Iso-surface not working?

Tags: #<Tag:0x00007fb87c4ca888> #<Tag:0x00007fb87c4ca720> #<Tag:0x00007fb87c4ca590>


I have an 8 bit binary stack & click Plugins > BoneJ > Isosurface

But nothing happens?

I’m using the latest versions of bothe ImageJ & BoneJ.

Is there something obvious I’m missing?


See the FAQ - it’s usually an installation issue and lately relates to a version collision between BoneJ1, ImageJ2, Java1.8, and 3D stuff. Check out Curtis’ advice here:


@mdoube @rimadoma And as of Tuesday, there is now an fully up-to-date Java-6 version of Fiji downloadable from here. Has anyone tested this package with BoneJ yet? It would be nice to know that all is working properly there.


I tested the previous lifeline version last Wednesday on Windows, and BoneJ1 worked out of the box.


The 2017-05-30 ‘all platforms’ version of Fiji works with BoneJ1 for me on Ubuntu - only quick and cursory testing done (Isosurface, which uses 3D libraries, works).


  • Downloaded all platforms zip file
  • Extracted to new directory
  • Double clicked on fiji-linux64
  • Allowed the updater to run (lots of things get removed, ij updates to 1.51)
  • Closed and restarted fiji-linux64
  • Drag 'n dropped BoneJ_.jar from onto Fiji
  • Restarted Fiji again
  • Opened a greyscale stack, converted to 8-bit, ran Plugins>BoneJ>Isosurface

Isosurface runs and makes a 3D rendering of the image in a 3D viewer window, and calculates the surface area which is logged in the Results table.


Thanks for testing, guys! :smile:

The things being removed all moved to the Fiji-Legacy update site.

The update is from 1.51h to 1.51n. This upgrade is actually a little problematic, because the 1.51n version of ImageJ 1.x is “too new” for the final Java-6 version of ij1-patcher to fully cope with (you’ll see a big stack trace relating to YesNoCancelDialog and how code couldn’t be patched). So I’d suggest not upgrading, actually. But it is not a huge deal, since things will largely still work either way.


Thanks it was a Java 3D thing.

Although I’m still having issues visualising in ImageJ (the 3d viewer window opens but remains empty), its exporting the iso-surfaces as STLs which is what I’m after at the end of the day.