pruning.bsh

// @ImagePlus(label="Skeleton image", description="Binary image skeletonized with Skeletonize3D") image
// @double(label="Length threshold", description="Minimum branch length to keep") threshold
// @OUTPUT ImagePlus prunedImage

// https://forum.image.sc/t/skeletonize-remove-or-prune-short-end-segments/4704

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" );