The following imageJ macro run in the Fiji script editor
produces the exception on Cilien-croped-3.tif image, 
but not on a similar image
Cilien-croped-2.tif. 

I wil attach the 2 image files to the bugzilla resport page. 

selectWindow("Cilien-croped-3.tif");
run("Smooth (3D)", "method=Gaussian sigma=1.000");
setAutoThreshold("Otsu dark stack");
run("Convert to Mask", "  black");
run("Skeletonize (2D/3D)");
run("Analyze Skeleton (2D/3D)", "prune=[lowest intensity voxel] show

java.lang.ArrayIndexOutOfBoundsException: 243
	at skeleton_analysis.AnalyzeSkeleton_.getNeighborhood(AnalyzeSkeleton_.java:2528)
	at skeleton_analysis.AnalyzeSkeleton_.getAverageNeighborhoodValue(AnalyzeSkeleton_.java:2493)
	at skeleton_analysis.AnalyzeSkeleton_.removeLowestIntensityVoxel(AnalyzeSkeleton_.java:787)
	at skeleton_analysis.AnalyzeSkeleton_.pruneCycles(AnalyzeSkeleton_.java:748)
	at skeleton_analysis.AnalyzeSkeleton_.run(AnalyzeSkeleton_.java:379)
	at skeleton_analysis.AnalyzeSkeleton_.run(AnalyzeSkeleton_.java:304)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:256)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:105)
	at ij.IJ.runUserPlugIn(IJ.java:195)
	at ij.IJ.runPlugIn(IJ.java:154)
	at ij.Executer.runCommand(Executer.java:150)
	at ij.Executer.run(Executer.java:81)
	at ij.IJ.run(IJ.java:269)
	at ij.macro.Functions.doRun(Functions.java:567)
	at ij.macro.Functions.doFunction(Functions.java:80)
	at ij.macro.Interpreter.doStatement(Interpreter.java:203)
	at ij.macro.Interpreter.doStatements(Interpreter.java:191)
	at ij.macro.Interpreter.run(Interpreter.java:102)
	at ij.macro.Interpreter.run(Interpreter.java:72)
	at CLI.Refresh_Macros.runScript(Refresh_Macros.java:56)
	at common.RefreshScripts.runScript(RefreshScripts.java:325)
	at fiji.scripting.TextEditor$Tab$6.execute(TextEditor.java:1197)
	at fiji.scripting.TextEditor$Executer$1.run(TextEditor.java:1757)



Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.6.8
  java.version => 1.6.0_26
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_26-b03-384-10M3425
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.1-b02-384
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: You wanted never to be reminded.

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  fiji.dir => /Applications/Fiji/Fiji.app

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