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

TVTotal Volumemm3
BVBone Volumemm3
BSBone Surfacemm2
BV/TVBone Volume Fraction%
BS/TVBone Surface Densitymm2/mm3
BS/BVSpecific Bone Surfacemm2/mm3
Conn.DConnectivity Density1/mm3
SMIStructure Model Index
Tb.NTrabecular Number1/mm
Tb.ThTrabecular Thicknessmm
Tb.SpTrabecular Separationmm
Tb.Th.SDStandard Deviation of Trabecular Thicknessmm
Tb.Sp/SDStandard Deviation of Trabecular Seperationmm
DADegree of Anisotropy
MILMean Intercept Length

Table 2. Cortical Bone Morphometric Indices

Tt.ArTotal Cross-Sectional Areamm2
Ct.ArCortical Bone Areamm2
Ma.ArMedullary Areamm2
Ct.Ar/Tt.ArCortical Area Fraction%
Ct.ThAverage Cortical Thicknessmm
Ps.PmPeriosteal perimetermm
Ec.PmEndocortical Perimetermm
IapMoment of Inertia Anteroposterior Axismm4
ImlMoment of Inertia Mediolateral Axismm4
ImaxMaximum Moment of Inertiamm4
IminMinimum Moment of Inertiamm4
JPolar Moment of Inertiamm4
Ct.PoCortical Porosity%
Po.NPore Numbern
Po.VTotal Pore Volumemm3
AvgPo.VAverage Pore Volumemm3
Po.V.SDStandard Deviation of Pore Volumemm3
Po.DnPore Density1/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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