Converting .STL file into stack of images

Tags: #<Tag:0x00007fb87cfec450> #<Tag:0x00007fb87cfec2c0> #<Tag:0x00007fb87cfec180> #<Tag:0x00007fb87cfec040>


Sorry about this. The reason I’m delaying a bit is that I need 1 package upstream to be officially released before the fix is really permanent. I am still watching this like a hawk, and will fix it as soon as ThreeDViewer can be built using release dependencies only.


@skalarproduktraum: ^ Your hard work has impact!


Hello everyone! I’m sorry that the scenery release, which is now holding up ThreeDViewer, is taking a little longer. The reason is that there have been quite a few things to figure out for me, which took longer than expected. Among them are

  • how to publish artifacts to a Maven repository, for the same release, from different CI build workers/operating systems
  • how to get a spot on Maven central, and put the resulting artifacts there in a stable way.
    This is now (mostly) done, I’m ironing out one more bug, then there will be a release, hopefully beginning of the next week.

I’ll also do a little write-up on the distributed native CI builds, so others might also enjoy this :smiley:

cheers and sorry again for the delay!


Well worth the wait!


No need whatsoever to apologize! I meant my comment encouragingly, like: your work is used and appreciated! People anxiously await, because it has impact!

Thank you very much for sorting that out.




Dear forum,
I am very excited to get to know this method. It has been a long time since this question was posted, but I was stuck at the very first few steps I think. I installed the Fiji imageJ, and I can import the stl file in the 3D viewer. But I cannot find the voxelize mesh button after I have done the update from the update sites. I attached the process from the very beginning as the followings:

(1) Download Fiji imageJ from;
(2) check the funimage update in the Fiji and click the apply changes;

(3) And here is my content

and plugin directory (I feel different from other people…);

(4) And here is in the 3D viewer of my imagej…

Could you please help me to find out which step I need to change or other things I need to do?

Sorry I didnt read the whole thing…I tried ThreeDviewer, but does not work, will wait until it works, thank you!


Report from Windows 10 user:. Bug tracking seems under construction so reporting here. FWIW, I updated my java from 8_111 to 8_121 but it didn’t help

The associated .jar list:

Clicking ThreeDViewer | Launch produces the following exceptions:

(Fiji Is Just) ImageJ 2.0.0-rc-43/1.51j; Java 1.8.0_121 [64-bit]; Windows 10 10.0; 109MB of 24425MB (<1%)
java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: graphics/scenery/SceneryDefaultApplication
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(
	at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(
	at ij.IJ.runPlugIn(
	at ij.Executer.runCommand(
Caused by: java.util.concurrent.ExecutionException: java.lang.NoClassDefFoundError: graphics/scenery/SceneryDefaultApplication
	at java.util.concurrent.FutureTask.get(
	at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(
	... 5 more
Caused by: java.lang.NoClassDefFoundError: graphics/scenery/SceneryDefaultApplication
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(
	at Method)
	at java.lang.ClassLoader.loadClass(
	at sun.misc.Launcher$AppClassLoader.loadClass(
	at java.lang.ClassLoader.loadClass(
	at org.scijava.thread.DefaultThreadService$
	at java.util.concurrent.ThreadPoolExecutor.runWorker(
	at java.util.concurrent.ThreadPoolExecutor$
	... 1 more
Caused by: java.lang.ClassNotFoundException: graphics.scenery.SceneryDefaultApplication
	at java.lang.ClassLoader.loadClass(
	at sun.misc.Launcher$AppClassLoader.loadClass(
	at java.lang.ClassLoader.loadClass(
	... 22 more


As far as I can see, that’s essentially the same error as in the :point_up: earlier post above by @darylhyun.

And as stated above, we should be patient until @skalarproduktraum and others have solved the issues with scenery :slight_smile:


I’m acknowledging that I see these updates. Apologies for the delay, progress is being made.


I can still not launch the threedviewer. Does the bugs fixed? Im looking forward to this function.


No, not yet.

@kephale I filed a PR to update the ThreeDViewer code to use the stable release of scenery et. al: kephale/ThreeDViewer#40.

@skalarproduktraum @kephale I would like to start managing the versions of ClearVolume etc. components in the pom-scijava Bill of Materials. Could you post a list of GAVs you want to be included? Our goal should be for ThreeDViewer to declare no explicit versions of any components in its POM.


Hi @ctrueden!

Sorry for the late reply, I managed to miss the notification. Could you clarify what the benefit of putting the GAVs into pom-scijava is? Is the idea to not have nasty issues with different plugins using different versions?



Yes. The idea is to become part of the global SciJava Bill of Materials—i.e., officially be part of the SciJava component collection. :smile: Then downstream components can depend on your stuff without worrying about version numbers.



@kephale First many thanks for providing such an excellent feature. I have the same Java problem as other users when launching ThreeDViewer. Are you still working on it? Look forward to your updates.



Yes, we’re putting a ton of effort in at the moment. The official rebranding will be SciView, and although we haven’t bothered with the public-facing documentation on the Wiki yet, that information will be available here: We will be rolling out early releases by early August.



Thank you very much and look forward to the releases.