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331 protocols using nrecon software

1

Maxillary Bone Microstructure Analysis

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All maxillary samples of the sheep were covered with Parafilm and scanned using Skyscan 1176 microtomography scanner (Bruker, Kontich, Belgium). MicroCT scanning was performed at a resolution of 18 µm with the following parameters: 90 kV, 278 µA, 0.5-mm aluminum filter, and 360-degree rotation range. All acquired images were reconstructed by using NRecon software (version 1.6.10.4; Bruker) with a Gaussian smoothing of 3, beam hardening correction of 40%, and ring artefact reduction of 12. DataViewer (version 1.5.2.4 64-bit; Bruker) was used to reorient the direction of the reconstructed images to the sagittal plane. Subsequently, all images were imported into CTAn software (version 1.15.4.0+; Bruker) for bone microstructural analysis.
The furcation areas enclosed by the buccal and lingual roots of premolars were defined as the region of interest (ROI) (Figure 1A). After selection of the ROIs, the automatic (Otsu method) threshold was applied for all images during the analysis. The bone microstructure parameters are presented in Table 1. Since the left and right sides were pooled together, the total number of samples was 36 and every group contained 6 samples taken after 4 and 12 weeks of retention.
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Micro-CT Analysis of Skull Bone Grafts

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The harvested specimens were scanned (SKYSCAN 1173, Bruker, Kontich, Belgium) using the following scanning parameters: voltage, 130 kV; current, 60 μA; pixel size, 13.85 μm; exposure, 500 ms; and frame averaging, 4. The acquired data were reconstructed using the NRecon software (version 1.7.0.4, Bruker). The grayscale threshold values for the bone blocks ranged from 50 and 70. Volumes of interest (VOIs) were determined along the outline of the block substitute materials on the outer surface of the skull. Newly formed bone along the lateral surface of each block was excluded from the VOIs for evaluation of the bone-block volume stability.
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High-Resolution Micro-CT Imaging of Rodents

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A Bruker Skyscan 1276 was used to acquire a series of images with a rotation step of 0.65° over a 360° rotation. Images were acquired with x-ray tube settings of 100 kV, 200 µA, and an exposure time of 90 ms with a 0.5-mm aluminum beam filter. A 4 × 4 detector binning was used for an isotropic resolution of 40.16 µm. Anesthesia was induced at 3% isoflurane and maintained at 2.0 to 2.5% during imaging, which lasted 76 s. Image reconstruction was performed using the Bruker NRecon software.
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Microarchitectural Analysis of Dental Restorations

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The µ-CT scanning was performed for all samples using an 1172 µ-CT scanner (SkyScan, Bruker, Belgium). The scanning settings were applied: 100 kV accelerating voltage, a 100 uA beam current, Al and Cu filters, pixel size of 6.7 µm, and flat field correction. The scans were reconstructed in 3D using NRecon software (Bruker), then reoriented in Data-Viewer (Bruker) to obtain 3D images of the restorations with a standardized Region of Interest (ROI) of 1460.6, 1460.6, and 3819 µm in XYZ planes. The generated standard-sized 3D images of the restorations were analyzed in CTAn software (SkyScan, Belgium) to measure the percent total porosity and the number and volume of closed pores. The analyzed 3D images were viewed on CTVol software (SkyScan, Belgium), after which 3D models were generated.
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Micro-CT Analysis of Chemobrionic Composite

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µ-CT was performed using a Skyscan1172 µ‐CT instrument (Bruker, USA). A section of chemobrionic composite was scanned with operating parameters of 80 kV source voltage, 100 µA current, 600 ms exposure time, 4 µm pixel size, rotation step of 0.1° and frame averaging of 20. The acquired slice data was reconstructed using NRecon software (Bruker, USA) and visualised using CTVox software (Bruker, USA).
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Micro-CT Analysis of Implanted Scaffolds

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Pre and post implanted scaffolds were wrapped in a transparent plastic film and mounted for scanning using submicron resolution μCT (Skyscan 1176, Skyscan, Belgium) and scan was performed with the settings: 45 kV X-ray voltage, 0.2 mm aluminium filter, source current 556 μA, 0.5° rotation step, exposure time of 180 ms for each section. Three-dimensional (3D) models were reconstructed using Skyscan NRecon software (Bruker micro-CT, Belgium) and reconstructed dataset was processed after segmentation and binarisation to analyse pore size, pore thickness, porosity % by CTAn software (Bruker micro-CT, Belgium), angiogenesis by CTVol software (Bruker micro-CT, Belgium) and volume degradation by Drishti software (ANU, Australia).
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Micro-CT Analysis of Collagen Scaffolds

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The collagen scaffolds (n = 20) were micro-CT scanned using a SkyScan 1272 desktop ex vivo device (Bruker micro-CT, Kontich, Belgium) with the following parameters: pixel size 4 μm, source voltage 60 kV, source current 166 μA, no filter, rotation step = 0.2°, frame averaging (2), rotation 180°, scanning time approximately 1 h. The same specimens were scanned once more following exposure to the relevant medium (SBF, PBS, blood plasma) and re-lyophilized. The total number of scanned specimens was 40. The specimens were mounted on specimen holders and scanned in the dry state in air. Projection images were reconstructed using NRecon software (v.2.8.0., Bruker, Kontich, Belgium). Visualizations were acquired using a DataViewer (v.1.5.2.4, Bruker, Kontich, Belgium) and a CTVox (v.1.5, Bruker, Kontich, Belgium). The volume of interest (VOI) was set inside the specimen so as to exclude those superficial parts which may have been altered via the handling of the specimens. The dimensions of the VOI were the same in all the specimens. The image processing (noise reduction, filtration, and despeckle operations) and binarization were conducted in CTAn software (v.1.18, Bruker, Kontich, Belgium) and optimized using TeiGen software [28 (link)]. The structure analysis was performed using 3D analysis in CTAn. The pore size evaluation was performed using a sphere-fitting algorithm.
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8

Microstructural Analysis of Mandible and Femur

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Microtomography (micro-CT) of the mandibles and femurs was performed using a SkyScan Model 1174 Microtome (Bruker), set at 50 Kv and 800 mA, image resolution of 1024 × 1024 × 1024 pixels (10.2 µm pixel size for the mandible and 20.4 µm for the femur). The pixel dimensions were used to scan the alveolar bone support region (interradicular septum) of the lower molars in the mandible and the proximal femoral epiphysis. To perform the morphometric analysis of structures of interest, the scanned images were imported into NRecon software (Bruker) for image reconstruction greyscale pattern. To obtain morphometric parameters, the software CT Analyzer (Bruker, Belgium) was used to perform the morphometric analysis. The parameters evaluated were bone surface (BS-mm 2 ), bone volume (BV-mm 3 ), trabecular thickness (Tb.Th-mm), trabecular number (Tb.N-1/mm), trabecular separation (mm), connectivity density (Conn.Dn-1/mm 3 ), bone surface density (BS/TV-1/mm) and total porosity (Po(tot) -%).
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9

High-Resolution μCT Analysis of Murine Tooth Morphology

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The mandibles of Mmp13−/− and WT mice were fixed in 70% ethanol and prepared for high-resolution µCT (SkyScan 1172, Bruker, Kontich, Belgium) of incisor and first molar teeth. A three-dimensional analysis was carried out to determine total volume, enamel volume, dentin volume, pulp volume, and total mineral density (TMD). The samples were scanned using a 10-MP digital detector, 10W of energy (70 kV and 142 mA), and a pixel size of 7.5microns, exposure 850 ms/frame rotation step 0.3° with ×10 frame averaging, 0.5 mm aluminum filter, and scan rotation of 180°. After scanning, the radiographs were reconstructed using NRecon software (version 1.7.3.0; Bruker). Reconstruction was conducted with NRecon using GPU acceleration. Gaussian smoothing was applied with a 2-voxel radius, ring artifact and beam hardening corrections were applied in reconstruction. Ring artefact reduction set to 7 pixels. Beam hardening correction was set to 40%. CTAn software (CTAn Micro-CT software, Bruker) was used to generate 2-D images for color density and 3-D images for CT volume.
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10

Micro-CT analysis of femoral bone microstructure

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Femur samples collected after sacrifice were fastened in 10% neutral buffered formalin (NBF) and rinsed with running water for 24 h. The femoral head was scanned by micro-CT referring to the protocol of a previous study [41 (link)] (SkyScan1176; Bruker Corporation; Kontich, Antwerpen, Belgium). Bone microstructural parameters such as BMD, bone volume/total volume (BV/TV), and trabecular separation (Tb.Sp) were also analyzed using NRecon software (Bruker Corporation).
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