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41 results for “X-ray Micro-Computed Tomography”
Simulated X-ray micro-computed tomography based particle tracking velocimetry dataset for validation purposes
<p>Authors: Tom Bultreys, Stefanie Van Offenwert, Wannes Goethals, Matthieu N. Boone, Jan Aelterman and Veerle Cnudde; Ghent University (Belgium)<br> Date: 8th February 2022<br> For any usage, please cite the accompanying publication: T. Bultreys, S. Van Offenwert, W. Goethals, M. N. Boone, J. Aelterman and V. Cnudde, "X-ray Tomographic Micro-Particle Velocimetry in Porous Media", Physics of Fluids, 34, 042008 (2022).<br> https://doi.org/10.1063/5.0088000<br> -----------------------------</p> <p>Validation dataset for micro-computed tomography based particle tracking velocimetry: a simulated micro-CT based velocimetry experiment with associated ground-truth particle trajectories</p> <p>- The ground truth trajectories were based on randomly dropping virtual particles in the pore space, and tracking their movement through a CFD-based velocity field (see below). The positions were calculated for the time corresponding to each radiograph of a micro-CT experiment. The folder "GroundTruthData" contains the locations of all particles at the central time of each micro-CT scan, as well as their radii. Check the associated readme file to read the data file.</p> <p>- The main data is contained in the directory "TimeFrames", containing the reconstructed 3D images at 7 time steps (70 seconds interval), with a voxel size of 11.8 µm, in 3D .tif format. This can be opened in for example Fiji/ImageJ.</p> <p>- The directory "clearFrame" contains an image of the pore space without particles, matching with the time frame images, in the same format and with the same voxel size as the time frame images.</p> <p>- The directory "SegmentedImage" contains two binary 3D images (same format as images before) which was created by segmenting the clearFrame image. There are two versions: the original segmentation, and a version where pores were eroded. The eroded segmentation was used to mask the pore space during particle detection (this avoids spurious detections near pore walls, caused by minor mis-alignments of the clearImage).</p> <p>- The original segmentation was used as input to simulate the velocity fields in the directory "simulatedVelocityFields", which contains 3D .tif images that represent the three components of the velocity vector field (the X-direction was the axis of the sample, equaling the flow direction). There is also an input text file and an output text file. The simulation was performed with the code from single-phase OpenFOAM implementation from Ali Raeini and others at Imperial College London: http://www.imperial.ac.uk/earth-science/research/research-groups/perm/research/pore-scale-modelling/</p> <p>- The trackingOutput folder contains the experimentally determined velocity points (.csv, only particles that could be tracked at least 6 time frames) and the experimentally determined velocity magnitude field (.tif, voxel size 23.6 µm)</p>
X-ray micro-computed tomography based X-ray particle tracking velocimetry dataset in a porous glass filter
<p>Authors: Tom Bultreys, Stefanie Van Offenwert, Wannes Goethals, Matthieu N. Boone, Jan Aelterman and Veerle Cnudde; Ghent University (Belgium)<br> Date: 8th February 2022<br> For any usage, please cite the accompanying publication: T. Bultreys, S. Van Offenwert, W. Goethals, M. N. Boone, J. Aelterman and V. Cnudde, "X-ray Tomographic Micro-Particle Velocimetry in Porous Media", Physics of Fluids, 34, 042008 (2022).<br> https://doi.org/10.1063/5.0088000<br> -----------------------------</p> <p>Dataset of a micro-computed tomography based particle tracking velocimetry experiment performed on a glass filter (ROBU P0; sample size 4 mm diameter by 1 cm).</p> <p>- The main data is contained in the directory "TimeFrames", containing the reconstructed 3D images at 59 time steps (35 seconds interval), with a voxel size of 11.8 µm, in 3D .tif format. This can be opened in for example Fiji/ImageJ.</p> <p>- The directory "clearFrame" contains a high-quality pre-scan taken before the main experiment, which was registered and resampled to the time frame images, in the same format and with the same voxel size as the time frame images.</p> <p>- The directory "SegmentedImage" contains two binary 3D images (same format as images before) which was created by segmenting the clearFrame image. There are two versions: the original segmentation, and a version where pores were eroded. The eroded segmentation was used to mask the pore space during particle detection (this avoids spurious detections near pore walls, caused by minor mis-alignments of the clearImage).</p> <p>- The original segmentation was used as input to simulate the velocity fields in the directory "simulatedVelocityFields", which contains 3D .tif images that represent the three components of the velocity vector field (the X-direction was the axis of the sample, equaling the flow direction). There is also an input text file and an output text file. The simulation was performed with the code from single-phase OpenFOAM implementation from Ali Raeini and others at Imperial College London: http://www.imperial.ac.uk/earth-science/research/research-groups/perm/research/pore-scale-modelling/</p> <p>- The trackingOutput folder contains the experimentally determined velocity points (.csv, only particles that could be tracked at least 20 time frames) and the experimentally determined velocity magnitude field (.tif, voxel size 23.6 µm)</p>
X-ray micro-computed tomography based particle tracking velocimetry dataset in a sandpack
<p>Authors: Tom Bultreys, Stefanie Van Offenwert, Wannes Goethals, Matthieu N. Boone, Jan Aelterman and Veerle Cnudde; Ghent University (Belgium)<br> Date: 8th February 2022<br> For any usage, please cite the accompanying publication: T. Bultreys, S. Van Offenwert, W. Goethals, M. N. Boone, J. Aelterman and V. Cnudde, "X-ray Tomographic Micro-Particle Velocimetry in Porous Media", Physics of Fluids, 34, 042008 (2022).<br> https://doi.org/10.1063/5.0088000<br> -----------------------------</p> <p>Dataset of a micro-computed tomography based particle tracking velocimetry experiment performed on a sand pack (grainsize 500-710 µm; sample size 4 mm diameter by 2 cm).</p> <p>- The main data is contained in the directory "TimeFrames", containing the reconstructed 3D images at 79 time steps (35 seconds interval), with a voxel size of 11.8 µm, in 3D .tif format. This can be opened in for example Fiji/ImageJ.</p> <p>- The directory "clearFrame" contains a high-quality pre-scan taken before the main experiment, which was registered and resampled to the time frame images, in the same format and with the same voxel size as the time frame images.</p> <p>- The directory "SegmentedImage" contains two binary 3D images (same format as images before) which was created by segmenting the clearFrame image. There are two versions: the original segmentation, and a version where pores were eroded. The eroded segmentation was used to mask the pore space during particle detection (this avoids spurious detections near pore walls, caused by minor mis-alignments of the clearImage).</p> <p>- The original segmentation was used as input to simulate the velocity fields in the directory "simulatedVelocityFields", which contains 3D .tif images that represent the three components of the velocity vector field (the X-direction was the axis of the sample, equaling the flow direction). There is also an input text file and an output text file. The simulation was performed with the code from single-phase OpenFOAM implementation from Ali Raeini and others at Imperial College London: http://www.imperial.ac.uk/earth-science/research/research-groups/perm/research/pore-scale-modelling/</p> <p>- The trackingOutput folder contains the experimentally determined velocity points (.csv, only particles that could be tracked at least 20 time frames) and the experimentally determined velocity magnitude field (.tif, voxel size 23.6 µm)</p>
FIGURE 4 in Benefits and limits of x-ray micro-computed tomography for visualization of colonization and bioerosion of shelled organisms
FIGURE 4. Ordovician bryozoan colony. One-half of hemispherical bryozoan, interior of object, bearing probably oldest boring attributable to ichnogenus Entobia Bronn, 1837. Besides semi-radial tunnels and exploratory threads, three bulbous chambers discovered near the center of the hemisphere. Darriwilian (middle Ordovician), Khrevitsa locality, St. Petersburg Region, Russia. Scale bar equals 1 cm.
FIGURE 7 in Benefits and limits of x-ray micro-computed tomography for visualization of colonization and bioerosion of shelled organisms
FIGURE 7. Three-dimensional visualization of a shell of the recent Foraminifera Amphistegina sp. illustrating the potential of micro-CT in investigations of recent marine shelled organisms. (A) A surface view of the whole shell. (B) A transversal section through the whole shell (C, D) Details of the shells´s surface.
FIGURE 5 in Benefits and limits of x-ray micro-computed tomography for visualization of colonization and bioerosion of shelled organisms
FIGURE 5. Minute conulariid specimen. (A) Conulariid specimen of Archaeoconularia fecunda and trepostome bryozoan colony; coated with ammonium chloride, no. NMP L21990, locality Loděnice, Upper Ordovician, Zahořany Formation (lower Katian) (B) Micro-CT visualizing of inner surfaces. Scale bar equals 5 mm.
FIGURE 3 in Benefits and limits of x-ray micro-computed tomography for visualization of colonization and bioerosion of shelled organisms
FIGURE 3. Siliceous nodules of the Šárka Formation. (A, B) Pricyclopyge binodosa, complete trilobite, no. NMP L 35055, locality Praha-Šárka, Middle Ordovician (Darriwilian), (A) Enrolled trilobite coated with ammonium chloride, exterior of objects. (B) Micro-CT image showing dense burrows, interior of objects. (C, D) Rostrum with eyes of a trilobite P. binodosa, no. NMP L46892, locality Praha-Šárka, Middle Ordovician (Darriwilian). (C) Rostrum coated with ammonium chloride, exterior of objects. (D) Micro-CT visualization of tunnels, interior of objects. (E) Bivalve Redonia deshayesi, micro-CT image showing trace fossils, interior of objects, no. NMP L 51722, locality Osek, Middle Ordovician (Darriwilian). All scale bars equal 5 mm.
FIGURE 2 in Benefits and limits of x-ray micro-computed tomography for visualization of colonization and bioerosion of shelled organisms
FIGURE 2. Custom-made holders specially adapted for each scanned specimen. (A) Plastic cup. (B) Polystyrene holder. (C) Aluminum holder for small specimens. (D) Plastic tube filled with polystyrene.
FIGURE 1 in Benefits and limits of x-ray micro-computed tomography for visualization of colonization and bioerosion of shelled organisms
FIGURE 1. (A) Single x-ray projection. Schematic representation of positioning of the investigated object inside x-ray device. (B) Multiple x-ray projections as the object rotates. Positioning of investigated object inside micro-CT device. (C) Example of 3D dataset, i.e., a group of 2D slice images acquired by the MicroCT scanner. (D) Examples of Volume rendering; technique in visualization and computer graphics, used to display object from 3D data set in different aspects and orientations.
FIGURE 6 in Benefits and limits of x-ray micro-computed tomography for visualization of colonization and bioerosion of shelled organisms
FIGURE 6. Tube fragments of the serpulid polychaete Pyrgopolon (Pyrgopolon) deforme. Left images show exterior of objects; right images show interior of objects. (A) Specimen encrusted with bryozoan colonies and serpulid worms, boreholes assigned to Entobia Bronn, 1837, representing the most common ichnogenus in the examined serpulid tubes, no. MHNLM EMV 2016.3.14. (B) Intensely bored specimen preserving tunnels of ichnogenera Entobia and Trypanites Mägdefrau, 1932, no. MHNLM EMV 2016.3.44. (C) Serpulid tube with Entobia boreholes and encrusting juvenile oyster, no. MHNLM EMV 2016.3.40. Scale bar equals 1 cm.
Figure 1 in The first extinct species of Acritus LeConte, 1853 (Histeridae: Abraeinae) from Eocene Baltic amber: a microscopic beetle inclusion studied with X-ray micro-computed tomography
Figure 1. Photomicrographs of Acritus sutirca sp. nov., holotype, no. 5541 (MAIG), habitus: (a) ventral view; (b) dorsal view; (c) left lateral view; (d) frontal view. Scale bar represents 0.2 mm.
Figure 2. X in The first extinct species of Acritus LeConte, 1853 (Histeridae: Abraeinae) from Eocene Baltic amber: a microscopic beetle inclusion studied with X-ray micro-computed tomography
Figure 2. X-ray micro-CT renderings of Acritus sutirca sp. nov., holotype, no. 5541 (MAIG), habitus: (a) dorsal view; (b) left lateral view; (c) ventral view; (d) right lateral view. Scale bar represents 0.2 mm.
Figure 4. X in The first extinct species of Acritus LeConte, 1853 (Histeridae: Abraeinae) from Eocene Baltic amber: a microscopic beetle inclusion studied with X-ray micro-computed tomography
Figure 4. X-ray micro-CT renderings of Acritus sutirca sp. nov., holotype, no. 5541 (MAIG): (a–d) aedeagus in dorsal, ventral view and lateral views; (e) antennae. Scale bar represents 0.1 mm.
Figure 3. X in The first extinct species of Acritus LeConte, 1853 (Histeridae: Abraeinae) from Eocene Baltic amber: a microscopic beetle inclusion studied with X-ray micro-computed tomography
Figure 3. X-ray micro-CT renderings of Acritus sutirca sp. nov., holotype, no. 5541 (MAIG), habitus: (a) frontal view; (b) caudal view. Scale bar represents 0.2 mm. Abbreviations: a1 – antennomere 1 (scape); ey – compound eye; py – pygidium; pp – propygidium.
FIGURE 2 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography
FIGURE 2. Reconstructed tomographic images of the specimen (1) and its internal structure in median section (2). The lower and upper jaws are enlarged in (3) and (4), respectively.
FIGURE 5 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography
FIGURE 5. Three-dimensional reconstruction of the upper and lower jaws preserved in the body chamber of the specimen. The reconstructed parts are inside the specimen (1). The jaws are preserved close to each other (2).
FIGURE 1 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography
FIGURE 1. Left lateral (1), dorsal (2) and ventral (3) views of Phyllopachyceras ezoensis with preserved upper and lower jaws in situ within the body chamber. UMUT MM 27831 (modified from Tanabe et al., 2013).
FIGURE 7 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography
FIGURE 7. Result of segmentation of the upper jaw of the specimen, from frontal (1), rear (2), left-lateral (3) views and the transverse section of the area (4) indicated as a square in (3). The three-dimensional reconstruction (5) shows areal distributions of the "chitinous" lamellae and the calcareous covering. The reconstruction of the transverse section (6), which corresponds to (4), shows the architecture of the outer lamella. The abbreviations are indicated in (5).
FIGURE 6 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography
FIGURE 6. Result of segmentation of the lower jaw of the specimen, from lateral view which is restricted to its anterior and posterior portion (1). Three-dimensional reconstruction (2) suggests a wide distribution of calcareous material. The outer calcareous layer on the outer "chitinous" layer is partly taken off in (2). The transverse section of the area indicated as a square in (1) shows that the calcareous covering of the lower jaw also covers the internal surface of the "chitinous" lamella (3). The abbreviation is indicated in (2).
FIGURE 4 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography
FIGURE 4. Linear absorption coefficient (LAC) of the internal portions of the specimen estimated by their mean luminance values in the tomographic images. The numbers (1)-(10) correspond to the materials in Table 1. The dashed lines indicate the known values for the materials (Chantler et al., 2005) that could be expected to be observed in the specimen. Note that glycine is the most dominant amino acid in jaws of Octopus vulgaris (Hunt and Nixon, 1981). The relationship between LAC values and luminance values is based on the assumption that the LAC values for the surrounding air are zero and that the crystals precipitated in the phragmocone are calcite.
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