Simple Segmentation ( IASimpleSegmentation )
Parameters:
Name |
Short Name |
Type |
Description |
Unused |
na1 |
boolean |
Legacy property. |
Unused |
na2 |
real |
Legacy property |
Unused |
na3 |
integer |
Legacy property |
Discard segments at edges |
noedges |
boolean |
Any segment that has at least 10% of its boundary at the edge of the image will be discarded. |
Data/Text Window Output |
textoutput |
boolean |
Whether to show progress and results of segmentation |
Description:
Segments binarized images using the pre set segmentation classifiers. Detects contiguous objects of pixel value "1" in frame by frame.
Each segment is marked by values corresponding to the label of the segment.
Use "Plot Morphological Parameters of Segments" function to create plots of mean segment data. Individual segment data are available for textual or Mathematica output.
Classifiers (gating) is applied, if present.
"Discard segments at edges": segments that have more than 1/10 of perimeter touching the edge of the image are removed. Use Classifiers to remove all segments touching the edge or ones are close by to the edge
Data/text window output: x,y : position of the center of the segment
z : time point or z position of the center of the segment
zspan : length of the segment in the third dimension (z or t)
V: volume
A: surface(maximum if present in multiple planes)
P: perimeter(maximum if present in multiple planes)
d: diameter(maximum if present in multiple planes)
S: surface
ShF: shape factor or circularity (mean if present in multiple planes) = 4*Pi*A/P^2
ShF3D: spherical shape factor = 36*Pi*V^2/S^3
Brnch: number branch points (for skeletonized objects)
The number of segments is limited only by the available memory.
Mathematica usage:
Result={number,{x,y,z},zspan, volume, maximal area, maximal perimeter, maximal diameter, surface, shape factor, spherical shape factor, number of branch points}