BoneJ
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:
- Our images are big (several gigabytes). Other software crashed when we tried to load more than 600MB.
- Other software failed to open even our small images. ImageJ opens a huge range of image formats.
- Some things we wanted to do were not implemented in other software.
- Or when they were implemented, code could not be examined. We didn't want a black box sitting in the middle of our experiments. BoneJ is open source (the source is in the .jar), so you can see where your results come from.
- Some useful things had become available for ImageJ, like the Local Thickness plugin.
- Licences are expensive, especially when compared to the cost of a postdoc's time.
- Java is 32- and 64-bit, multithreaded and runs on lots of OS's (Linux, Mac OS X, Windows, Solaris). Where there is Java, ImageJ and BoneJ can run.
- Our project is funded by the BBSRC, which means British taxpayers pay for much of (but not all of) BoneJ. So, in the spirit of public openness, BoneJ is available to all our funders.
Install BoneJ
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. Please install the 31.03.2010 version only. 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 623 times since March 2010, and is now version 1.1.10 (29 July 2010).
For Trabeculae
- Analyse Skeleton
- Classify, count and measure skeleton branches and junctions. Based on Ignacio Arganda Carreras' AnalyzeSkeleton_.
- Anisotropy
- Use the mean intercept length (MIL) method to determine degree of anisotropy.
- Connectivity
- Calculates the Euler characteristic of an image, and works out the connectivity density (Conn.D), which can be interpreted as trabecular number per mm3.
- Fractal Count
- Uses the box counting method to calculate fractal dimension.
- Plateness
- Fits star volumes to the structure using a skeleton as starting points. An experimental replacement for the structure model index (SMI).
- Isosurface
- Creates and optionally displays a 3D surface mesh and measures the surface area, to calculate bone surface (BS).
- Purify
- Prepares an image for connectivity analysis.
- Skeletonise 3D
- Find the skeleton of a structure using a topology-maintaining medial axis thinning algorithm implemented by Ignacio Arganda Carreras.
- Structure Model Index
- Calculates the structure model index (SMI), a measure of how rod- or plate-like trabeculae are. The user can choose between mesh-based (Hildebrand & Rüegsegger method, preferred) and voxel-based (SkyScan) structure dilation.
- Optimise Threshold
- Uses a histogram from whole stack (rather than the current slice) to autothreshold, and optionally attempts to choose a threshold that minimises connectivity.
- Thickness
- Calculates the thickness of foreground and background to give trabecular thickness (Tb.Th) and separation (Tb.Sp). Based on Bob Dougherty's Local Thickness plugin.
- Volume Fraction
- Determines the proportion of the image volume that is foreground (BV/TV).
For Whole Bones
- Fit Ellipsoid
- Finds the best-fitting ellipsoid from a set of point ROI's in the ROI Manager.
- Fit Sphere
- Finds the best-fitting sphere from a set of point ROI's in the ROI Manager.
- Moments 3D
- Calculates the moments of inertia of a structure, such as a whole bone.
- Neck Shaft Angle
- Works out the neck-shaft angle and curvature of the femur.
- Slice Geometry
- Calculates cross-sectional parameters such as second moment of area and section modulus.
For Particles
- Particle Analyser
- Finds and measures particles in a 3D binary image stack. Draws interactive 3D graphical output. Installs under Plugins->Analyze->Particle Analyser. Particle Analyser is an experimental branch of the 3D Object Counter, which is being maintained at Fiji and on the Wiki.
Running in Batch Mode
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.
Email List
If you'd like to be kept up to date with news relating to BoneJ, please write me an email, and I'll add you to the list. Your email address will be kept confidential, and you can request to be taken off the list at any time.
Changes
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.
Debugging and Feature Requests
If there's something that's broken:
- Make sure you have the latest BoneJ_.jar
- Make sure your Java and ImageJ installations are up to date
- Ensure you are using ImageJ 3D Viewer version 31.03.2010, and that you have run the 3D Viewer to install Java's 3D libraries
- Read the BoneJ User Guide
- Use the power of Google, or other search engine
- Then, write me an email describing what you're trying to do and what actually happened. Attach any error or exception messages to your email.
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.
Licences and Authorship
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 Cordelires and Jonathan Jackson | Public Domain |
