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opencc-by-4.0Dec 2018View details →

FIGURE 4. A in Testing the impact of two key scan parameters on the quality and repeatability of measurements from CT scan data

FIGURE 4. A video moving through slices of a pteropods shell scanned at 500 ms exposure time, with five xray radiographs averaged per view and an overall scan time of 75 minutes. There are streak artefacts perpendicular to the shell edge that are likely caused by beam hardening or shell movement during the scan. For video file, see https://palaeo-electronica.org/content/2020/ 2923-investigating-ct-scan-quality.

opencc-by-4.0Mar 2019View details →

Micro-CT scans, whole-test meshes, and internal chamber segments of planktonic foraminifera for three-dimensional analysis of inter- and intra-specific variation in ontogenetic growth trajectories

Here, we release tomographic reconstructions of 42 planktonic foraminifera from plankton tows and sediment traps, along with meshes and shrinkwrap meshes the whole tests and internal meshes of segmented chambers. Shrinkwrap meshes are test meshes that have been modified to close all pores and apertures in the test. Additionally, we have provided sample metadata for each specimen and volumetric measurements for the tests and chambers. This dataset was used in a study of ontogenetic growth in planktonic foraminifera and its variation within and among species.  The CT-scans and reconstructions were obtained at Naturalis Biodiversity Center in Leiden, the Netherlands with a Zeiss Xradia 520 Versa micro-CT scanner. The meshes and segments were created at Yale University. <ol> <li>Sample_Metadata.csv: Spreadsheet containing information on the sampling localities and dates for all specimens.</li> <li>Scan_data.csv: Spreadsheet containing metadata for all micro-CT scans including current strength, pixel size, voltage, image height, image width, and the number of images taken.</li> <li>Whole_Test_Measurements.csv:  Spreadsheet containing measurements of linear dimensions (axis1, axis2, axis 3), total number of chambers, calcite test volume, calcite test surface area, shrinkwrap volumes, and and shrinkwrap surface areas for all specimens.</li> <li>Chamber_Measurements.csv: Spreadsheet containing measurements of individual internal chamber segments, including position from the final chamber (F-chamber), position from the first chamber (Chamber), volume, and surface area.</li> <li>CT_Scan_Stacks.zip: reconstructed micro-CT image stacks (.tif files) for each specimen.</li> <li>Meshes.zip: Meshes of the test calcite, the shrinkwrap, and the internal chamber segments for each specimen (.stl 3D mesh files). Regular test meshes are named with the format “SampleID.stl”, and shrinkwrap meshes are named “SampleID-WRAP.stl”. Chamber meshes are named “SampleID-CH#.stl” and “SampleID-CH#-Wrap.stl”. Chambers are numbered in relation to their position from the final chamber, with “CH1” being the final chamber and “CH2” being the penultimate chamber.</li> </ol> This data is described and analyzed in the manuscript “Three-Dimensional Analysis of Inter- and Intraspecific Variation in Ontogenetic Growth Trajectories of Planktonic Foraminifera” submitted to the journal Marine Micropaleontology.

Fig. 10 in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 10. Comparison of the dorsal view of the preserved cranium of Messapicetus cf. longirostris (MDM-2029) with some stem beaked whales. The dotted ovals indicate the extent of the prenarial basin.

Fig. 7. 3D in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 7. 3D reconstruction resulting from the CT-scan of the ziphiid cetacean Messapicetus cf. longirostris Bianucci, Landini, and Varola, 1992 skull MDM-2029) inside two limestone slabs from the Tortonian of Menorca (Balearic Islands, Spain); in left lateral view (A1), left lateral view without the mandibles (A2), detail of the orbital area (A3).

Fig. 8 in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 8. CT-scan of the ziphiid cetacean Messapicetus cf. longirostris Bianucci, Landini, and Varola, 1992 skull (MDM-2029) inside two limestone slabs from the Tortonian of Menorca (Balearic Islands, Spain). A. Transverse section of the rostrum. B. Dorsal outline of the cranium showing the position of the section. C. Variation of the gray-value density along the transverse section of the rostrum.

Fig. 6. 3D in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 6. 3D reconstruction resulting from the CT-scan of the ziphiid cetacean Messapicetus cf. longirostris Bianucci, Landini, and Varola, 1992 skull (MDM-2029) inside two limestone slabs from the Tortonian of Menorca (Balearic Islands, Spain); in right lateral view (A1), right lateral view without the mandibles (A2), detail of the pterygoid hamuli showing the well-preserved transverse crests (A3).

Fig. 4. 3D in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 4. 3D reconstruction resulting from the CT-scan of the ziphiid cetacean Messapicetus cf. longirostris Bianucci, Landini, and Varola, 1992 skull (MDM-2029) inside two limestone slabs from the Tortonian of Menorca (Balearic Islands, Spain); in anterior view, showing transverse cross sections of the rostrum (A1–A4) made at different distances from the rostrum base. Not to scale.

Fig. 9 in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 9. CT-scan 3D reconstruction of the posterior portion of the left mandible of the ziphiid cetacean Messapicetus cf. longirostris Bianucci, Landini, and Varola, 1992 skull (MDM-2029) inside two limestone slabs from Tortonian of Menorca (Balearic Islands, Spain); in anterior (A1) lateral (A2) posterior (A3), and medial (A4) views.

Fig. 3. 3D in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 3. 3D reconstruction resulting from the CT-scan of the ziphiid cetacean Messapicetus cf. longirostris Bianucci, Landini, and Varola, 1992 skull MDM-2029) inside two limestone slabs from the Tortonian of Menorca (Balearic Islands, Spain), in dorsal (A1) and anterodorsal (A2) views.

Fig. 2 in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 2. The two limestone slabs showing longitudinal cross sections of the Messapicetus cf. longirostris skull (MDM-2029) from the Tortonian of Menorca (Balearic Islands, Spain). A. Surface of slab 1 (A1, top; A2, bottom), details of A2 (A3, A4, explanatory drawing). B. Surface of slab 2 (B1, top; B2, bottom).

Fig. 5. 3D in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 5. 3D reconstruction resulting from the CT-scan of the ziphiid cetacean Messapicetus cf. longirostris Bianucci, Landini, and Varola, 1992 skull (MDM- 2029) inside two limestone slabs from the Tortonian of Menorca (Balearic Islands, Spain); in ventral view (A1), ventral view without the mandibles (A2).

Fig. 11 in A new beaked whale record from the upper Miocene of Menorca, Balearic Islands, based on CT-scan analysis of limestone slabs

Fig. 11. Geographic distribution of fossil remains of Messapicetus from upper Miocene deposits worldwide (see text for data sources).

opencc-by-4.0Aug 2024View details →

CT-Scan Image Dataset of Residual Fluid-Driven Fracture in a Molasse de Villarlod Sandstone Core - Post-Radial Hydraulic Fracture Experiment - M04 Sample

<h3>Dataset Description</h3> This dataset contains high-resolution CT-scan images that capture the residual fracture surface within a core sample of Molasse de Villarlod Sandstone. The core sample was extracted after conducting a radial hydraulic fracture experiment on a 25 × 25 × 25 cm cubic block of sandstone (M04 Smaple). The experiment was designed to simulate fluid-driven fracture propagation and closure, and the resulting fracture path was preserved in the core sample. Core Location in the M04 Cube Sample: <ul> <li>Z: 12.5 cm</li> <li>South-North: 12.5 cm</li> <li>West-East: 13.5 cm to 23.3 cm (Coring direction)</li> </ul> This spatial information specifies the exact location and orientation of the core extraction within the M04 cube sample. <h4>CT-scan instrument details:</h4> The M04 sample was analyzed using an X-ray micro-CT scanner (RX-Solutions Ultratom) under consistent scanning protocols and parameters. A reflective 230 kV microfocus X-ray source (Hamamatsu L10801) equipped with a 0.2 mm thick copper filter, a tungsten cathode, and a tungsten target was employed for the imaging process. The scans were conducted with a voltage of 120 kV and a current intensity of 80 mA. The volume data acquisition was performed in continuous helical mode, ensuring complete coverage of the sample’s height. For sample M04, 5 full rotations were executed, with 1312 projections captured for each 360° rotation, allowing for highly precise volume reconstruction. The X-ray beam attenuation was recorded by an XL Varex Paxscan 2530HE plane detector with a resolution of 2176 x 1792 pixels, and an exposure time of 0.50 seconds per projection. The acquired projections were processed using RX-Solutions X-act software with Filtered Backprojection to reconstruct a corrected volume. This reconstruction yielded approximately 9000 slices in 16-bit TIFF format, with voxel dimensions of 10 x 10 x 10 microns, providing detailed insights into the internal structure of the sample. <h4>Key Features:</h4> <ul> <li> Fracture Characteristics: The fracture observed in the CT-scans represents a residual opening that remains post-fracturation. It is entirely contained within the core, showcasing the internal fracture geometry resulting from the hydraulic fracturing process. </li> <li> CT-Scan Details: The CT-scans were taken perpendicular to the fracture surface, offering a detailed cross-sectional view of the fracture at different depths. This orientation is critical for accurately capturing the fracture morphology and allows for the reconstruction of the fracture surface in 3D. </li> <li> Material Information: The core sample is composed of Molasse de Villarlod Sandstone, a sedimentary rock which is porous (18% porosity) and permeable. This material choice is relevant for studying fracture closure subjected to the leak-off of the fluid inside the porous medium. </li> <li> Experimental Context: The radial hydraulic fracture experiment aimed to simulate the propagation of hydraulic fracture and its closure due to the leakage of fluid inside fracture into the porous medium. The dataset provides valuable insights into fracture propagation patterns, surface roughness, and the effects of fluid-driven fractures in porous media. </li> </ul> <h4>Applications:</h4> This dataset is particularly valuable for researchers and engineers involved in: <ul> <li>Fracture mechanics and surface characterization</li> <li>3D reconstruction and visualization of fracture surfaces</li> <li>Surface roughness analysis</li> <li>Hydraulic fracturing studies</li> <li>Geomechanical modeling</li> </ul> <h4>File Structure:</h4> The dataset is organized into zip-folder contains .tif images corresponding to different depths within the core. Each tif-image is a CT-scan for that specific depth, labeled according to their position along the fracture path. <h4>Processing code:</h4> Follow the URL repository in the software section to access to the code for processing these images and reconstructing the fracture surfaces. Acknowledgment: We would like to extend our deepest thanks to Gary Perrenoud, Albert Taureg, and Lionel Pittet, the technical specialists of the PIXE platform at École Polytechnique Fédérale de Lausanne (EPFL). Their expertise and support in operating the CT-scan machine were important to the success of this research. We greatly appreciate their dedication and the high-quality work they provided. Contact and Support: Email: Brice Lecampion: brice.lecampion@epfl.ch Mohsen Talebkeikhah: m.talebkeikhah@gmail.com

opencc-by-nc-sa-4.0Sep 2024View details →

CT Scans of Spine with Metastases (Lytic, Sclerotic)

This dataset comprises 38 CT scans of the spine with identified and segmented metastatic lesions, focusing on two types of metastases: lytic and sclerotic. The dataset was used in the research article, "Artificial Intelligence Assisted Detection and Localization of Spinal Metastases." Each CT scan includes detailed metadata, such as: <ul> <li>Type of Metastasis: Classified as either lytic or sclerotic.</li> <li>Primary Site of Metastasis: The original location of the cancer that metastasized to the spine, including sites such as melanoma, lungs, ovary, breast, prostate, kidney, blader, large intestine, multiple myeloma, stomach.</li> <li>Sex: Patient gender (male or female).</li> </ul> This dataset was collected for research purposes and can serve as a valuable resource for further studies in oncology, radiology, and artificial intelligence-assisted diagnostics. The dataset is anonymized to ensure patient confidentiality. Edelmers, E.; Ņikuļins, A.; Sprūdža, K.L.; Stapulone, P.; Pūce, N.S.; Skrebele, E.; Siņicina, E.E.; Cīrule, V.; Kazu&scaron;a, A.; Boločko, K. AI-Assisted Detection and Localization of Spinal Metastatic Lesions. Diagnostics 2024, 14, 2458. https://doi.org/10.3390/diagnostics14212458

Fig. 40 in Morphology of the Braincase in the Cretaceous Hybodont Shark Tribodus limae (Chondrichthyes: Elasmobranchii), Based on CT Scanning

Fig. 40. Basicranial circulation in other elasmobranchs. A, Egertonodus (Hybodus) basanus, after Maisey, 1983; B, extant Heterodontus, after Maisey, 1983; C, extant Chlamydoselachus, after Allis, 1923 (reproduction from Maisey, 1983: fig. 25; positions of ''ora'' and ''opha'' changed from original figure to reflect their correct positions); D, Cladodoides, after Maisey, 2005; E, Tamiobatis, after Maisey, 2005 (left side: interpretation of Williams, 1998; right side: interpretation of Maisey, 2005); F, Orthacanthus, after Schaeffer, 1981. No scale.

Fig. 39 in Morphology of the Braincase in the Cretaceous Hybodont Shark Tribodus limae (Chondrichthyes: Elasmobranchii), Based on CT Scanning

Fig. 39. Oblique medial view of the Tribodus braincase showing the foramina for the efferent pseudobranchial and ophthalmic arteries. The internal carotid arteries emerge on the internal floor of the braincase after tunneling through the basicranial cartilage, and diverge to form a posterolaterally curving branch, which further diverges into the efferent pseudobranchial and ophthalmic arteries external to the cartilage, and an anterolaterally curving branch, the optic artery, which exits through the optic foramen. Compare with figure 38. No scale.

Fig. 33 in Morphology of the Braincase in the Cretaceous Hybodont Shark Tribodus limae (Chondrichthyes: Elasmobranchii), Based on CT Scanning

Fig. 33. Lateral view of the Egertonodus braincase (NHM P60110), anterior to the left (surface rendering). No scale.

Fig. 32 in Morphology of the Braincase in the Cretaceous Hybodont Shark Tribodus limae (Chondrichthyes: Elasmobranchii), Based on CT Scanning

Fig. 32. Transverse CT scan slices of the Egertonodus braincase, BM(NH) P60110. Otic and occipital regions. No scale.

Fig. 34 in Morphology of the Braincase in the Cretaceous Hybodont Shark Tribodus limae (Chondrichthyes: Elasmobranchii), Based on CT Scanning

Fig. 34. Medial view of the Egertonodus braincase (NHM P60110), sliced through the sagittal plane, anterior to the left (surface rendering). No scale.

Fig. 28. Tribodus limae cephalic spines. A–C, AMNH 13957, left cephalic spine. A in Morphology of the Braincase in the Cretaceous Hybodont Shark Tribodus limae (Chondrichthyes: Elasmobranchii), Based on CT Scanning

Fig. 28. Tribodus limae cephalic spines. A–C, AMNH 13957, left cephalic spine. A, lateral; B, dorsal; C, mesial views. D–E, AMNH 13959, right cephalic spine. D, mesial; E, lateral views. Scale bar is 1 cm.