At 3 and 6mpf zebrafish were euthanized and fixed in 3.7% formaldehyde (Sigma-Aldrich) in PBS overnight. Length, weight and sex were recorded, and fish were stored in 70% ethanol until scanning. A total of 55 fish were scanned (3mpf: lrp5-/- n=15, lrp5+/+ n=15; 6mpf: lrp5-/- n=12, lrp5+/+ n=13) using a 1172 SkyScan micro-computed tomography (micro-CT) scanner (Bruker, Kontich, Belgium). The whole body of fish was scanned at pixel size of 12 μm (scan settings 49 kV, 100 μA, filter Al 0.25mm). The scanned files were reconstructed with NRecon Software (Bruker). The BMD was measured from reconstructed files using CTAnalyzer Software (Bruker) calibrated to the phantoms with known mineral density (0.25 and 0.75 g.cm−3 hydroxyapatite, Bruker). The 3D tomography images of zebrafish whole body were generated using CTvox software (Bruker). The morphometrical measurements of nasofacial angle (NA) and parasphenoid (PD) distance between two limits were done on 3D reconstructed micro-CT scanned zebrafish using Meshy online tool from GitHub platform (https://0x00019913.github.io/meshy/ ). Prior to the measurements, the reconstructed zebrafish heads were saved in 3D models using CTAnalyzer Software (Bruker).
Ct analyzer software
Manufactured by Bruker
Sourced in Belgium
The CT Analyzer software is a tool designed for the analysis of computed tomography (CT) data. Its core function is to provide users with comprehensive tools for visualizing, processing, and analyzing CT images. The software offers features for data import, segmentation, quantification, and reporting.
Automatically generated - may contain errors
Lab products found in correlation
Nrecon software, by Bruker (18 mentions)
Ctvox software, by Bruker (10 mentions)
Skyscan 1172, by Bruker (9 mentions)
Skyscan 1176, by Bruker (9 mentions)
Skyscan 1174, by Bruker (3 mentions)
Dataviewer software, by Bruker (3 mentions)
Skyscan 1176 micro ct, by Bruker (3 mentions)
Dataviewer, by Bruker (2 mentions)
Formaldehyde, by Merck Group (1 mentions)
Skyscan 1072 scanner, by Bruker (1 mentions)
Nrecon software v 1.6.9, by Bruker (1 mentions)
Skyscan 1172 system, by Bruker (1 mentions)
Formalin, by Merck Group (1 mentions)
Mimics research software, by Materialise (1 mentions)
Pentobarbital sodium, by Merck Group (1 mentions)
Nrecon reconstruction software, by Bruker (1 mentions)
Micro ct skyscan 1276 system, by Bruker (1 mentions)
Micro ct scanning, by Bruker (1 mentions)
Skyscan 1176 x ray microtomography, by Bruker (1 mentions)
Skyscan 1272, by Bruker (1 mentions)
46 protocols using ct analyzer software
1
Zebrafish Skeletal Morphometrics via Micro-CT
2
Microcomputed Tomography Analysis of Tibiae
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Microcomputed tomography (µCT) analysis was performed on the tibiae using the Skyscan 1072 scanner (Bruker, Aartselaar, Belgium) and imaged with an X-ray tube voltage of 50 kV and current of 201 µA with a 0.5 mm aluminum filter. Scanning angular rotation was 180° with an angular increment of 0.70°. The voxel size was 4.48 µm isotropically. NRecon software (v.1.6.9; Bruker) was used for image reconstruction. CT Analyzer software (Bruker) was used for trabecular and cortical bone analysis. For trabecular bone parameters, trabecular bone distal to the proximal growth plate was selected for analysis within a conforming volume of interest (cortical bone excluded), commencing at a distance of 650 μm from the growth plate and extending a further longitudinal distance of 134 µm in the distal direction. For cortical bone, the diaphyseal region was analyzed 2.36 mm distal from the growth plate and extended a further longitudinal distance of 134 µm in the distal direction, corresponding to ∼37% of the length of the tibia from the proximal end. The equipment was calibrated with ceramic standard samples (calibration phantoms, calcium hydroxyapatite 0.25 and 0.75 g/cm3; Bruker) for measurements of BMD.
3
Determination of Pore Size Distribution
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Pore sizes were determined using the 3D object analyser tool within the CTAnalyzer software (Bruker, Belgium). The data were plotted as the mean pore size ± s.d. of the pore size distribution.
4
Distal Femur Microarchitecture Analysis
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Distal femur µCT images were taken on the high resolution Skyscan 1172 system (Bruker, Kontich, Belgium). The scanner X-ray source was set at a voltage of 50 kV and a current of 200 µA and a 0.5 mm aluminum filter was applied. Scans were taken with a pixel size of 5 µm, the scanning angular rotation was 180° with an angular increment of 0.4° and with a frame averaging of 2. Serial tomographs were reconstructed from raw data with the cone-beam reconstruction software (NRecon software, Skyscan, Bruker) based on the Feldkamp algorithm [16] . 3D morphometric analysis of reconstructed datasets was performed using the CT Analyzer software (CTAn, Bruker). Cortical and trabecular volumes of interest were manually selected [2 -2.5 mm (cortical) and 0.5 -1.5 mm (trabecular) under the selected reference point (point were trabecular bone is fully separated into four compartments on a transverse plane)]. Cortical and trabecular regions of interest were selected using the "automated trabecular and cortical bone selection method" (Method note, Bruker). Binary images for analysis were generated using a global thresholding of 80-255 (cortical) or 75-255 (trabecular). 3D models were constructed with the CTvox software (Bruker) using different selections [2.35 -2.5 mm (cortical) and 0.25 -2.75 mm (trabecular) under the same reference point].
5
Calvarial Bone Regeneration Analysis
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Calvarial specimens were collected and preserved in 10 % formalin (Sigma-Aldrich) at 4 and 8 weeks after surgery. To assess bone regeneration in the defect areas, a high-resolution μCT (SkyScan 1176, Bruker Corporation, Billerica, MA, USA) was employed with the following parameters: 65 kV, 385 mA, and 1 mm Al filter. The three-dimensional (3D) reconstruction was performed using Mimics Research software (Materialise, Leuven, Belgium). The region of interest (ROI) reconstruction area for the defect consisted of a consistent segment centered on the calvarium. CT Analyzer software (Bruker) was used to calculate bone volume ratio (BV/TV, %), trabecular thickness (Tb.Th., μm), and bone mineral density (BMD, g/cm3) for evaluating bone microstructure.
6
Micro-CT Analysis of Bone Loss Suppression
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The separated femurs (n = 6) were scanned by micro-CT to evaluate the suppression on bone loss, and an upper 2.2 mm region of bone trabecula beginning to distal femur metaphysis was set as ROI. 3D reconstruction images of bone trabecula on lateral and coronal views were visualized using CTvox software (Bruker), and the parameters like BV/TV, bone mineral density (BMD), number of trabecular bone tissue (Tb.N) and separation of trabecular bone tissue (Tb.S) were quantified using CT Analyzer software.
H&E and Masson staining were performed to evaluate the number of trabecular bone in distal femur metaphysis. Additionally, the TRAP staining was used to specially color the osteoclasts on the surface of bone trabecula, and representative indexes of bone resorption, like osteoclast surface relative to trabecular bone surface (OC.S/BS) and number of osteoclast per trabecular bone surface (N.OC/BS), were quantified via measuring 5 sections of each femoral metaphysis as previously reported [36 (link)].
H&E and Masson staining were performed to evaluate the number of trabecular bone in distal femur metaphysis. Additionally, the TRAP staining was used to specially color the osteoclasts on the surface of bone trabecula, and representative indexes of bone resorption, like osteoclast surface relative to trabecular bone surface (OC.S/BS) and number of osteoclast per trabecular bone surface (N.OC/BS), were quantified via measuring 5 sections of each femoral metaphysis as previously reported [36 (link)].
7
Ovariectomy Rat Model for Osteoporosis
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The osteoporotic rat model was prepared via bilateral ovariectomy as previously described [35 (link)]. Briefly, SD rats weighing about 200 g were anesthetized with injection of pentobarbital sodium (30 mg/kg, Sigma) by intraperitoneal injection. Subsequently, 2 cm-length skin incisions were made in the lower abdomen to expose the ovary of rat. Then, some rats underwent bilateral ovariectomy (OVX) and some rats, which were cut off an equal volume of parovarian fat, acted as control (Sham). After 3 months, the rats were sacrificed under overdose injection of pentobarbital sodium, and the femurs of rat were collected and subjected to micro-CT (Skyscan 1176, Bruker, Germany) and histological analysis. For micro-CT analysis, an upper 2.2 mm region beginning at 1.0 mm proximal to the medial condyle of femur was set as the region of interest (ROI). Analysis of micro-CT data using CT Analyzer software (Bruker) and H&E staining of distal femoral metaphysis were accomplished to evaluate the degree of bone loss in ovariectomized rat.
8
Microarchitectural Bone Analysis by microCT
9
Quantification of Scaffold Morphometry
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To quantify morphometric parameters, scaffolds were subjected to X-ray micro-computed tomography (XCT) analysis using a Bruker Skyscan 1174 tomographic system (Bruker, Billerica, MA, USA). As shown in Table 1 , scaffold projections were obtained at V = 50 kV and I = 800 A using the experimental settings listed in Table 1 . The conditions under which projections were processed in stacks of cross-sectional slices using Nrecon reconstruction software (version 1.7.1.6) (Bruker) are also detailed in Table 1 .
DO and RD scaffolds for each compound composition were analyzed with CT-analyzer software (Version 1.18) (Bruker). Morphometric parameters examined were micro-porosity (%) and total porosity (%).
DO and RD scaffolds for each compound composition were analyzed with CT-analyzer software (Version 1.18) (Bruker). Morphometric parameters examined were micro-porosity (%) and total porosity (%).
10
Micro-CT Analysis of CDM Discs
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