According to previous studies [23 (link)–25 (link)]. the ankle joints were fixed with 4% PFA for 48 h and subsequently scanned using SkyScan1276 Micro-CT (Bruker, Kontich, Belgium) with the following parameters: Source Voltage of 70 kV, Source Current of 200 µA, Exposure time of 388ms, and no 360-degree rotation. Three-dimensional (3D) reconstruction of the two-dimensional joint scan images was performed using Recon software (Bruker, Kontich, Belgium). A cuboid area in the right calcaneus (size: 2.0268 × 1.0134 × 1.0134 mm3) was selected as the Region of Interest (ROI) for analyzing trabecular bone changes. The percent bone volume (BV/TV), bone mineral density (BMD), trabecular number (Tb.N), Trabecular thickness (Tb.Th), Trabecular separation (Tb.Sp), and Trabecular pattern factor (Tb.Pf) were measured using CTAn software (Bruker, Kontich, Belgium). Each parameter was measured at least three times.
Recon software
Manufactured by Bruker
Sourced in Belgium
Recon software is a data processing and analysis tool developed by Bruker. It is designed to handle and interpret data generated by Bruker's analytical instruments. The software's core function is to provide users with the necessary tools to process, visualize, and analyze their experimental data.
Automatically generated - may contain errors
5 protocols using recon software
1
Micro-CT Analysis of Ankle Joint Trabecular Bone
2
Micro-CT Analysis of Enamel Mineral Density
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Three hemi-mandibles from 2- to 3-month-old heterozygous and homozygous Enamp.S55I mutant and wild-type mice were dissected and fixed as described for scanning electron microscopy followed by mounting in sealed polypropylene micro tubes (to prevent drying out) together with hydroxyapatite standards. Micro X-ray computed tomography was carried out using a Skyscan 1172 CT scanner (Bruker, Kontich, Belgium). Scans were obtained using a tube voltage of 75 kV at a constant power of 10 W. Image pixel resolution was 8–10 µm and a 0.5 mm aluminium filter was used to reduce beam hardening. The scanner was used in oversize scan mode which allowed hydroxyapatite standards to be imaged along with each individual sample for mineral density calibration purposes. The standards used had relative densities of 0.25, 0.75 (Bruker, Kontich, Belgium) and 2.9 (Himed, Old Bethpage, USA). Projection images were reconstructed using Recon software (Bruker, Kontich, Belgium). Quantitative mineral density maps were generated using ImageJ software (http://imagej.nih.gov/ij/ ) and 3D rendered videos produced using CTVox software (Bruker, Kontich, Belgium).
The exfoliated human AI tooth and a corresponding healthy control tooth along were scanned as described above except the tube voltage was increased to 100kV and the aluminium and copper filter were engaged to reduce beam hardening.
The exfoliated human AI tooth and a corresponding healthy control tooth along were scanned as described above except the tube voltage was increased to 100kV and the aluminium and copper filter were engaged to reduce beam hardening.
3
Geometric Morphometric Analysis of Bone
4
Micro-CT Analysis of Bone Regeneration
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Rats undergoing limb muscle punch surgery were anesthetized by 1% pentobarbital (3 mL kg−1) at 5 weeks after operations, which were tested by X-ray. They were then sacrificed to obtain limb samples containing implanted scaffolds. After being fixed with 4% paraformaldehyde, the samples were tested by a micro-CT imaging system (SkyScan 1276 system, Bruker, Germany) under a source voltage of 45 kV, a current of 200 μA, and an aluminum filter of 0.25 mm with an image pixel size of 6.5 μm. NRecon software (Bruker, USA) was used to reconstruct the scanned images. DataViewer (Bruker, USA) and CTAn software (Bruker, USA) were used to analyze the newly formed bone volume (BV).
Rats undergoing surgery for critical calvarial defects were sacrificed at 8 weeks to obtain calvarial samples containing defects. The samples were fixed with 4% paraformaldehyde and then examined by a micro-CT imaging system (SkyScan 1276 system, Bruker, Germany) under a source voltage of 45 kV, a current of 200 μA, and an aluminum filter of 0.25 mm with an image pixel size of 6.5 μm. The raw data were reconstructed by Recon software (Bruker, USA). The parameters reflecting bone regeneration were analyzed by DataViewer (Bruker, USA) and CTAn software (Bruker, USA), which included the newly formed BV, BV/tissue volume (BV/TV), trabecular number (Tb. N), and trabecular spacing (Tb.Sp).
Rats undergoing surgery for critical calvarial defects were sacrificed at 8 weeks to obtain calvarial samples containing defects. The samples were fixed with 4% paraformaldehyde and then examined by a micro-CT imaging system (SkyScan 1276 system, Bruker, Germany) under a source voltage of 45 kV, a current of 200 μA, and an aluminum filter of 0.25 mm with an image pixel size of 6.5 μm. The raw data were reconstructed by Recon software (Bruker, USA). The parameters reflecting bone regeneration were analyzed by DataViewer (Bruker, USA) and CTAn software (Bruker, USA), which included the newly formed BV, BV/tissue volume (BV/TV), trabecular number (Tb. N), and trabecular spacing (Tb.Sp).
5
Micro-CT-Based Craniofacial Morphometrics
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Reconstruction of microCT data was performed using Bruker Recon software. Hemimandible, pre-maxilla, maxilla, palatine and occipital bones were segmented and landmarks were placed using Amira software (Ho et al., 2015 (link); Welsh et al., 2018 (link)). x-y-z coordinates were imported into the R Geomorph package that was used to calculate Procrustes distances, calculate inter-landmark absolute distances and perform ANOVA statistics to determine significance. For boxplots representing inter-landmark distance measurements, a significant reduction in size of the mutant mandibles is labeled as a percentage of the wild-type mandible. Hotelling tests were performed using Procrustes transformed data, and the hotelling.test function in R. Plotting was performed in R. Numbers of embryos analyzed is indicated in the figure legends.
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