate results during operator execution
Save intermediate results
disables/enables the saving of intermediate results to disk
Save intermediate results path
path where to save intermediate results
Verbose
disables/enables output of additional messages on console