Can't display area map using Show in 3D in TrakEM2 on Mac

I recently installed the latest version of Fiji on an iMac running OS X 10.11.3 [3.5 GHz Intel Core i7; 32 GB 1600 MHz DDR3; NVIDIA GeForce GTX 780M 4096 MB]. I also removed all older versions of Java and their Frameworks from the computer and installed a fresh copy of jdk-8u74-macosx-x64. In Fiji, I included Java 3D in the update sites and made sure all plugins were current. Tests of Marching Cubes and Java 3D seemed to work fine. Loading one of the test projects provided by TrakEM2 -Membranes.xml-seems to work fine. However, when I selected one of the area_lists, made it visible, and selected Show in 3D, I get the following error message:

ERROR:
java.lang.reflect.InvocationTargetException
	at java.awt.EventQueue.invokeAndWait(EventQueue.java:1319)
	at java.awt.EventQueue.invokeAndWait(EventQueue.java:1294)
	at javax.swing.SwingUtilities.invokeAndWait(SwingUtilities.java:1348)
	at ini.trakem2.display.Display3D.get(Display3D.java:320)
	at ini.trakem2.display.Display3D$6.call(Display3D.java:469)
	at ini.trakem2.display.Display3D$6.call(Display3D.java:404)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.NoSuchMethodError: ij3d.Image3DUniverse.getViewer()Lcom/sun/j3d/utils/universe/Viewer;
	at ini.trakem2.display.Display3D.<init>(Display3D.java:102)
	at ini.trakem2.display.Display3D.<init>(Display3D.java:55)
	at ini.trakem2.display.Display3D$2.run(Display3D.java:321)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:301)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
==> Caused by: java.lang.NoSuchMethodError: ij3d.Image3DUniverse.getViewer()Lcom/sun/j3d/utils/universe/Viewer;
	at ini.trakem2.display.Display3D.<init>(Display3D.java:102)
	at ini.trakem2.display.Display3D.<init>(Display3D.java:55)
	at ini.trakem2.display.Display3D$2.run(Display3D.java:321)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:301)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
	at java.awt.EventQueue.access$500(EventQueue.java:97)
	at java.awt.EventQueue$3.run(EventQueue.java:709)
	at java.awt.EventQueue$3.run(EventQueue.java:703)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

Could not get a proper 3D display for node area_list #104

I have tried another project that I created with the same result. I am at a loss as to what to try next. Any help would be greatly appreciated. Thank you.

Unfortunately, TrakEM2 has not yet been updated for Java 8. So if you enable the Java-8 update site, you cannot use TrakEM2’s 3D capabilities. The only way to do that on OS X currently is to stick with Java 6 with the Java-8 update site disabled. This is a known issue which we hope to resolve relatively soon.

Thanks for the explanation. I will give using Java 6 a try.

I uninstalled Java 8, installed Java 6, and turned off the Java-8 update site. When I load a project into Fiji, select an area_list I wish to view in the 3D viewer, and select view in 3D the viewer window opens without any errors. After clicking OK to select the default resample value, the program seems to process the area_list, but no image shows up in the 3D viewer window. This behavior is the case whether or not I have the jogamp-fat.jar and jogamp-fat-test.jar files in the extension (this was a suggestion made in some other forum to fix the viewing problem). At this point I have no idea how to get an area_list to display in the 3D viewer. Any other ideas? Thanks for your help.

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I was having the same issue with the newest release of Fiji. I found downloading the Fiji Life-Line Version, 2015 December 22 solved the issue.
Cheers, G

2 Likes

Thank you so much for your suggestion. This did the trick. Rob Lasher

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has this been resolved?

Welcome to the forum, @Jonathan_Perelmuter.

Yes, the issue discussed here was resolved long ago. If you continue to have trouble with TrakEM2, please start a new topic here describing your issue in detail, and we will try to help!

But there are still issues with 3D Viewer, TrakEM2 and Java8 correct?

Are there? I don’t know. Are you personally having problems? If so, what sort of problems?

I am having problems on a Mac running OS 10.12.6 (FIJI with Java8). Trying to load AreaLists into 3D Viewer and just getting a black screen. The lifeline version of FIJI w/Java6 doesn’t work either. It’s not urgent, as I have everything working on a PC, but wouldn’t mind getting this working on the Mac if there is a fix.

I am having the exact same issue. Get a black screen when I load a set of area lists into the 3D viewer using MAc running 10.12.6 with FIJI and java8. Specifically trying to do a 3 D view of area lists from TRAKEM2 project. Is this still a known issue? In Feb 2016 this was the case, but it is unclear to me whether this has been resolved?

@Jonathan_Perelmuter @MLNonet Sorry for the late reply. If you are still having problems, and wish to see them resolved, could you please post step-by-step instructions for reproducing the issue? Then we can investigate, or at least file an issue in the TrakEM2 GitHub repository, so the problem can be worked on when someone has time. Thanks!

I haven’t tried to see if it works since it posted in July.
I will try and see if works this afternoon and respond.

Good morning, I have the same problem in MacOS 10.14.1. When I try to visualize my stack in 3d viewer it works well. Instead when I create an area list in TrakEM2 and want to see it in 3D (with Show in 3d) it doesn’t work: a black window of 3D viewer appear and Fiji tells that it is processing the image but the processing doesn’t move on, also with little stacks.
Thank you very much!