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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:
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->Update Menus.
There is one important dependency - Benjamin Schmid's 3D Viewer. Recent versions of ImageJ include this plugin, but if you don't have it 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 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.
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, open BoneJ_.jar in your favourite compression
program and look for a file called plugins.config, in which there's a line that looks like:
# Version: 1.0.5
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 |
| Fast Fourier Transform | Stephan Preibisch | GNU GPL 2 |
| 3D Erode and Dilate | Benjamin Schmid | Public Domain |
| Mines JTK | Dave Hale | Eclipse CPL |
| 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 Cordelires and Jonathan Jackson | Public Domain |
This file last modified 1705hrs 03 March 2010 © Michael Doube 2004-2010 :: Designed to be interoperable and standards-compliant. Looks best with Mozilla Firefox