ArticleRoyal Society open science2021
A new straightforward method for semi-automated segmentation of trabecular bone from cortical bone in diverse and challenging morphologies.
Article in Royal Society open science, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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8 citing papers in PubMed, 15 citations in OpenAlex.
- In Situ Profiling of Nanoscale Strains Uncovers Mechano-Architectural Predictors of Aging and Osteoarthritis Emergence.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Diets Differently Affect Bone Health: Murine Models.International journal of molecular sciences · 2026Article
- Micro-CT-based analysis of the murine osteochondral unit: a review and recommendations for standardized subchondral bone assessment.JBMR plus · 2026Review
- Age-related bone loss in mouse lumbar vertebrae is affected by region, sex, and level: Implications for spinal loading and analysis methods.Bone reports · 2025Article
- Segmentation of cortical bone, trabecular bone, and medullary pores from micro-CT images using 2D and 3D deep learning models.Anatomical record (Hoboken, N.J. : 2007) · 2025Article
- Absence of E2f1 Negates Pro-osteogenic Impacts of p21 Absence.Calcified tissue international · 2024Article
- A new method for segmentation and analysis of bone callus in rodent fracture models using micro-CT.Journal of orthopaedic research : official publication of the Orthopaedic Research Society · 2023Article
- 3D profiling of mouse epiphyses across ages reveals new potential imaging biomarkers of early spontaneous osteoarthritis.Journal of anatomy · 2023Article
Corrections and comments
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Authors and funding
6 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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