BoneJ (ImageJ)
Author Michael Doube
Maintainer Michael Doube
Source on GitHub
Development status Active

BoneJ is a plugin for bone image analysis in ImageJ. It provides free, open source tools for trabecular geometry and whole bone shape analysis.

Experimental release

There's a new experimental, modernized BoneJ available through the ImageJ updater. It's update site is BoneJ experimental. Detailed installation instructions are available on GitHub. This software is not yet stable, but it works with the latest Fiji.


Imagej1-icon.png BoneJ was designed to work with plain ImageJ 1.x.

Fiji-icon.png BoneJ can be installed into Fiji, but you must use the Java-6 version of Fiji, not the current Java-8 version:

  • Download the final Java-6 version of Fiji labeled “2017 May 30” from here.
  • Unpack it somewhere beneath your home folder.
  • Download and install BoneJ_.jar into that installation's plugins folder.
  • Launch Fiji and run Plugins  ▶ 3D Viewer to trigger installation of the 3D Viewer.
  • Restart Fiji.

For technical details about ImageJ and Fiji using Java 6 vs. Java 8, see the Java 8 page.

BoneJ and pQCT

BoneJ and pQCT plug-ins are in the process of separation. The latter have their own update site, and they don't need BoneJ to work. However, if you download BoneJ_.jar from it still includes older versions of the pQCT tools.