Pattern Recognition 41 (2008) 2358 – 2368 www.elsevier.com/locate/pr A constrained region growing approach based on watershed for the segmentation of low contrast structures in bone micro-CT images Z. Peter a , b, c , d , ∗ , V. Bousson e , f , C. Bergot e , g , F. Peyrin a , b, c , d a CNRS, UMR 5220, F-69621, Villeurbanne, France b Inserm, U630, F-69621, Villeurbanne, France c INSA-Lyon, laboratoire CREATIS-LRMN, F-69621, Villeurbanne, France d ESRF, BP 220, F-38043, Grenoble, France e Université Paris 7 Denis Diderot, UFR de Médecine, UMR CNRS 7052, F-75010 Paris, France f Service de Radiologie Ostéo-Articulaire, H ˆ opital Lariboisière, Paris, France g Service de Radiologie, H ˆ opital Saint Louis, F-75010 Paris, France Received 15 March 2007; received in revised form 23 November 2007; accepted 21 December 2007 Abstract Quantitative synchrotron micro-CT makes it possible to visualize remodeling zones having different mineral concentrations within bone tissue. However, so far their segmentation has only been performed by simple thresholding which is insufficient due to noise and weak contrast. In this paper, we propose a new customized region growing approach to segment each remodeling zone taking into account some biological prior.A constrained region growing strategy based on distance map and watershed is developed to control the shape of the detected regions. The statistical analysis of the results on synthetic noisy images and the application to experimental micro-CT data show the efficiency of the method.  2008 Elsevier Ltd. All rights reserved. Keywords: Image segmentation; Anisotropic diffusion; Bones; X-ray tomography 1. Introduction New techniques providing three-dimensional (3D) images of biological tissues are being developed. Among these, 3D micro- tomography (micro-CT) which is a version of X-ray comput- erized tomography (CT) at the micrometer scale encounters a definite success [1]. A number of micro-CT systems are now commercialized and may provide images of various materials at spatial resolution up to a few micrometers. The development of this technique has mainly been motivated by research on bone tissue [2]. At the microscopic level, trabecular bone constituted of small struts (around 100 m) called trabeculae is surrounded by cortical bone. The microscopic architecture of bones could not be resolved by clinical CT due to insufficient spatial ∗ Corresponding author at: ESRF, BP 220, F-38043 Grenoble, France. Tel.: +33 4 38 88 19 63; fax: +33 4 76 88 22 52. E-mail address: zpeter@esrf.fr (Z. Peter). 0031-3203/$30.00  2008 Elsevier Ltd. All rights reserved. doi:10.1016/j.patcog.2007.12.011 resolution and was rather investigated by 2D histology. Micro- CT offers several advantages as compared to histology since it is non-destructive and may provide 3D information. Three- dimensional morphometric parameters of trabecular bone micro-architecture are typically calculated after segmenting bone from background [1]. However, densitometric informa- tion within the bone phase is generally not available due to beam hardening and limited signal to noise ratio when using standard X-ray sources. Coupling micro-CT to synchrotron sources allows overcom- ing these limitations and provides quantitative images with high signal to noise ratio [3]. This capability is mainly related to the use of high fluxes monochromatic X-ray beams. In pre- vious works, we proved that synchrotron micro-CT enabled to estimate the mean mineral concentration in bone tissue, also called the degree of mineralization of bone. The accuracy of the system was evaluated by using solutions mimicking hydroxya- patite, the main component of bone, at different known concen- trations [4]. The method was applied to analyze the effect of a