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How To Download BoneJ?

Published Aug 29, 2025 4 min read
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The recommended and most straightforward way to download and install the latest version of BoneJ is by using the built-in update manager in Fiji, a popular distribution of the ImageJ software.

BoneJ is a powerful, open-source plugin for ImageJ designed specifically for analyzing bone image data, including trabecular geometry and whole bone shape.

Pre-installation: Get Fiji (ImageJ)

Before you can install BoneJ, you must have Fiji, a "batteries-included" distribution of ImageJ, which simplifies installation and management of plugins.

  1. Visit the Fiji website. Navigate to the official ImageJ website at imagej.net.
  2. Download Fiji. Choose the latest version of Fiji for your operating system (Windows, macOS, or Linux) and download the installer.
  3. Launch Fiji. Once the download is complete, run the installer and launch the Fiji application.

Installation: Use the Fiji update manager

The Fiji update manager automatically handles dependencies and ensures you get the correct version of BoneJ for your ImageJ installation.

  1. Open the update manager. In Fiji, go to the menu and select Help > Update....
  2. Manage update sites. In the update manager window, click the Manage update sites button.
  3. Enable BoneJ. Scroll through the list of available update sites and check the box next to BoneJ.
  4. Close and apply changes. Click Close and then click Apply changes to start the download and installation.
  5. Restart Fiji. After the downloads are complete, close and restart Fiji to finalize the installation. You should now find the BoneJ plugins under the Plugins menu.

Alternative installation methods

While the Fiji update manager is the most reliable method, there are other scenarios where you might choose a different approach.

Manual installation (Legacy BoneJ 1.x)

This method is primarily for users who need to run a specific legacy version of the software for reproducibility or compatibility reasons. The developers recommend using the update manager for the latest features and support.

  1. Download the legacy .jar file. Visit the legacy BoneJ website (bonej.org/legacy) and download the final BoneJ_.jar file.
  2. Install into the plugins folder. Save the .jar file directly into your ImageJ/plugins directory.
  3. Refresh plugins. In ImageJ, go to Help > Refresh Menus.
  4. Install the 3D Viewer dependency. Legacy BoneJ requires the 3D Viewer plugin. Install it by dragging its .jar file into ImageJ, saving it to the plugins folder, and refreshing the menus.
  5. Restart ImageJ. Close and reopen ImageJ to ensure all plugins are correctly loaded.

Command-line installation (BoneJ Headless)

For advanced users who need to automate processing of large datasets without a graphical user interface (GUI), there is a Python-based tool called BoneJ Headless. This is designed for scripting and batch processing on Linux OS.

  1. Install Fiji. Ensure you have Fiji installed and a working Python environment.
  2. Download BoneJ Headless scripts. Access the repository on GitHub (github.com/DIDSR/BoneJ_Headless) to get the necessary Python scripts.
  3. Run scripts from the command line. Use the provided scripts to call BoneJ functionalities directly from your terminal, allowing for automated, high-throughput image analysis.

Troubleshooting common installation issues

BoneJ menu items are missing after installation

  • Restart Fiji: After running the update manager, you must close and restart Fiji for the changes to take effect.
  • Check update sites: Double-check that the BoneJ update site was correctly enabled in the Manage update sites menu.
  • Check Java version: If you are trying to use a legacy version of BoneJ 1.x, you must use a compatible Java-6 version of Fiji. The modern updater method automatically handles Java compatibility.

Errors related to 3D functionality

  • Install the 3D Viewer: Legacy BoneJ requires the 3D Viewer plugin. Ensure it is installed and you have run it at least once to trigger the installation of Java's 3D libraries.
  • Run as Administrator: On some operating systems, you may need administrative permissions to install the Java 3D libraries correctly. Try running Fiji as an administrator.

Sluggish performance

  • Allocate more memory: BoneJ, particularly with large datasets, can be memory-intensive. Increase the memory available to Fiji by going to Edit > Options > Memory & Threads.
  • Use a modern computer: For very large datasets, using a machine with more RAM and a supported GPU (for BoneJ+) will significantly improve performance.
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