Skyscan 1173

Specimens were placed in the scanning chamber of the SkyScan-1173 high energy Micro-CT machine (BrukerSkyScan, Belgium) in a certain pre-marked position (orientation) to enable the same position during the second scanning of specimens. After adjusting the appropriate parameters (675 ms exposure time, 36.8 µm image-pixel size, 0.5 mm brass-filter, 0.4 rotation-step for 360° angle, frame-average of 4, and 8 random-movement), samples were scanned by the SkyScan-1173 Micro-CT machine (BrukerSkyScan, Belgium). A flat-field correction was performed before scanning procedures to correct variations in the camera pixel sensitivity. Using the ©N-Recon software version 1.6.9.4 (BrukerSkyScan), the projected images were reconstructed to produce 2-dimensional (2-D) cross-sectional images of the samples’ inner structure. A 5 ring artifact reduction, 25% beam hardening compensation, and 2 smoothing using Gaussian kernel were applied. The reconstructed images were loaded to the Data-viewer software (version 1.5.6.2) (BrukerSkyScan) to determine images’ quality, reorient, resize, and to enable more accurate positioning and visual inspection. The registration data-set was saved and loaded in the ©CTAn software (version 1.20.8.0) (BrukerSkyScan) to analyse images selectively and then to measure the volume of the root-canal fillings.

The specimen was measured using Micro-CT (SkyScan1173; Bruker-CT, Kartuizersweg 3B 2550 Kontich, Belgium). SkyScan1173 control software (ver 1.6, Bruker-CT) was used for obtaining the measurements, with a tube voltage of 130 kVp, a tube current of 60 μA, 1 mm aluminum filtration (Filter), an exposure time of 500 ms, (2240 × 2240) pixels, and a pixel size of 7.14 μm. The rotation angle was rotated by 0.3˚ and 180˚ to obtain 800 high-resolution images. For cross-sectional reconstruction, an image of 2240 × 2240 pixels was obtained using Nrecon (ver 1.7.0.4, Bruker-CT), and the cross-sectional image was aligned using Dataviewer (ver 1.5.1.2, Bruker-CT). For data analysis, CTAn (ver 1.17.7.2, Brooker-CT) was used to set the inside of the Trephine drill as an area, and the volumes of the nephrotic area and this parameter were analyzed by setting the threshold to 45–61 for the amount of bone present in the area. Bone mineral density was obtained using Bruker’s standard sample phantom and applied to the specimen to be analyzed. Bone mineral density was analyzed using CTAn (ver 1.17.7.2, Bruker-CT).

To evaluate dimensional discrepancies between modeled and 3D printed splints microcomputed tomography images were acquired in a µCT (SkyScan 1,173, Bruker) at 60 kV and 50 µA with a resolution of 10.0 µm voxel size. DICOM images of splints were post-processed into ImageJ (Fiji) software (Schindelin et al., 2012 (link)). Masks were created to calculate volume discrepancies in the splints.

The wet constructs were scanned with a calibrated micro CT scanner (Bruker Skyscan 1173, Bruker, Kontich, Belgium) at 30 kV, 180 μA, integration time 3200 ms, nominal resolution of 5 μm, and without a filter. Scaffolds were scanned in wet conditions, except empty scaffolds for porosity analysis were scanned dry. Using medtool (Version 4.3; Dr. Pahr Ingenieurs e.U., Pfaffstätten, Austria), the µCT scans were processed. First, raw image files from Brucker were imported into Medtool, and the region of interest was cropped. Second, registration was performed using the iterative selection method to find a single level threshold at the minimum between the scaffold constructs and calcified regions. Third, the equivalent bone volume to total volume was calculated as the number of calcified voxels divided by the voxels’ total number in one scaffold.

Tooth histology was examined non‐destructively with X‐ray tomographic imaging. Jaws and teeth of different sizes were scanned using three different micro‐computed tomography (CT) devices: SkyScan1173 micro‐CT device (Bruker, Kontich, Belgium) at the Department of Palaeontology (University of Vienna); Xradia MicroXCT‐system (Zeiss, Oberkochen, Germany) at the Department of Theoretical Biology (University of Vienna); and VISCOM X8060 NDT X‐ray (Viscom AG, Hannover, Germany) at the Department of Evolutionary Anthropology (University of Vienna). The applied device and settings for each specimen are summarized in the Table S2. The generated slice file stacks were loaded into the Amira software package (version 5.4.5; FEI Visualization Sciences Group, Hillsboro, OR, USA) to create isosurfaces and virtual sections through different planes of the examined teeth to investigate their internal anatomy. All raw data are stored on servers in the Department of Palaeontology (University of Vienna). Figures of the resulting two‐dimensional images were finalized with Adobe Photoshop CS6 (version 13.0; Adobe Systems, San José, CA, USA) in regard to editing colour balance, contrast and labelling.