Ctan software

Manufactured by Bruker

Sourced in Belgium, United States, Germany

CTAn software is a tool for the analysis and visualization of 3D data from micro-computed tomography (micro-CT) imaging. It provides core functions for image processing, analysis, and quantification of various morphological parameters.

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Lab products found in correlation

Nrecon software, by Bruker (71 mentions) Skyscan 1172, by Bruker (31 mentions) Ctvox software, by Bruker (29 mentions) Ctvol software, by Bruker (26 mentions) Dataviewer software, by Bruker (24 mentions) Skyscan 1176, by Bruker (23 mentions) Skyscan 1272, by Bruker (18 mentions) Dataviewer, by Bruker (17 mentions) Ctvox, by Bruker (14 mentions) Nrecon, by Bruker (13 mentions) Skyscan 1076, by Bruker (10 mentions) Skyscan 1174, by Bruker (8 mentions) Skyscan 1276, by Bruker (8 mentions) Ctvol, by Bruker (6 mentions) Nrecon reconstruction software, by Bruker (6 mentions) Skyscan 1276 system, by Bruker (5 mentions) Skyscan 1275, by Bruker (4 mentions) Skyscan 1173, by Bruker (3 mentions) Skyscan 1172 x ray microtomograph, by Bruker (3 mentions) Skyscan 1176 scanner, by Bruker (3 mentions)

Spelling variants of this product

SkyScan CTAn software (8 citations) SkyScan CT Analyzer (CTAn) Software (3 citations) 3D Ctan software (3 citations) CTAn Micro-CT Software (3 citations) CTAn 3D analysis software (2 citations) SkyScan CT-Analyser (CTAn) software (2 citations) CTAn reconstruction software (2 citations) CT Analyzer Software (CTAn; (2 citations) 2D/3D Image analysis CT-analyser (CTAn) software (2 citations) CTAn/CTVol software (2 citations)

246 protocols using ctan software

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. N Recon 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).

Hao Z., Feng Q., Wang Y., Wang Y., Li H., Hu Y., Chen T., Wang J., Chen R., Lv X., Yang Z., Chen J., Guo X, & Li J. (2023). A parathyroid hormone related supramolecular peptide for multi-functionalized osteoregeneration. Bioactive Materials, 34, 181-203.

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Micro-CT Analysis of Trabecular and Cortical Bone

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High-resolution scans with an isotropic voxel size of 5 µm were acquired with a µCT system (60 kV, 0.5 mm aluminium filter, 0.6° rotation, Skyscan 1172; Bruker Daltonics). Scans were reconstructed using NRecon software (Bruker Daltonics). A 1,000-µm section of the metaphysis 250 µm off the reference plate was taken for analysis of the trabecular bone. The base of the growth plate was used as a standard reference point. A 250-µm metaphysis section of the mid-diaphysis, 1,500 µm below the reference plate, was scanned for the analysis of cortical structure. Data were analysed with CTAn software (Bruker Daltonics). The following parameters were analysed using CTAn software (Bruker Daltonics): percentage bone volume/trabecular bone volume (%BV/TV), trabecular number (Tb.N;/mm), trabecular patten factor (Tb.Pf), bone mineral density (BMD; g/cm³), trabecular thickness (Tb.Th; mm), trabecular separation (Tb. Sp) and the structure model index (SMI) were evaluated. In the cortical bone, %BV/TV, BMD (g/cm³), cortical thickness, cross-sectional area (mm²), the percentage of closed pores and polar moment of inertia (mm⁴) were evaluated.

HUESA C., STAINES K.A., MILLÁN J.L, & MacRAE V.E. (2015). Effects of etidronate on the Enpp1−/− mouse model of generalized arterial calcification of infancy. International Journal of Molecular Medicine, 36(1), 159-165.

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Quantifying Bone Morphometry and Osteoclasts

Cited 2 times

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Bone morphometric parameters of formaldehy-fixed tibias were measured using high-resolution micro-computed tomography (μCT, Skyscan 1272; Kontich, Belgium) with a source voltage of 60 kV, current of 166 μA and resolution of 8 μm. Bone volume per total volume (BV/TV), bone mineral density (BMD), trabecular separation (Tb. Sp.), and trabecular number (Tb. N.) were evaluated using CTAn software (Bruker; Kontich, Belgium) as reported previously [37 (link),38 (link)]. Three-dimensional bone structure images were generated using CTAn software (Bruker; Kontich, Belgium).
For histomorphometric analysis, fixed tibias were decalcified in 12% EDTA and embedded in paraffin. Tissue sections were prepared using a microtome (Leica Biosystems, Nussloch, Germany) for hematoxylin and eosin (H&E) and tartrate resistant acid phosphatase (TRAP) staining. The number of osteoclasts per bone perimeter (N. OC/B. Pm) was assessed in sections stained for TRAP [39 (link)].

Ihn H.J., Kim J.A., Lim S., Nam S.H., Hwang S.H., Lim J., Kim G.Y., Choi Y.H., Jeon Y.J., Lee B.J., Bae J.S., Kim Y.H, & Park E.K. (2019). Fermented Oyster Extract Prevents Ovariectomy-Induced Bone Loss and Suppresses Osteoclastogenesis. Nutrients, 11(6), 1392.

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Micro-CT Analysis of Printed Samples

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μCT scanning was performed using a SkyScan 1272 micro-computer (Bruker Corporation, Billerica, MA, USA) tomograph at room temperature by rotating the object in front of the source (voltage 45 kV, current 110 mA) for 180 degrees with a rotation step of 0.3 degrees; each frame resulted from an average of 4 projections per frame (550 ms/frame). The scanning resolution (image pixel size) was set at 15 μm for all printed samples. Tomograms were reconstructed from the raw data in Bruker NRecon software (Bruker Corporation, Billerica, MA, USA). Bruker CTAn software (Bruker Corporation, Billerica, MA, USA) was employed to analyze the tomograms and measure the morphological parameters of the printed objects (total porosity, pore/wall size distribution, etc.) and to generate the secondary color-coded dataset depicting pore size variations. All procedures were performed after thresholding (binarization; white pixels for solid sample and black pixels for pores) and despeckling (removal or residual scanning artifacts) and were based on the image pixel size for metric unit conversion.

Boretti G., Giordano E., Ionita M., Vlasceanu G.M., Sigurjónsson Ó.E., Gargiulo P, & Lovecchio J. (2023). Human Bone-Marrow-Derived Stem-Cell-Seeded 3D Chitosan–Gelatin–Genipin Scaffolds Show Enhanced Extracellular Matrix Mineralization When Cultured under a Perfusion Flow in Osteogenic Medium. Materials, 16(17), 5898.

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Trabecular Bone Microarchitecture Analysis via μCT

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Trabecular bone samples (length/width/height about 0.5–0.7 cm) were cut out directly from the bone pieces after receiving the samples and stored frozen at −80°C until μCT analysis. Samples were scanned in a micro-computed tomography system with a voxel size of 12 μm (Röntgenprüfsystem v| tome| x s 240 Research/Edition V2.5, GE Sensing and Inspection Technologies GmbH, Wunstorf, Germany, DFG number: INST 102/11-1 FUGG). Following parameters were used for scanning: X-ray tube was operated at 45 kV and 260 μA; integration time of 333 ms and 1,500 images/360°. Automatic geometry calibration without using further filters was used for reconstruction of the data. Bone microarchitecture was analyzed with the Bruker CtAN Software (Bruker Corporation, Billerica, MA, United States).

Niedermair T., Lukas C., Li S., Stöckl S., Craiovan B., Brochhausen C., Federlin M., Herrmann M, & Grässel S. (2020). Influence of Extracellular Vesicles Isolated From Osteoblasts of Patients With Cox-Arthrosis and/or Osteoporosis on Metabolism and Osteogenic Differentiation of BMSCs. Frontiers in Bioengineering and Biotechnology, 8, 615520.

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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.

Le M.H., Noor Hayaty A.K., Zaini Z.M., Dom S.M., Ibrahim N, & Radzi Z.B. (2019). Alveolar restoration following rapid maxillary expansion with and without corticotomy: A microcomputed tomography study in sheep. Korean Journal of Orthodontics, 49(4), 235-245.

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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).

Sawadkar P., Mandakhbayar N., Patel K.D., Buitrago J.O., Kim T.H., Rajasekar P., Lali F., Kyriakidis C., Rahmani B., Mohanakrishnan J., Dua R., Greco K., Lee J.H., Kim H.W., Knowles J, & García – Gareta E. (2021). Three dimensional porous scaffolds derived from collagen, elastin and fibrin proteins orchestrate adipose tissue regeneration. Journal of Tissue Engineering, 12, 20417314211019238.

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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.

Suchý T., Bartoš M., Sedláček R., Šupová M., Žaloudková M., Martynková G.S, & Foltán R. (2021). Various Simulated Body Fluids Lead to Significant Differences in Collagen Tissue Engineering Scaffolds. Materials, 14(16), 4388.

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High-Fat Diet Induced Obesity Protocol

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The mice were fed with HFD (MP Biomedicals) containing 60 kcal% calorie value, which was replaced every three days and weighted to calculate food intake. When necessary, mice were subcutaneously injected with either vehicle or LPZ (10 mg/kg) daily until the completion of the experiments, when serum, different adipose depots and liver samples were dissected and weighted for subsequent analysis. The bone and fat volume of mice was recorded using the SKyScan micro-CT scanner (Bruker). Volumetric micro-CT data were post-processed via Gaussian smoothing, and analyzed using the CTAn software (Bruker), wherein regions of interest were manually delineated. Energy expenditure was measured by the Promethion calorimetry system (Sable Systems International).

Wu Y., Xin J., Li X., Yang T., Liu Y., Zhao Y., Xie W, & Jiang M. (2024). Repurposing lansoprazole to alleviate metabolic syndrome via PHOSPHO1 inhibition. Acta Pharmaceutica Sinica. B, 14(4), 1711-1725.

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Cortical and Trabecular Bone Analysis

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The mouse bones were scanned in the Bruker Skyscan 1174 at a nominal resolution of 9.6 μm employing an aluminum filter 0.5 mm thick and an applied x-ray tube voltage of 50 kV. Camera pixel binning was not applied. The scan orbit was 180/360 degrees with a rotation step of 0.4 degrees. Reconstruction was carried out with a modified Feldkamp algorithm using the SkyScanTM NRecon software accelerated by GPU3. Gaussian smoothing, ring artefact reduction and beam hardening correction were applied.
The stack of the reconstructed images was analyzed in CTAn software. Fifty slices from the mid diaphysis were selected for each type of bone to calculate the cortical bone parameters. The minimum threshold was set to 55 and maximum was set to 255 for all the bones. Hundred slices from distal femur and proximal tibiae were selected to calculate the trabecular bone parameters. The minimum threshold was set to 45 and maximum was set to 95 for both femur and tibiae. We used Bruker's CTAn software to calculate these parameters in which we are able to isolate the cortical and the trabecular bone regions using polygonal ROI tool. The software calculates the total volume based on our ROI and the respective bone volume within the selected ROI in either cortical or trabecula region. Trabecular bone analysis was not done on ulnae.

Mumtaz H., Dallas M., Begonia M., Lara-Castillo N., Scott J.M., Johnson M.L, & Ganesh T. (2020). Age-related and sex-specific effects on architectural properties and biomechanical response of the C57BL/6N mouse femur, tibia and ulna. Bone Reports, 12, 100266.

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