VolumeJ - Frequently Asked Questions

ImageJ is running out of memory during rendering
Increase the amount of memory available for ImageJ. Look at the "Memory" section of the installation notes for your OS at

     http://rsb.info.nih.gov/ij/docs/install/

I am trying to render confocal microscopy stacks (volumes) and they renderings don't look good.
This is because VolumeJ assumes the voxels are as thick as they are wide. To make the stack seem thicker, increase the z-aspect ratio setting to something like 4 or 6. This will make the voxels look very elongated. Even better is to use the reconstructor plugin and reconstruct the stack using the same aspect ratio.


The rendering (for example mri-stack.tif) is almost invisible because it is so dark.
This problem most often occurs with stacks that were used in NIH Image. The examples on the ImageJ website are one example. These volume stacks are inverted (i.e. black is 255 or 32768 and white is 0) and then the light position is inverted also. Either invert the stack (using Edit->Invert) or set the light to 1,1,10 instead of 1,1,-10 for correct renderings.

Why is rendering slower than with the Volpack library (or the IX library, VTK, MacVol or XYZ package)?
First, VolumeJ
was written in Java, an interpreted language, and the other packages have been written in C(++). The advantage of VolumeJ is that it is automatically multiplatform. Secondly, most other packages use more sophisticated algorithms, such as run-length encoding, octrees and other optimizations. VolumeJ is not optimized in this way. The advantage is that the software is easier to understand (and thus more easy to reuse by others), easier to write new classes for classification or non-scalar volumes, and finally, that it was easier and faster for me to write and debug.  

Actually, isosurface rendering is superfast and <1s for most volumes. Please contact me for details and licensing.

Where can I learn more about volume rendering, classification etc.?
See the literature section
, which admittedly needs work.

Why are updates so haphazard?
VolumeJ is not a project, but a service to the imaging community.
As my work on visualization evolves, I update VolumeJ based on  ideas from there.

Where can I find other volumes to download?
I am sorry I cannot supply you with my volumes, as all of them contain patient data. The only suggestion I have is to look on the web. Remember that ImageJ can load just about any series of images as a stack. The example renderings
page is starting to be a repository for example volume links.

ImageJ prints:
PlugIn not found: Volume_Renderer.
Windows: Take care that the
class files are in the  plugins\VolumeJ, plugins\bijnum and plugins\volume directories.
Windows: Take care that if you are running ImageJ from the commandline, the java CLASSPATH variable should be
    SET CLASSPATH=
<wherever_ij.jar_is_located_path>/ij.ImageJ;
Sometimes this message appears and  VolumeJ will still run. It was a problem in the ImageJ classloader, which has now been replaced by Wayne Rasband.

ImageJ prints:
Exception occurred during event dispatching:
java.lang.NoClassDefFoundError: bijnum/SVDCException
         at vr.MatrixTransform.... etc

This has been a problem with previous versions of VolumeJ on Sun systems. It should not occur anymore. It was caused by java doing load-time instead of run-time binding of class names. It is not supposed to do this. Contact me if this problem keeps arising after updating to the newest  VolumeJ version.

ImageJ prints:
java.lang.NoClassDefFoundError: VolumeJ/VJClassifierLevoyDepthCueing
This has been a problem with VolumeJ on Mac OS X systems. It should not occur anymore. It was caused by this version of java not accepting class names longer than 32 characters. This does not happen on Windows/Linux Java implementations as far as I know, so I onyl found out when Mac users started having problems. Contact me if this problem keeps arising after updating to the newest  VolumeJ version.

The plugins do not run, and the VolumeJ, bijnum and volume directories/folders are not there:
Make sure that when you extract in Winzip, the "Use folder names" checkbox is checked, otherwise the proper folders are not created and you end up with a mess of .class files.

If this FAQ doesn't solve your problem: let me know and I will post it here (hopefully with the solution).

(c) 1999-2003, Michael Abramoff. Last updated 08-Dec-03.

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