分析骨骼

// Takes a binary image as input
var imp = IJ.getImage(); // get current open image

// Skeletonize the image
IJ.run(imp, "Skeletonize (2D/3D)", "");

// Initialize AnalyzeSkeleton_
var skel = new AnalyzeSkeleton_();
skel.calculateShortestPath = true;
skel.setup("", imp);

// Perform analysis in silent mode
// (work on a copy of the ImagePlus if you don't want it displayed)
// run(int pruneIndex, boolean pruneEnds, boolean shortPath, ImagePlus origIP, boolean silent, boolean verbose)
var skelResult = skel.run(AnalyzeSkeleton_.NONE, false, true, null, true, false);

// Read the results
var shortestPaths = skelResult.getShortestPathList().toArray();
var branchLengths = skelResult.getAverageBranchLength();
var branchNumbers = skelResult.getBranches();

var totalLength = 0;
for (var i = 0; i < branchNumbers.length; i++) {
    totalLength += branchNumbers[i] * branchLengths[i];
}

var cumulativeLengthOfShortestPaths = 0;
for (var i = 0; i < shortestPaths.length; i++) {
    cumulativeLengthOfShortestPaths += Number(shortestPaths[i]);
}

// Use the readout within the script
IJ.log(totalLength);
IJ.log(cumulativeLengthOfShortestPaths); ###按长度树枝

import sc.fiji.analyzeSkeleton.AnalyzeSkeleton_;
import sc.fiji.analyzeSkeleton.Edge;
import sc.fiji.analyzeSkeleton.Point;
import ij.IJ;

// analyze skeleton
skel = new AnalyzeSkeleton_();
skel.setup("", image);
skelResult = skel.run(AnalyzeSkeleton_.NONE, false, false, null, true, false);

// create copy of input image
prunedImage = image.duplicate();
outStack = prunedImage.getStack();

// get graphs (one per skeleton in the image)
graph = skelResult.getGraph();

// list of end-points
endPoints = skelResult.getListOfEndPoints();

for( i = 0 ; i < graph.length; i++ )
{
    listEdges = graph[i].getEdges();

    // go through all branches and remove branches under threshold
    // in duplicate image
    for( Edge e : listEdges )
    {
        p = e.getV1().getPoints();
        v1End = endPoints.contains( p.get(0) );
        p2 = e.getV2().getPoints();
        v2End = endPoints.contains( p2.get(0) );
        // if any of the vertices is end-point 
        if( v1End || v2End )
        {
            if( e.getLength() < threshold )
            {
                if( v1End )
                    outStack.setVoxel( p.get(0).x, p.get(0).y, p.get(0).z, 0 );
                if( v2End )
                    outStack.setVoxel( p2.get(0).x, p2.get(0).y, p2.get(0).z, 0 );
                for( Point p : e.getSlabs() )
                    outStack.setVoxel( p.x, p.y, p.z, 0 );
            }
        }
    }
}

prunedImage.setTitle( image.getShortTitle() + "-pruned" ); 请注意，由于删除了端点和板而不是交汇点，可能会创建小分支（以防止破坏某个值的分支）。因此，您可能需要运行该脚本几次才能删除所有不需要的分支。

import sc.fiji.analyzeSkeleton.AnalyzeSkeleton_;
import sc.fiji.analyzeSkeleton.Edge;
import sc.fiji.analyzeSkeleton.Point;
import ij.IJ;
import ij3d.Image3DUniverse;
import org.scijava.vecmath.Point3f;
import org.scijava.vecmath.Color3f;
 
// analyze skeleton
skel = new AnalyzeSkeleton_();
skel.setup("", image);
skelResult = skel.run(AnalyzeSkeleton_.NONE, false, false, null, true, false);
 
// get calibration
pixelWidth = image.getCalibration().pixelWidth;
pixelHeight = image.getCalibration().pixelHeight;
pixelDepth = image.getCalibration().pixelDepth;
 
// get graphs (one per skeleton in the image)
graph = skelResult.getGraph();

// create 3d universe
univ = new Image3DUniverse();
univ.show();

// list of end-points
endPoints = skelResult.getListOfEndPoints();
// store their positions in a list
endPointList = new ArrayList();
for( Point p : endPoints )
    endPointList.add( new Point3f(
        (float)( p.x * pixelDepth ),
        (float)( p.y * pixelHeight ),
        (float)( p.z * pixelDepth ) ) );
// add end-points to the universe as blue spheres
univ.addIcospheres( endPointList, new Color3f( Color.BLUE ), 2, 1f, "End-points");

// list of junction voxels
junctions = skelResult.getListOfJunctionVoxels();
// store their positions in a list
junctionList = new ArrayList();
for( Point p : junctions )
    junctionList.add( new Point3f(
        (float)( p.x * pixelDepth ),
        (float)( p.y * pixelHeight ),
        (float)( p.z * pixelDepth ) ) );
// add junction voxels to the universe as magenta spheres
univ.addIcospheres( junctionList, new Color3f( Color.MAGENTA ), 2, 1f, "Junctions");

for( i = 0 ; i < graph.length; i++ )
{
    listEdges = graph[i].getEdges();
 
    // go through all branches and add slab voxels 
    // as orange lines in the 3D universe
    j=0;
    for( Edge e : listEdges )
    {
        branchPointList = new ArrayList();
        for( Point p : e.getSlabs() )
            branchPointList.add( new Point3f(
                (float)( p.x * pixelDepth ),
                (float)( p.y * pixelHeight ),
                (float)( p.z * pixelDepth ) ) );
        // add slab voxels to the universe as orange lines
        univ.addLineMesh( branchPointList, new Color3f( Color.ORANGE ), "Branch-"+i+"-"+j, true );
        j++;    
    }
} ## API文档