Analyze 12.0

Visualization and Analysis Software for Medical Imaging

Bone Microarchitecture Analysis Add-On

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Bone Microarchitecture Analysis Add-On

The Bone Microarchitecture Analysis (BMA) module is a new add-on available for Analyze 12.0. BMA is a powerful pre-clinical research application designed for the evaluation of 3D microCT image data. The module provides researchers the ability to process single whole bone specimens and isolated 3D samples of cortical and trabecular bone tissue. It generates an extensive set of bone morphometric indices as described by Bouxsein et al.

The BMA add-on provides automatic and user-guided isolation of bone from non-bone tissue by means of threshold-based segmentation and a novel segmentation algorithm that separately identifies the cortical and trabecular bone in whole-bone specimens. The BMA add-on uses the segmented regions to automatically drive the calculation of common bone morphometric indices that provide researchers with a quantitative description of bone microarchitecture. The microarchitectural characteristics of the trabecular and cortical bone are listed below (table 1 and 2).


Table 1. Trabecular Bone Morphometric Indices

Abbreviation Description Unit
TV Total Volume mm3
BV Bone Volume mm3
BS Bone Surface mm2
BV/TV Bone Volume Fraction %
BS/TV Bone Surface Density mm2/mm3
BS/BV Specific Bone Surface mm2/mm3
Conn.D Connectivity Density 1/mm3
SMI Structure Model Index
Tb.N Trabecular Number 1/mm
Tb.Th Trabecular Thickness mm
Tb.Sp Trabecular Separation mm
Tb.Th.SD Standard Deviation of Trabecular Thickness mm
Tb.Sp/SD Standard Deviation of Trabecular Seperation mm
DA Degree of Anisotropy
MIL Mean Intercept Length

Table 2. Cortical Bone Morphometric Indices

Abbreviation Description Unit
Tt.Ar Total Cross-Sectional Area mm2
Ct.Ar Cortical Bone Area mm2
Ma.Ar Medullary Area mm2
Ct.Ar/Tt.Ar Cortical Area Fraction %
Ct.Th Average Cortical Thickness mm
Ps.Pm Periosteal perimeter mm
Ec.Pm Endocortical Perimeter mm
Iap Moment of Inertia Anteroposterior Axis mm4
Iml Moment of Inertia Mediolateral Axis mm4
Imax Maximum Moment of Inertia mm4
Imin Minimum Moment of Inertia mm4
J Polar Moment of Inertia mm4
Ct.Po Cortical Porosity %
Po.N Pore Number n
Po.V Total Pore Volume mm3
AvgPo.V Average Pore Volume mm3
Po.V.SD Standard Deviation of Pore Volume mm3
Po.Dn Pore Density 1/mm3

Bone Microarchitecture Analysis Workflow


The BMA add-on module requires that bone specimens are isovolumetric. If the image data contains multiple bones the bone of interest must be isolated and orientated into the correct anatomical orientation. All tools needed for data preprocessing are provided with Analyze 12.0.arrow-down


Cortical Bone Segmentation

Once the image data is loaded the BMA add-on will conduct a preliminary segmentation which will allow the module to identify the cortical shell, cortical pores and trabecular tissue regions.arrow-down


Trabecular Bone Segmentation

Upon user approval the add-on will now complete the segmentation process by identifying the trabecular bone in the trabecular region. Two new regions, the trabecular bone and intra-trabecular space will be derived.arrow-down


Calculate Bone Morphometric Indices

Measurements are automatically calculated for the trabecular and cortical bone and output in several comma-separated value (.csv) files. A utility is also provided to convert CT numbers (HUs) to Bone Mineral Density (BMD) in units of mg/CC.


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All the tools you need to evaluate microCT bone data in one package.

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