Issue with Level Sets


The following is copy-pasted from some other threads I’ve made before. So, I am currently researching neuronal ultrastructure in the brain, and have obtained a stack of images from doing serial-section SEM on a tissue sample. We have loaded them all up for use in FIJI as a large image stack. Long story short, we intend to use FIJI’s TrakEM2 plugin to segment (so, “color in”, across the different layers, so to speak) various structures using AreaLists. Then, we want to create 3D models of these structures (not the entire image stack; just the colored-in structures of interest), and make them easily understandable/viewable in the 3D graphics software, Blender.

As our data sets grow, we are seeking ways to improve the efficiency and time required to segment the cells. While the fast-marching tool is great, it is occasionally slow (10-20 seconds adds up after hundreds of stacks and multiple areas per stack). We are seeking ways to improve our automatic segmentation. I came across this page on Level Sets ( However, when I attempt to use Level Sets from the Plugins>Segmentation menu after having pointed out an area, I get the following error:

(Fiji Is Just) ImageJ 2.0.0-rc-43/1.50e; Java 1.6.0_24 [64-bit]; Windows NT (unknown) 6.2; 149MB of 49066MB (<1%)
java.lang.ArrayIndexOutOfBoundsException: 16
	at ij.process.TypeConverter.convertByteToShort(
	at ij.process.TypeConverter.convertToShort(
	at ij.process.ImageProcessor.convertToShort(
	at levelsets.ij.ImageContainer.<init>(
	at levelsets.ij.LevelSet.execute(
	at ij.IJ.runUserPlugIn(
	at ij.IJ.runPlugIn(
	at ij.Executer.runCommand(

This is complete gibberish to me, so any help would be much appreciated, either about speeding up automatic tracing or fixing this error. Thanks a lot in advance!


I cannot reproduce this error on an up-to-date Fiji installation with Java 8.

Can you try if running Fiji on Java 8 with the Java-8 update site enabled (the easiest way is to download a new Fiji) fixes things for you?

The Java-6 version of Fiji doesn’t receive updates any more for a few months now, for details see here.