Skyscan ct analyzer ctan software

Microarchitecture of the cortical and cancellous compartments of the tibia was quantified by μCT using the SkyScan 1272 system (Bruker). For cancellous bone morphology, the proximal tibia was scanned at 3.5 μm resolution. A 400 μm region of interest was 3D reconstructed with a 450 μm offset from the proximal growth plate. This region was auto-contoured using SkyScan CT Analyzer (CTAn) Software (Bruker) to select for the cancellous region. Cancellous parameters such as Bone Volume (BV, mm³), Tissue Volume (TV, mm³), percent Bone Volume (BV/TV, %), Trabecular Spacing (Tb.Sp, mm), Trabecular Thickness (Tb.Th, mm), and Trabecular Number (Tb.N, 1/mm) were quantified following standard μCT guidelines (Bouxsein et al., 2010 (link)). For the analysis of cortical bone microstructure, the tibia was scanned at 12 μm resolution. A 300 μm region that was 200 μm proximal to the tibio-fibular junction (TFJ) was auto-contoured to analyze cortical bone parameters such as Marrow Area (Ma.Ar, mm²), Cortical Area (Ct.Ar, mm²), Endocortical Perimeter (Ec.Pm, mm), Periosteal Perimeter (Ps.Pm, mm), and Cortical Thickness (Ct.Th, mm).

Images of the femurs were acquired by micro-CT using a Bruker Skyscan 1176 (Bruker, Kontich, Belgium) (X-ray voltage = 50 kV, X-ray current = 200 µA, filter = 0.5 mm aluminum, resolution = 9 µm, rotation step = 1°). For reconstruction of trabecular and cortical femurs, the region commenced ~0.215 mm and 1.935 mm from the growth plate in the direction of the metaphysis and was extended by 1.29 mm and 0.43 mm, respectively. Structural indices were determined by Bruker’s Skyscan CT Analyzer (CTan) software. The calculated trabecular and cortical parameters are presented in Fig. 3. Three-dimensional models were created using CT-volume.
In fractured femurs, the region of interest was defined as the periosteal callus between both inner pin holes. The BV/TV was determined using a global threshold of 642 mgHA·cm^–2 as described previously^{70 (link)}.

MicroCT (μCT) scanning was performed to measure morphological indices of metaphyseal regions of femurs. Bone samples were rotated around their long axes and images were acquired using Bruker Skyscan 1172 (Kontich, Belgium) with the following parameters: pixel size = 6 μm3; peak tube potential = 59 kV; X-ray intensity = 167 μA; 0.4° rotation step. Raw images were reconstructed by the SkyScan reconstruction software (NRecon) to 3-dimensional cross-sectional image data sets using a 3-dimensional cone beam algorithm. Structural indices were calculated on reconstructed images using the Skyscan CT Analyzer (CTAn) software (Bruker). Cortical and trabecular bone were separated using a custom processing algorithm in CTAn, based on the different thicknesses of the structures. Cortical bone was analysed by a region of 150 slices, starting 9 mm distal to the metaphysis. Cortical parameters included BMD and cortical thickness (Ct.Th). Trabecular bone was analysed in the proximal metaphysis region starting just distal to the metaphysis and continued distally for 200 slices. Trabecular parameters included BMD, bone volume fraction (BV/TV), number (Tb.N), thickness (Tb.Th), separation (Tb.Sp) and Fractal dimension.