More problems with TrakEM2 (3D showing)

so I’m still trying to make this work and I’ve managed to paint all the layers of a cell after aligning a decent chunk of images, but when I try to show it in 3D the PC thinks for a few minutes and then pops this error:

‘’’
Mesh generation failed for “test_slices/dendrites/[area_list #51] #51” from area_list #51 [area_list]

ERROR:
java.lang.OutOfMemoryError: Java heap space
at org.scijava.java3d.utils.geometry.NormalGenerator.createHardEdges(NormalGenerator.java:205)
at org.scijava.java3d.utils.geometry.NormalGenerator.generateNormals(NormalGenerator.java:816)
at customnode.CustomTriangleMesh.createGeometry(CustomTriangleMesh.java:142)
at customnode.CustomMesh.update(CustomMesh.java:95)
at customnode.CustomMesh.(CustomMesh.java:78)
at customnode.CustomTriangleMesh.(CustomTriangleMesh.java:55)
at ini.trakem2.display.Display3D$8.call(Display3D.java:895)
at ini.trakem2.display.Display3D$8.call(Display3D.java:772)
at ini.trakem2.display.Display3D$6$2.call(Display3D.java:509)
at ini.trakem2.display.Display3D$6$2.call(Display3D.java:504)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
‘’’

anyone knows a solution?

also I had the “resample” option set at 12, because it ame by default but I haven’t found it’s purpose, so that might be the problem.

Thanks for your time

PD: after some more research, I’ve found it is an allocable RAM problem, and that I should just enter a commang to allow more RAM to be used, but I can’t find how to access the command console for Java (or does it use the main PC console?)

PD2, electric boogaloo: I managed to find it and increased the Heap Space too 2Gb, and now I only get one error message:
‘’’
Mesh generation failed for “test_slices/dendrites/[area_list #51] #51” from area_list #51 [area_list]

ERROR:
java.lang.OutOfMemoryError: Java heap space
‘’’

I don’t know if this is good or bad

1 Like

Hi @meperegri,

Sorry for not catching this post earlier.

Quick follow up question:
How big is your stack? I.e. how big is each 2d image and how many z-section are there?

This could be it, but I’ll have to dig a little to look into it…

John

Sorry about the wait, @bogovicj, I can only get to this computer on weekdays.

the stack is 13 5MB (2560x2048 pixels) images in TIF format.

Problem solved: I just had to use the Java6 version, with Java8 the 3D viewer does not work, it seems.