Example on how to script Simple Neurite Tracer (see http://forum.imagej.net/t/macro-able-segmentation-of-filamentous-structures-axons-in-3d/5533/3?u=tferr)

SNT_Scripting_Example.groovy

//@LogService log
//@UIService ui

import ij.IJ
import ij.gui.Overlay
import features.ComputeCurvatures
import tracing.TracerThread
import tracing.Path


start = [330, 390, 0]    // Beginning of structure to be traced (pixel coordinates)
end = [565, 50, 0]       // End-point (goal) of structure to be traced (pixel coordinates)  
timeout = 60             // If things go awry give up tracing after how many seconds?
timeoutCheckRate = 3000  // How many miliseconds should timeout be evaluated?
reciprocal = true        // use reciprocals when calculating the cost of moving to a new point?

log.info("Retrieving sample image...")
IJ.run("ddaC Neuron (84K)")
imp = IJ.getImage()
cal = imp.getCalibration()

log.info("Calculating Hessian curvatures...")
hessian = new ComputeCurvatures(imp, cal.pixelWidth, null, true)
hessian.run();

log.info("Running tracer...")
tracer = new TracerThread(imp, 0, 255, timeout, timeoutCheckRate,
                          start[0], start[1], start[2], end[0], end[1], end[2],
                          reciprocal, true, hessian, 4, null, true)
tracer.run()

log.info("Retrieving traced path...")
result = tracer.getResult();
result.setName(imp.getTitle())

log.info("Displaying path")
overlay = new Overlay()
result.drawPathAsPoints(overlay) 
imp.setOverlay(overlay)

ui.showDialog(result.toString(), "Path details")