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128 results for “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 5 in New look at Concavicaris woodfordi (Euarthropoda: Pancrustacea?) using micro-computed tomography
FIGURE 5. Inner layer of Concavicaris woodfordi (Cooper, 1932). A–C, anterior part of the specimen. A, tomogram (transversal slice). B, tomogram (transversal slice; colour-marked). C, anterior view (3D rendering). D–F, posterior part of the specimen. D, tomogram (transversal slice). E, tomogram (transversal slice; colour-marked). F, cross-section (3D rendering). G, cross-section of cephalothorax of a reptantian decapod (after Glaessner, 1969). H, I, cross-section of the carapace structure of a myodocopan (Euphilomedes japonica (Müller, 1890); after Yamada, 2019). H, attached region. I, duplicated region. Arrow indicates the rotation of the posterior part of the inner layer. Abbreviations: am, adductor muscles; app, appendage; cb, chitinous body; ef, epimeral fold; g, gills; hi, hinge; il, inner layer of the shield; ila, anterior part of the inner layer; ilp, posterior part of the inner layer; mua, attractor muscles; ol, outer layer of the shield; pl, pleural part; pta, posterior trunk appendages; so, shield outline; st, sternal part; te, tergal part. Scales: 5 mm.
FIGURE 2 in New look at Concavicaris woodfordi (Euarthropoda: Pancrustacea?) using micro-computed tomography
FIGURE 2. General view of Concavicaris woodfordi (Cooper, 1932). A, B, Right and left lateral views. C, line drawing (lateral view). D, location of virtual slices presented in the figures (dorsal view). Abbreviations: vld, ventro-lateral depression. Arrows indicate the anterior side of the specimen. Yellow doted lines indicate longitudinal sections. Green dotted lines indicate transversal sections. Scales: 10 mm. Photos: T. A. Hegna.
FIGURE 8 in New look at Concavicaris woodfordi (Euarthropoda: Pancrustacea?) using micro-computed tomography
FIGURE 8. Muscular structures of Concavicaris woodfordi (Cooper, 1932). A, tomogram. B, tomogram (colourmarked). C, gastric muscles (3D rendering). D, cross-section (3D rendering). E, adductor muscles (3D rendering). Abbreviations: am, adductor muscle; gm, gastric muscles; il, inner layer; lvp, latero-ventral pouch; s, shield; sto, stomach. Scales: A, B, D, 5 mm; C, E, 2 mm.
FIGURE 1 in New look at Concavicaris woodfordi (Euarthropoda: Pancrustacea?) using micro-computed tomography
FIGURE 1. Position and geology of the fossil locality. A, Map of USA with the position of Oklahoma (red area) and of Arbuckle Mountains (grey area). B, Map of Arbuckle mountains with the position of the type locality of Concavicaris woodfordi (Cooper, 1932). C, Section of the upper Woodford Shale at Interstate 35 road-cut section (I-35) (sec. 25, T2S, R2E, Arbuckle Mountains, Oklahoma, USA; redrawn after Over [1992]).
FIGURE 4 in New look at Concavicaris woodfordi (Euarthropoda: Pancrustacea?) using micro-computed tomography
FIGURE 4. Anatomy of Concavicaris woodfordi (Cooper, 1932). A, longitudinal virtual section. B, longitudinal virtual section (colour-marked). C, dorsal view (3D rendering). D, lateral view (3D rendering). Abbreviations: am, adductor muscles; cs, cylindrical structure; g2–7, gills; gm, gastric muscles;ila, anterior part of the inner layer; ilp, posterior part of the inner layer; lvp, latero-ventral pouch; pta, posterior trunk appendages; ra1–3, raptorial appendages; so, shield outline; sto, stomach. Arrows indicate the anterior side of the specimen. Scales: 10 mm.
FIGURE 3 in New look at Concavicaris woodfordi (Euarthropoda: Pancrustacea?) using micro-computed tomography
FIGURE 3. Marginal fold of Concavicaris woodfordi (Cooper, 1932). A, B, anterior part of the shield (tomogram and drawing). C, close-up of marginal fold in the anterior part of the shield (tomogram). D, E, middle part of the shield (tomogram and drawing). F, close-up of marginal fold in the middle part of the shield (tomogram). Abbreviations: il, inner layer; mf; marginal fold; so, shield outline. Scales: A, B, D, E, 5 mm; C, F, 1 mm.
FIGURE 7 in New look at Concavicaris woodfordi (Euarthropoda: Pancrustacea?) using micro-computed tomography
FIGURE 7. Digestive, reproductive, and circulatory systems of Concavicaris woodfordi (Cooper, 1932). A, longitudinal virtual section. B, longitudinal virtual section (colour-marked). C, D, digestive and reproductive systems (3D rendering). C, anterior view. D, right lateral view. E, F, G, circulatory system. E, tomogram. F, tomogram (colour-marked). G, 3D rendering of the left part. Abbreviations: cs, cylindrical structure; g1–8, gills; go, gonads; il, inner layer; lvp, lateroventral pouch; sto, stomach. Arrows indicate the anterior side of the specimen. Scales: A, B, 10 mm; C–G, 5 mm.
FIGURE 6 in New look at Concavicaris woodfordi (Euarthropoda: Pancrustacea?) using micro-computed tomography
FIGURE 6. Internal anatomy of Concavicaris woodfordi (Cooper, 1932). A, right lateral view (3D rendering). B, anterior view (3D rendering). C, dorsal view (3D rendering). D, longitudinal section (3D rendering). Abbreviations: am, adductor muscles; cs, cylindrical structure; g1–8, gills; gm, gastric muscles; go, gonads; lvp, latero-ventral pouch; pta1–3, posterior trunk appendages; r, rostrum; ra1, 3, raptorial appendages; s, shield; so, shield outline; sto, stomach. Arrows indicate the anterior side of the specimen. Scales: A, C, D, 10 mm; B, 5 mm.
FIGURE 10 in New look at Concavicaris woodfordi (Euarthropoda: Pancrustacea?) using micro-computed tomography
FIGURE 10. Hypothetical reconstruction of Concavicaris woodfordi (Cooper, 1932). Morphology of anterior and posterior sides of the shield, eyes and number of posterior trunk appendages are reconstructed based on Concavicaris submarinus (Jobbins et al., 2020). Abbreviations: ce, compound eyes; g, gills; go, gonads; il, inner layer: lvp, lateroventral pouch; pt, posterior trunk; pta, posterior trunk appendages; r, rostrum; ra, raptorial appendages; s, shield; sto, stomach. Arrow indicates the anterior side of the specimen. Scales: 10 mm.
FIGURE 9 in New look at Concavicaris woodfordi (Euarthropoda: Pancrustacea?) using micro-computed tomography
FIGURE 9. Appendages of Concavicaris woodfordi (Cooper, 1932). A, longitudinal section (3D rendering). B, raptorial appendages (3D rendering). C, tomogram. D, close-up of third posterior trunk appendage. E, posterior trunk appendages (3D rendering). Arrow indicates the third posterior trunk appendage. Abbreviations: il, inner layer; pta1–3, posterior trunk appendages; ra1–3, raptorial appendages; s, shield. Arrow indicates the anterior side of the specimen. Scales: A–C, 10 mm; D, G, 2 mm; E, 5 mm; F, 1 mm.
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.
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