bonej.org .
BoneJ is a plugin for bone image analysis in ImageJ. It provides free, open source tools for trabecular geometry and whole bone shape analysis.
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, Cordelières 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
The author manuscript is available here.
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.
BoneJ has been downloaded 4414 times by 2665 unique hosts since March 2010, and is now version 1.3.6 (29 April 2012).
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 sign up for the Google group here:
Subscribe to the BoneJ Users and Developers Google group
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:
If there's something that you think BoneJ could do, but doesn't, please write me an email describing your study's objectives, your images and the data you want to get, and I might be able to help you out.
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 |
