BoneJ is a plugin for bone image analysis in ImageJ. It provides free, open source tools for trabecular geometry and whole bone shape analysis.
BoneJ 1.x is now legacy software. BoneJ2 is available to download and install from its own ImageJ update site.
Development on BoneJ started for a number of practical and ethical reasons:
If you use BoneJ in your work, please cite:
Doube M, Kłosowski MM, Arganda-Carreras I, Cordeliéres F, Dougherty RP, Jackson J, Schmid B, Hutchinson JR, Shefelbine SJ. (2010) BoneJ: free and extensible bone image analysis in ImageJ. Bone 47:1076-9. doi: 10.1016/j.bone.2010.08.023
Remember to list the version numbers of BoneJ (Help > About Plugins... > BoneJ) and ImageJ (Help > About ImageJ) because these represent defined states of the programs, which can be looked up and examined thanks to Git tagging.
The green OA author manuscript is available here.
All users are encouraged to switch to BoneJ2, available from the ImageJ2 updater.
Legacy versions of BoneJ 1.x and its documentation will remain available here for reproducibility purposes
To install BoneJ, make sure you have a recent version of ImageJ and drag this link to BoneJ_.jar onto ImageJ, or save it in your ImageJ/plugins directory and refresh ImageJ's plugins with Help->Refresh Menus.
There is one important dependency - Benjamin Schmid's 3D Viewer. Installation is the same as for BoneJ; drag the link to the .jar file onto ImageJ or save the .jar in your ImageJ/plugins directory. Make sure to run ImageJ 3D Viewer, which will prompt you to install Java's 3D libraries if you don't already have them.
BoneJ1 was downloaded 50,932 times between March 2010 and May 2020, and its final version was 1.4.3 (8 August 2018).
BoneJ plugins are designed to be called from ImageJ macros, to make them easy to run on a whole directory of images. This is an example batch macro that measures BV/TV, Tb.N, Tb.Sp and Tb.Th on a directory of cropped, binary image stacks.
dir1 = getDirectory("Choose Source Directory ");
list = getFileList(dir1);
setBatchMode(true);
for (i=0; i<list.length; i++) {
showProgress(i+1, list.length);
open(dir1+list[i]);
title = getTitle();
run("Volume Fraction", "start=1 end="+nSlices());
run("Purify");
run("Connectivity");
run("Thickness", "thickness spacing");
close();
}
The easiest way to modify this script is to record your desired sequence of menu commands with ImageJ's macro recorder (Plugins-Macros-Record), and copy-paste the new commands into the macro.
If you'd like to be kept up to date with news relating to BoneJ, please follow the BoneJ tag on forum.imagej.net
Archived user and developer messages are posted at the old Google group, which is closed to new users and messages.
BoneJ is in active development. If you'd like to help develop BoneJ or you just want to see the code, have a look at BoneJ at github. The Java source code is included in BoneJ_.jar, if you would like to see where your results come from. If you want to know the version of BoneJ you have, run Help > About Plugins > BoneJ.
If there's something that's broken:
BoneJ is intended to be transparent and free. All the new code is Copyright Michael Doube and licensed under GNU General Public License version 3. Code incorporated in BoneJ has come from several sources. Use of BoneJ implies that you accept the terms of the licenses of all the individual plugins. Terms are generally not onerous, but it's worth checking them out so you know where you stand.
| Plugin | Author | Licence |
|---|---|---|
| Fractal Count | Per Christian Henden and Jens Bache-Wiig | Public Domain |
| Skeletonize 3D Analyze Skeleton |
Ignacio Arganda-Carreras | GNU GPL |
| 3D Erode and Dilate | Benjamin Schmid | Public Domain |
| Local Thickness | Bob Dougherty | BSD Licence |
| JAMA | Joe Hicklin, Cleve Moler and Peter Webb from The MathWorks, and Ronald F. Boisvert, Bruce Miller, Roldan Pozo and Karin Remington from NIST. | Public Domain |
| 3D Object Counter | Fabrice Cordelières and Jonathan Jackson | Public Domain |
