It is not possible to run the 3D viewer from MATLAB anymore. 

The demo posted on the MATLAB FEX (see link) hooks forever when trying to instantiate the 3D universe. This most likely originates from MATLAB itself rather than from a Fiji component. 

I copy below the very detailed report from Eric Siggia (thanks to him) that thoroughly investigated the issue. 

"

	I am on a Mac 10.9.2, using matlab 2013b, I downloaded FIJI yesterday, and checked no further updates needed.
	I worked though the file Matlab3DViewerIntroduction and everything looks fine including…

InstallJava3D
Testing if Java3D is already installed...
Java3D is already installed.
Installed version is 1.5.
This is good enough, you have nothing to do.
Exiting.

I can run the demo  at http://fiji.sc/Miji  eg
MIJ.run('Embryos (42K)’);
etc

and all looks OK. I can open the 3D viewer directly via FIJI or ImageJ and it rotates normally.

However the demo Matlab3DViewerDemo_1.m  hangs matlab at the command (with ‘busy’ on command window)…
universe = ij3d.Image3DUniverse();

and I have to force quit matlab to exit.

This error was encountered before by Ran Shadmi and your fix was an update of Fiji, but I am updated…(and have opened and closed all apps numerous times)

scripts> pwd
/Applications/FIJI.app/scripts
scripts> ls
InstallJava3D.m			Matlab3DViewerIntroduction.m
IsJava3DInstalled.m		Miji.m
Matlab3DViewerDemo_1.m		Miji_Test.m
Matlab3DViewerDemo_2.m		bfopen.m
Matlab3DViewerDemo_3.m		importTrackMateTracks.m

On the same MAC I have matlab2010a installed and I get the error noted in Dec 2011 by S Mehta, which is a similar issue.

I also tried Matlab2014a on the same MAC and also run into problems on the same command (a query you posted 09 april 2014)
universe = ij3d.Image3DUniverse();

What I do not understand are the following responses…

ij3d
Undefined function or variable 'ij3d'. 
ij3d.setup()
Undefined variable "ij3d" or class "ij3d.setup". 
universe = ij3d.Image3DUniverse();  %%%%% and then it hangs, but it did not recognize the ij3d class before and I assume this last line is a method in this class


On a different MAC running OS 10.6.8 and Matlab 2012a everything runs fine!
"