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Michael Doube: BoneJ: a collection of ImageJ plugins for bone image analysis


Bones are commonly imaged in computed tomographic (CT) and X-ray microtomographic (µCT) systems for research purposes, such as investigating trabecular and cortical changes in osteoporosis and non-destructive examination of fossil skeletons. We had hundreds of CT and µCT scans of whole bones and trabecular bone cubes to analyse for studies on allometric bone scaling. Many of our scans were over 1 GB, but available software crashed when processing small (~ 60 MB) datasets, required a per-machine licence fee, or didn't implement our required features. We needed to pre-process and analyse scans on several different computers, remote from scanning hardware. We took advantage of the existing functionality and flexible plugin architecture of ImageJ and implemented standard bone measurements as a new plugin, BoneJ (, to make full use of our computer hardware. We first incorporated well-defined parameters commonly measured by the bone research community, using definitions in primary references, standardised nomenclature, and pre-existing code. Model-independent methods were preferred over techniques that make assumptions of underlying geometry. Stereological techniques that assume rod- or plate-like trabecular structure were avoided where a good alternative existed. For trabeculae, three-dimensional methods were used exclusively. Cross-sectional diaphyseal parameters such as second moment of area and section modulus were calculated directly from pixel positions without assuming circular or ellipsoidal geometry. Where possible, users were given the choice between surface-mesh based methods and voxel-based methods. BoneJ is open source and free for anyone to download, use, modify and distribute, and we hope it grows to incorporate new developments in bone morphometry.


bone, trabeculae, tomography, foam, particle

Administrative data

Presenting author: Michael Doube
Organisation: Department of Bioengineering, Imperial College London

co-authors: Michał M Kłosowski, Ignacio Arganda Carreras, Fabrice Cordelires, Robert P Dougherty, Jonathan Jackson, Benjamin Schmid, John R Hutchinson, Sandra J Shefelbine

Type: Poster (portrait)

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