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Ctan v1

Manufactured by Bruker
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Sourced in Belgium, United States, Germany

The CTAn v1.9 is a software package for the analysis of 3D X-ray micro-computed tomography (micro-CT) data. It provides a comprehensive set of tools for visualizing, segmenting, and quantifying features within the 3D dataset.

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Lab products found in correlation

Nrecon v1, by Bruker (15 mentions) Skyscan 1172, by Bruker (8 mentions) Ctvol v2, by Bruker (8 mentions) Skyscan 1176, by Bruker (6 mentions) Skyscan 1272, by Bruker (3 mentions) μctvol v2, by Bruker (2 mentions) Skyscan 1174, by Bruker (2 mentions) Dataviewer v 1, by Bruker (2 mentions) Nrecon software, by Bruker (2 mentions) Skyscan 1176 μct, by Bruker (1 mentions) Ct analyzer software, by Bruker (1 mentions) Micro ct device, by Bruker (1 mentions) Ivis lumina xr, by PerkinElmer (1 mentions) Skyscan 1176 micro ct system, by Bruker (1 mentions) Xenolight d luciferin, by PerkinElmer (1 mentions) Forane, by Abbvie (1 mentions) Micro ct, by Bruker (1 mentions) Skyscan, by Bruker (1 mentions) Skyscan 1076, by Bruker (1 mentions) Nrecon 1, by Bruker (1 mentions)

39 protocols using ctan v1

1

Micro-CT Analysis of Root Canal Obturation

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After all canals were obturated, the roots were once again scanned by micro-CT using the same parameters described previously. All sections were reconstructed with the NRecon software (Bruker-MicroCT). The length of the root canal obturations was measured in millimeters using the CTAn v.1.14.4 software (Bruker-MicroCT). Images were converted to NRRD file format using the Image J 1.50d software (National Institutes of Health, Bethesda, Maryland, United States). Subsequently, the images were captured using the 3D Slicer v1.5.1.2 software (
www.slicer.org, MIT Artificial Intelligence Laboratory, Brigham & Women's Hospital Surgical Planning Laboratory, and Harvard Medical School, Massachusetts, United States). Voids were quantified by subtraction of the models before and after root canal obturation was completed. The volume of the voids was measured using the Image J software (National Institutes of Health). Finally, three-dimensional models were generated with the CTAn v.1.14.4 software (Bruker-MicroCT) and visualized in the CTVol v.2.3.1 software (Bruker-MicroCT) (
Fig. 2). After that, the percentage of voids in relation to the volume of the prepared canal was calculated for each tooth at the evaluated levels.
Penha da Silva P.J., Marceliano-Alves M.F., Provenzano J.C., Dellazari R.L., Gonçalves L.S, & Alves F.R. (2021). Quality of Root Canal Filling Using a Bioceramic Sealer in Oval Canals: A Three-Dimensional Analysis. European Journal of Dentistry, 15(3), 475-480.
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2

Micro-CT Analysis of Entheses Healing

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Entheses samples (n = 6 per each of the 4 groups) harvested at 12 weeks after surgery were scanned using a Skyscan 1176 μCT (Bruker, Kontich, Belgium) at 90 kV and 277 µA. A 0.1 mm Cu filter was used. Images were acquired at a resolution of 35 µm. Image reconstruction was performed using NRecon v2.0.4 (Bruker, Kontich, Belgium), and analysis was performed using CTAn v1.13 (Bruker, Kontich, Belgium). Briefly, a region of interest (ROI) was selected by excluding the patella and tibia bones but including the area of the enthesis defect. Next, global thresholding of 90 to 255 was implemented for the binarization of images and further calculations using built-in algorithms in CTAn.
Peniche Silva C.J., Müller S.A., Quirk N., Poh P.S., Mayer C., Motta A., Migliaresi C., Coenen M.J., Evans C.H., Balmayor E.R, & van Griensven M. (2022). Enthesis Healing Is Dependent on Scaffold Interphase Morphology—Results from a Rodent Patellar Model. Cells, 11(11), 1752.
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3

Micro-CT and Histology of Tibiae

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The tibiae were harvested for μCT imaging and histology. Micro-CT was performed using Skyscan 1172 (Bruker-MicroCT, Kontich, Belgium). Using manufacturer-provided software, scans were performed at pixel size 8.99 μm, and the images were reconstructed (nRecon v1.6.9.18, Bruker-MicroCT) and analyzed (CTan v1.13, Bruker-MicroCT). We focused on the proximal tibia, 1 mm thick along the length of the tibia, distal to the growth plate. In histology, H&E staining and immunohistochemistry were conducted as described previously [54 (link),58 (link)]. The samples were blinded for data analysis.
Feng Y., Liu S., Zha R., Sun X., Li K., Robling A., Li B, & Yokota H. (2021). Mechanical Loading-Driven Tumor Suppression Is Mediated by Lrp5-Dependent and Independent Mechanisms. Cancers, 13(2), 267.
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4

Microstructural Analysis of Dental Tissues

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We used CTAn v.1.13 software (Bruker MicroCT) to define different volumes of interest (VOIs) for each structural feature (dentin, dentin bridge and pulp tissue/pores) by manual definition of the regions of interest (ROIs) using the full-axial slices dataset. Dataviewer software and the corresponding histology were used as support references. An automatic thresholding method (Otsu 2D) was applied for segmenting dentin and the dentin bridge from the pulp tissue/pores. CTVox software (Bruker MicroCT) was used to render the volume and to merge the different structural features on the 3D models.
Pedano M.S., Li X., Camargo B., Hauben E., De Vleeschauwer S., Yoshihara K., Van Landuyt K., Yoshida Y, & Van Meerbeek B. (2020). Injectable phosphopullulan-functionalized calcium-silicate cement for pulp-tissue engineering: An in-vivo and ex-vivo study. Dental materials : official publication of the Academy of Dental Materials, 36(4).
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5

Micro-CT Analysis of Bone Volume

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The implants were scanned with Skycan® Micro-CT (Bruker Corporation) at 65 kV, 80 µA with an isotropic resolution of 12 µm of three spatial dimensions, using CTAn v1.18 (Bruker Corporation) analysis for each experimental group. Bone volume (BV) was calculated using the closed volume triangular surface corresponding to the tetrahedron. Total bone volume was the volume of the entire sample being examined.
Zhang Y., Zhou L., Zhang Z., Ren F., Chen L, & Lan Z. (2020). miR-10a-5p inhibits osteogenic differentiation of bone marrow-derived mesenchymal stem cells. Molecular Medicine Reports, 22(1), 135-144.
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6

Micro-CT Analysis of Biomaterial Scaffolds

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Freeze-dried samples were scanned using a SkyScan 1172 (Bruker, Billerica, MA, USA) with a source voltage of 34 kV, current of 210 µA, rotation step of 0.28°, and pixel size of 1.23 µm. Reconstruction was performed using NRecon v1.0 (2018, Bruker) with ring artefact reduction (4), smoothing (2), and beam hardening correction (65%). Quantitative analysis was performed in CTAn v1.18 (2018, Bruker) following thresholding between 110 and 255 to include mineral only and the removal of white speckles smaller than 20 voxels to remove scanning artefacts. While some smaller HAp particles will be removed for the analysis, the chosen scanning parameters were required to ensure the visualization of both the inorganic and organic phases of the material. Organic content was calculated as the difference between the thresholded, mineral-only volume and the total volume of the scaffold.
Naseri S., Cooke M.E., Rosenzweig D.H, & Tabrizian M. (2021). 3D Printed In Vitro Dentin Model to Investigate Occlusive Agents against Tooth Sensitivity. Materials, 14(23), 7255.
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7

Micro-CT Analysis of Bone Implants

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Bruker Skyscan 1172® (Billerica, MA, USA) with a 50 mm image field width and 11 Mp X-ray camera was used at a resolution of 2000 × 2000 px for the micro-CT scanning. We analysed a region of interest of a round shape, and a diameter of 120 mm centred on the implant. The length of the area of interest was 600 slices (8.1 mm) starting from the distal metaphysis proximally. The Bruker CTAn® v.1.18. software was used to calculate bone volume (BV), percent bone volume (BV%), bone surface (BS), bone surface/volume ratio (BS/VR), tissue surface (TS), mean total cross-sectional bone area, trabecular number (TN), cross-sectional thickness, and trabecular diameter (TD). The measurements were performed while the examinator was unaware of group allocation.
Apostu D., Berechet B., Oltean-Dan D., Mester A., Petrushev B., Popa C., Gherman M.L., Tigu A.B., Tomuleasa C.I., Barbu-Tudoran L., Benea H.R, & Piciu D. (2022). Low-Molecular-Weight Heparins (LMWH) and Synthetic Factor X Inhibitors Can Impair the Osseointegration Process of a Titanium Implant in an Interventional Animal Study. Medicina, 58(11), 1590.
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8

High-resolution microCT Analysis of Human Musculoskeletal Tissues

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Human tissues were fixed overnight in 10% formalin and analyzed by high-resolution μCT (Skyscan1172, Skyscan1272, Bruker microCT, Kontich, Belgium) and included the hip joint (the femoral head with ligaments and the acetabular labrum with ligaments), the spinous process with the interspinous ligament, and the supraspinous ligament and/or the ligamentum flavum from both healthy patients and AS patients. The scanner was set at a voltage of 60 kV and a resolution of 9 μm per pixel. Images of perfusion computed tomography (PCT) were used to perform three-dimensional (3D) histomorphometric analyses. The region of interest was defined to cover the whole PCT compartment (the femoral head or acetabular labrum with ligaments, single spinous process or joint spinous process with the interspinous ligament, supraspinous ligament, and/or ligamentum flavum). The images were reconstructed with NRecon v1.6 software (Bioz, Inc., Palo Alto, CA, USA), analyzed by CTAn v1.9 software (Bruker microCT), and visualized using the 3D model visualization software CTVol v2.0 (Bruker microCT).
Yu T., Zhang J., Zhu W., Wang X., Bai Y., Feng B., Zhuang Q., Han C., Wang S., Hu Q., An S., Wan M., Dong S., Xu J., Weng X, & Cao X. (2021). Chondrogenesis mediates progression of ankylosing spondylitis through heterotopic ossification. Bone Research, 9, 19.
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9

Femur Microarchitecture Analysis in Klotho Mice

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The mice were sacrificed and We dissected femur specimens of both sides from kl/kl mice and WT mice, all adapted mice were 4-week-old males. Then specimens were fixed overnight in 10% formalin and analyzed by high-resolution µCT (Skyscan1272, Bruker microCT, Kontich, Belgium). There were 24 samples in total, including 12 specimens from kl/kl mice and 12 specimens from WT mice. The scanner was set at a voltage of 60 kV and a resolution of 12 µm per pixel. Images of perfusion computed tomography (PCT) were used to perform three-dimensional (3D) histomorphometric analyses. The region of interest was defined to cover the whole PCT compartment (the femoral head and the femoral shaft). The images were reconstructed with NRecon v1.6 software (Bioz, Inc., CA, USA), analyzed by CTAn v1.9 software (Bruker microCT), and visualized using the 3D model visualization software CTVol v2.0 (Bruker microCT).
Yu T., Dou C., Lu Y., Duan L., Tan J., Li J., Kang F., Dong S., Bai Y, & Xu J. (2021). Klotho upregulates the interaction between RANK and TRAF6 to facilitate RANKL-induced osteoclastogenesis via the NF-κB signaling pathway. Annals of Translational Medicine, 9(19), 1499.
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10

Tibia Microstructure Analysis via μCT

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Tibia specimens from different mice groups were fixed overnight in 4% paraformaldehyde. The specimens were scanned using micro-computed tomography (μCT; Skyscan1272, Bruker microCT, Kontich, Belgium). The scanner was set to a voltage of 60 kV and a resolution of 8 μm per pixel. NRecon v1.6 software (Bioz, Inc., United States) was used to reconstruct the scanned image. The reconstruction was analyzed using CTAn v1.9 software (Bruker micro-CT), and CTVol v2.0 software (Bruker micro-CT) was used to visualize the 3D model. The area of interest was defined according to the “fracture callus analysis” section of Bruker micro-CT method annotation.
Bai Y., Yu T., Deng J., Yang Y., Tan J., Dai Q., Zhang Z., Dong S, & Xu J. (2021). Connective Tissue Growth Factor From Periosteal Tartrate Acid Phosphatase-Positive Monocytes Direct Skeletal Stem Cell Renewal and Fate During Bone Healing. Frontiers in Cell and Developmental Biology, 9, 730095.
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