Particle Analyszer Java Exception

java-8
java3d
bonej
Tags: #<Tag:0x00007fb87cdbcdb0> #<Tag:0x00007fb87cdbcb80> #<Tag:0x00007fb87cdbca18>

#1

HELP! I regularly use the Particle Analyzer function in FIJI and Image J, but it currently keeps crashing on my system, with the following error:

(Fiji Is Just) ImageJ 2.0.0-rc-54/1.51g; Java 1.8.0_66 [64-bit]; Mac OS X 10.12.1; 2381MB of 31966MB (7%)
 
java.lang.ClassCastException: org.scijava.vecmath.Point3f cannot be cast to javax.vecmath.Point3f
	at org.doube.bonej.ParticleCounter.getSurfacePoints(ParticleCounter.java:984)
	at org.doube.bonej.ParticleCounter.run(ParticleCounter.java:253)
	at ij.IJ.runUserPlugIn(IJ.java:217)
	at ij.IJ.runPlugIn(IJ.java:181)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)

I am running Fiji with no problem at home, but for some reason it has a slightly different version of Java SDK/RE on it (1.8.0_73) on an otherwise identical iMac. I’ve done a quick search, and have updated Java in my Mac OS settings, but I believe I need to replace the Java folder within FIJI/ImageJ. However, I don’t know quite what to do here: I must have done it sometime recently on my iMac at home, but cannot recall how I did this…

Any suggestions very much appreciated!

Simon


#2

Dear @Simon_Carr,

this looks like some version skew in one of you installations, I guess one of your installations has a newer version of 3D Viewer. But I guess @mdoube might have some information on the issue.

Best,
Stefan


#3

BoneJ1 does not (yet) work with Java 8, see these posts:


So, you can:

  • use a Life-line version of Fiji as proposed in the linked posts, or
  • use ImageJ’s own Particle Analyzer (Analyze > Analyze Particles…)

depending on what you need to do.