A new straightforward method for semi-automated segmentation of trabecular bone from cortical bone in diverse and challenging morphologies

Abstract

Many physiological, biomechanical, evolutionary and clinical studies that explore skeletal structure and function require successful separation of trabecular from cortical compartments of a bone that has been imaged by X-ray micro-computed tomography (micro-CT) prior to analysis. Separation often involves manual subdivision of these two similarly radio-opaque compartments, which can be time-consuming and subjective. We have developed an objective, semi-automated protocol which reduces user bias and enables straightforward, user-friendly segmentation of trabecular from the cortical bone without requiring sophisticated programming expertise. This method can conveniently be used as a ‘recipe’ in commercial programmes (Avizo herein) and applied to a variety of datasets. Here, we characterize and share this recipe, and demonstrate its application to a range of murine and human bone types, including normal and osteoarthritic specimens, and bones with distinct embryonic origins and spanning a range of ages. We validate the method by testing inter-user bias during the scan preparation steps and confirm utility in the architecturally challenging analysis of growing murine epiphyses. We also report details of the recipe, so that other groups can readily re-create a similar method in open access programmes. Our aim is that this method will be adopted widely to create a reproducible and time-efficient method of segmenting trabecular and cortical bone.

3D profiling of mouse epiphyses across ages reveals new potential imaging biomarkers of early spontaneous osteoarthritis

“…This contrasts with our data showing increased cortical thickness from 8–11 to 18–20 weeks, which levelled off in both strains thereafter (Figure 3 ). These disparities may be explained by the regions analysed; Stok et al included only proximal epiphysis cortical bone (extending just past the growth plate) whilst we included cortical bone of the entire epiphysis, up to but not including growth plate bridges (Herbst et al, 2021 ).…”

“…We implemented the semi‐automated segmentation algorithm developed by Herbst et al ( 2021 ) to isolate each entire tibial epiphysis and segment from them the trabecular bone, cortical bone (including articular calcified cartilage), and marrow space into three separate non‐overlapping 3D volumes in Avizo. We sealed large foramina manually for a high‐precision segmentation, although sensitivity studies in mouse epiphyses show that foramen‐sealing does not greatly affect parameters such as trabecular BV/TV, trabecular volume/cortical volume and trabecular degree of anisotropy (Herbst et al, 2021 ). Isolated epiphyses were viewed as 2D image stacks and as a 3D model, at which point four damaged specimens were identified and discarded.…”

“…We developed an open‐access, semi‐automated method enabling segmentation of the tibial epiphysis from μCT scans, which can then isolate cortical from trabecular bone and marrow space as non‐overlapping 3D volumes for quantitative analysis (Herbst et al, 2021 ). Here, we apply our method to analyse both the entire STR/Ort epiphyses and the closely related parental CBA control strain, to identify reliable imaging biomarkers for OA.…”

A new method for segmentation and analysis of bone callus in rodent fracture models using micro‐CT

“…Other methods including our own 23 are described for semiautomated bone segmentation but have not been applied to callus. The excellent methods of Buie et al 24 and Kohler et al 25 solved many issues related to automated segmentation of cortical from trabecular bone.…”