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BoneJ is a collection of Fiji/ImageJ plug-ins for skeletal biology. It provides free, open source tools for trabecular geometry and whole bone shape analysis. This repository hosts the modern incarnation of BoneJ in development. If you use BoneJ in your work please cite:

Domander R, Felder AA, Doube M. 2021 BoneJ2 - refactoring established research software. Wellcome Open Res. 6. doi:10.12688/wellcomeopenres.16619.1


For legacy ImageJ1 plug-ins, which are no longer maintained, please visit


The code is in two main modules: Legacy and Modern. The code in Legacy is originally from BoneJ1, but it has been refactored to manage its dependencies via Maven. Unlike BoneJ1, the plug-ins in Legacy work with Java 8 and the latest version of Fiji. However some of them still depend on 3D_Viewer, which is known to have issues with the latest versions of MacOS (see the forum).

The main development happens in the Modern module. It hosts the modernized versions of BoneJ plug-ins, which fully comply with the current ImageJ API. Our goal is that as code matures, Modern hosts only "thin" wrapper plug-ins. They should be responsible only for interacting with the user, and collecting and displaying results. The wrappers call algorithms from the Ops framework, specialised algorithms from BoneJ's own Ops, and utility code from imagej-common, scifio and other such core libraries.

Contributing to BoneJ

If you'd like to improve the code in BoneJ or add new features, we'd greatly appreciate it! To get started have a look at the contribution guidelines. The wiki and forum are good places to find info on how to develop ImageJ based software.