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Xmreconstructor

Manufactured by Zeiss
Sourced in Germany

The XMReconstructor is a software tool developed by Zeiss that enables the reconstruction of 3D models from X-ray microscopy data. It provides the core functionality to process and visualize volumetric data acquired through X-ray imaging techniques.

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15 protocols using xmreconstructor

1

Micro-CT Scanning of Contrasted Animal Heads

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Micro-CT scans were performed using an X-ray microscope (Xradia MicroXCT-200; Carl Zeiss Microscopy GmbH, Jena, Germany) that uses a 90-kV/8 W tungsten X-ray source and switchable scintillator-objective lens units as described by Sombke et al. (2015) (link). The heads of fixed animals (Bouin; two specimens) were contrasted in iodine solution (2% iodine resublimated (Cat. #X864.1; Carl Roth GmbH, Karlsruhe, Germany) in 99.5% ethanol), critical point-dried using a fully automatic critical point dryer Leica EM CPD300 (Leica Microsystems, Wetzlar, Germany) and scanned dry (scan medium air). Tomography projections were reconstructed using the reconstruction software XMReconstructor (Carl Zeiss Microscopy GmbH, Jena, Germany), resulting in image stacks (DICOM format) with a pixel size of about 5.8 µm for the 4 × objective and 1.9 µm for the 10 × objective.
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2

X-ray Micro-CT Analysis of PFA and PEEK Cells

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X-ray micro-CT was performed on the PFA and PEEK in-situ cells with a lab-based micro-CT instrument (Zeiss Xradia Versa 520, Carl Zeiss Inc., Oberkochen, Germany). The instrument consisted of a polychromatic micro-focus sealed source set to an accelerating voltage of 80 kV on a tungsten target at a maximum power of 7 W. The scintillator was coupled to either a 20× or 40× objective lens and 2048 × 2048 pixel CCD detector with a pixel binning of 1, which results in a pixel size of ca. 460 nm and a field of view of ca. 940 μm for the 20× objective and ca. 230 nm and a field of view of ca. 470 μm for the 40× objective. There was no significant geometric magnification since the sample was set close to the detector to reduce the effects of penumbral blurring arising from the cone beam nature of the source. The sample was rotated through 360° with radiographs collected at discrete angular intervals amounting to a total of 1601 projections. The radiographic projections were then reconstructed with proprietary reconstruction software (Version 11.1.8043, XMReconstructor, Carl Zeiss Inc.) by using a modified Feldkamp-David-Kress (FDK) algorithm for cone beam geometry.
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3

μ-CT Analysis of K. biedouwense

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For μ-CT analysis, we used one male K. biedouwense. Sample preparation and μ-CT scanning was conducted according to Sombke et al. [25 (link)]. The abdomen was cut off, dehydrated in an ascending ethanol series and stained in 1% iodine solution (Carl Roth GmbH + Co. KG, Germany) for 24 h. The sample was then transferred back to 100% ethanol, critical-point dried (Leica EM CPD300, Leica Microsystems, Germany), and mounted on a pin head using glue from a glue gun. The sample was scanned on an Xradia MicroXCT-200 imaging system (Carl Zeiss AG, Germany) with a 4x magnification, 40 kV voltage, 8 W power, and 0.7 s exposure time (180° scan). Resulting pixel sizes were 5.33 μm. Tomography projections were reconstructed using the software XMReconstructor (Carl Zeiss AG, Germany), resulting in an image stack of 995 pictures. Visualization and 3D reconstruction were done with Amira 6.4.0 software (Visualization Sciences Group, FEI Company, OR, USA). Images of the reconstructions were subsequently edited with Adobe Photoshop (CS4, Adobe Systems Inc., USA).
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4

3D Imaging and Segmentation of Insect Genitalia

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X-ray micro-computed tomography was conducted using a Zeiss Versa XRM-520 X-ray microscope (Zeiss, Oberkochen, Germany) at the Centre for Microscopy, Characterization and Analysis at the University of Western Australia. Full details of sample mounting and scanning parameters can be found in the electronic supplementary material. The software XMReconstructor (Zeiss) was used to construct the 3D volumetric data upon completion of scanning. A beam hardening constant of 0 and automatic center shift were used.
The manual segmentation of female and male genitalia was conducted using Avizo v9.2.0 software (Thermo-Fisher Scientific, USA), where the right female receptaculum and left male gonopod were isolated from each 3D volume. Full details of the workflows can be found in the electronic supplementary material. Once segmentations were complete, each female receptaculum and male gonopod was exported as a surface mesh file in the Polygon File format (.ply). Each .ply file was then checked for holes and non-manifold edges in MeshLab (v2021.10) [38 ] so that no surfaces with missing data were included in downstream analyses.
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5

Quantifying Periodontal Ligament Space

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Each specimen was scanned using X-ray micro-computed tomography (Micro-XCT 200, Carl Zeiss, Pleasanton, CA) at 4X magnification with LE#2 filter, 80 W of power, and 40 kV of voltage. X-ray projections were reconstructed into volumes utilizing XMReconstructor (Carl Zeiss, Pleasanton, CA). Reconstructed images were further processed by AVIZO® software (2019.1, Thermo Fisher Scientific, Hillsboro, Oregon) to evaluate the PDL space between the roots of molars and respective alveolar bone sockets in control (without infection) and experimental (with infection) groups. The normalized frequency of PDL space for each specimen was plotted for control and experimental groups. The parameters for peak value and peak width were estimated through a Gaussian fit using MATLAB Curve Fitting Tools (R2019a, The MathWorks, Inc., Natick, MA). Student’s t test was used to obtain significant differences (p < 0.05) between groups with a 95% confidence interval.
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6

High-resolution X-ray Microscopy of Barnacle Structure

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A Zeiss Xradia Versa 520 (Carl Zeiss XRM, Pleasanton, CA, USA) was used to carry out high-resolution XRM non-destructive imaging; this was achieved using a CCD (charge coupled device) detector system with scintillator-coupled visible light optics and a tungsten transmission target. Initial scans of the barnacle region block were undertaken with an X-ray tube voltage of 130 kV, a tube current of 89 µA, an exposure of 4000 ms. A total of 1601 projections were collected. A filter (LE4) was used to filter out lower energy X-rays, and an objective lens giving an optical magnification of 4 was selected with binning set to 2, producing an isotropic voxel (three-dimensional (3D) pixel) size of 3.45 µm. The tomograms were reconstructed from 2D projections using a Zeiss Microscopy commercial software package (XMReconstructor) and an automatically generated cone-beam reconstruction algorithm based on the filtered back-projection. Individual plates were also scanned (not in the resin block); these were collected using the 4X objective lens at 60 kV and 84 µA, with an exposure time of 12 000 ms and a resulting (isotropic voxel size) of 0.5 µm. A filter (LE1) was used to filter out low-energy X-rays, and 1601 projections were collected. The scout and zoom methodology was used to create high-resolution regions of interest (ROIs) within the sutures.
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7

Evaluating Peri-Implant Bone Microstructure

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To evaluate microstructure of peri-implant bone more precisely, samples were randomly selected for scanning using X-ray microscopy (ZEISS Xradia Versa 520, USA) with the following parameters: an X-ray source voltage of 80 kV, power of 7 W, and pixel size of 10 μm. Then the three-dimensional images of implants and peri-implant bone were reconstructed by XMReconstructor (Carl Zeiss, USA). To evaluate the inner zone of peri-implant bone response, the region of interest (ROI) of peri-implant bone in each tomography was selected from middle 30 layers of implant body and was defined as a rectangle extending 500 μm from the implant surface, with the entire length of the implant screw [40 (link)]. Next, the bone morphometry indices were measured from three-dimensional images at ROIs in the compressive and tensile sides, including BV/TV, Tb.N, Tb.Sp, Tb.Th and SMI, which were calculated using CTAn software (Skyscan, Belgium) [41 (link)].
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8

High-Resolution Nano-CT Imaging Protocol

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High-resolution imaging was performed using a nano-CT (Zeiss Xradia Ultra 810), which operates at a constant X-ray photon energy of 5.4 keV (monochromatic, no beam-hardening artifacts) with parallel beam geometry (no cone-beam artifacts) and a rotating chromium anode. The minimum voxel size in high-resolution mode is 16 nm. For the experiments, absorption contrast imaging in large field of view mode (minimum voxel size 64 nm) was used. Image reconstruction was performed by means of the software Zeiss XMReconstructor (Version 10.0.3878.16108).
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9

Micro-CT Imaging Protocols and Considerations

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Low-resolution and medium-resolution measurements were performed using a micro-CT (Zeiss Xradia VERSA 510) with a polychromatic X-ray source, a rotating tungsten anode, a maximum acceleration voltage of 160 keV, and a maximum power of 10 W. Compared to conventional X-ray micro-CT systems, an additional optical system increases magnification by a factor of 10. This two-step magnification gives a minimum voxel size of 0.3 μm. Reconstruction was done using the software Zeiss XMReconstructor (Version 11.1.8043) with the aim of minimizing manipulations in preprocessing (smoothing, beam-hardening correction). No beam hardening was visible in the reconstructed slices. Due to the cone beam artifact, 50 slices were removed from the top and bottom of the data set before image postprocessing. A summary of relevant artifacts related to micro-CT measurements is given by Boas & Fleischmann (2012) and Davis & Elliott (2006) .
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10

Micro-CT Analysis of Graphite Electrode Structure

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The graphite electrodes of different thicknesses (50 and 100 μm, corresponding to 2 and 4 mAh cm−2) were cut into disks of ~500 μm in diameter using a laser cutter (A Series/Compact Laser Micromachining System, Oxford Lasers, Oxford, UK). The electrode disks were then scanned at 0.2 μm voxel size using a lab-based X-ray micro-CT system (Zeiss Xradia Versa 520 X-ray microscope, Carl Zeiss, CA, USA)55 (link) at the X-ray tube voltage of 80 kV (tungsten emission). In total, 2001 projections were collected over the 360° rotation of the sample. The projections were then reconstructed using commercial software (Zeiss XMReconstructor) employing a proprietary Feldkamp-Davis-Kress (FDK) algorithm56 . Microstructural characterization of the electrode was carried out in commercial software Avizo V9.5 (Avizo, Thermo Fisher Scientific, Waltham, Massachusetts, U.S.). The geometrical metrics of graphite particles (orientation, size and shape etc) were analyzed by extracting the moments of inertia of its ellipsoid template and the eigenvalues of the covariance matrix57 .
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