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444 results for “CT scan”
CT scans of COVID-19 patients
<p>Datasets contain CT scans of COVID-19 patients from Faculty hospital of Královké Vinohrady in DICOM (and TIFF) used in paper <em>Estimation of Covid-19 lungs damage based on computer tomography images analysis</em> presenting the tool is available on F1000reserach DOI: <a href="http://dx.doi.org/10.12688/f1000research.109020.1">10.12688/f1000research.109020.1</a>. The tool sued for the analysis of the dataset is published in Zenodo (<a href="https://doi.org/10.5281/zenodo.5805990">10.5281/zenodo.5805990</a>). Data were anonymized before exporting. Each patient has a folder with a unique ID, subfolder contains TIFF image for reach CT slice, and whenever possible DICOM files are added. All files contain ID and data format in the name. The CT data overview is in CSV for the whole dataset.</p> <p>Contributions:<br> Martin SCHÄTZ: Dataset preparation and couration<br> Olga RUBEŠOVÁ: Data selection and cleaning<br> David GIRSA: Data measuring and selection<br> Katarína NAĎOVA: Data measuring and selection</p> <p>The work was funded by the Ministry of Education, Youth and Sports by grant ‘Development of Advanced Computational Algorithms for evaluating post-surgery rehabilitation’ number LTAIN19007. The work was also supported from the grant of Specific university research – grant No FCHI 2022-001.</p>
Dual energy CT scan of ordinary objects
<p>Dual energy CT scan of ordinary objects: wires, pen, fruits (orange, avocado), pastery, bacon, butter, cheese.</p> <p>The purpose of these scans is to enable experimenting with CT scans using various kernels and iterative reconstructions. For instance, studying metal artifacts at different energies, material identification using dual energy index, examining the relation between reconstruction kernel sharpness, iterative reconstruction strength and noise.</p> <p>The dataset also can be used to set up mock trials, e.g. where readers have to choose the sharpest image, or the one with least disturbing metal artifacts. Similarly, it could serve debug purposes, e.g. testing the workflow, DICOM readers, etc.</p> <p>Zenodo-get ( https://doi.org/10.5281/zenodo.1261812 ) could be used to download the whole record at once.</p>
CT-Scan Image Dataset of Residual Fluid-Driven Fracture in a Molasse de Villarlod Sandstone Core - Post-Radial Hydraulic Fracture Experiment - M03 Sample
<h3><strong>Dataset Description</strong></h3> <p>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 (M03 sample). The experiment was designed to simulate fluid-driven fracture propagation and closure, and the resulting fracture path was preserved in the core sample.</p> <p><strong>Core Location in the M03 Cube Sample:</strong></p> <ul> <li><strong>Z:</strong> 12.5 cm</li> <li><strong>South-North:</strong> 12.5 cm</li> <li><strong>West-East:</strong> 11.5 cm to 1.36 cm (Coring direction)</li> </ul> <p>This spatial information specifies the exact location and orientation of the core extraction within the M03 cube sample.</p> <h4><strong>CT-scan instrument details:</strong></h4> <p>The M03 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.</p> <p>The volume data acquisition was performed in continuous helical mode, ensuring complete coverage of the sample’s height. For sample M03, 6 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.</p> <p>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.</p> <h4><strong>Key Features:</strong></h4> <ul> <li> <p><strong>Fracture Characteristics</strong>: 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.</p> </li> <li> <p><strong>CT-Scan Details</strong>: 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.</p> </li> <li> <p><strong>Material Information</strong>: 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.</p> </li> <li> <p><strong>Experimental Context</strong>: 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.</p> </li> </ul> <h4><strong>Applications:</strong></h4> <p>This dataset is particularly valuable for researchers and engineers involved in:</p> <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><strong>File Structure:</strong></h4> <p>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.</p> <h4><strong>Processing code:</strong></h4> <p>Follow the <strong>URL repository</strong> in the software section to access to the code for processing these images and reconstructing the fracture surfaces.</p> <p><strong>Acknowledgment:</strong></p> <p>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.</p> <p><strong>Contact and Support:</strong></p> <p>Email:</p> <p>Brice Lecampion: brice.lecampion@epfl.ch</p> <p>Mohsen Talebkeikhah: m.talebkeikhah@gmail.com</p>
Dataset of CT scans, slice photographs, and visual browning scores of 120 'Kanzi' apples
<p><strong>Summary</strong></p><p>This dataset is a collection of CT scans, slice photographs, and visual browning scores of 120 'Kanzi' apples.</p><p><br><strong>Description</strong></p><p><i>Sample information</i></p><p>In 2022, 120 'Kanzi' apples that had been stored under CA conditions (4 °C, 1 kPa O2, 1.5 kPa CO2) for 8 months were obtained from FruitMasters, The Netherlands. The fruit was grown in orchards surrounding Geldermalsen, the Netherlands, and harvested at physiological maturity in 2021.</p><p><i>CT acquisition</i></p><p>The dataset is acquired in the FleX-ray Laboratory, developed by TESCAN-XRE, located at CWI in Amsterdam. The CT scanner consists of a cone-beam microfocus polychromatic X-ray point source, and a 1944x1536 pixel, 14-bit, flat detector panel (Dexela1512NDT). Full details can be found in [Coban 2020]. A cone beam geometry with a circular trajectory was used to acquire 1440 projection images at an exposure time of 100ms, a tube peak voltage of 90kV, a current of 550uA, and 2 times binning, halving the detector resolution. Volumes were reconstructed with the FDK algorithm and a voxel size of 129.3um. Beam hardening correction was used from the FleXbox package [Kostenko 2020]. To make sure that the grey values could be compared between scans the spectral sensitivity of the scanner was first estimated for each scan individually and the average of these estimates was used for beam hardening correction on all CT scans. All apples were scanned with the stem side on top. Moreover, a line was drawn on all apples from the stem to the calyx. The apples were put in the CT scanner so that the line was facing the X-ray source.</p><p>The CT volumes are saved as .tiff stacks. All volumes have been cropped to remove the background.</p><p><i>Slicing and photograph acquisition</i></p><p>One day after CT scanning, the apples were sliced using a modified meat-slicing machine (CaterChef, house brand of EMGA, Mijdrecht, The Netherlands), which is illustrated in the file slicing_machine_labels.png. The sliding surface of the meat-slicing machine was replaced by a transparent acrylic sheet, and a camera was placed behind the slicing surface. While in the machine, each apple was kept in place by a suction cup so that it could not rotate during the slicing. All apples were sliced from the stem end to the calyx end, with a slice thickness of roughly 4mm. Every time before slicing, a picture was taken of the remaining part of the apple through the transparent sliding surface. To ensure that all apples were roughly aligned to the CT scans, the apples were oriented so that the line drawn earlier was on top.</p><p>The slice photographs are saved as .png files. All photographs have been cropped to remove the background and to center the apple in the image.</p><p><i>Visual browning scores</i></p><p>After each apple was sliced it was also visually inspected, and a score from one to ten was given to describe the amount of browning in the apple.</p><p><strong>Related paper</strong></p><p>When using this dataset please consider citing the following paper. It explains how the dataset was collected and used for the first time:</p><p>Dirk Elias Schut, Rachael Maree Wood, Anna Katharina Trull, Rob Schouten, Robert van Liere, Tristan van Leeuwen, Kees Joost Batenburg, "Detecting internal disorders in fruit by CT. Part 1: Joint 2D to 3D image registration workflow for comparing multiple slice photographs and CT scans of apple fruit", 2023, <a href="https://arxiv.org/abs/2310.01987">arXiv preprint arXiv:2310.01987</a></p><p><br><strong>Research group</strong><br>This dataset was produced in a collaboration between the Computational Imaging group at Centrum Wiskunde & Informatica (CWI), and GREEFA.</p><p><a href="https://www.cwi.nl/research/groups/computational-imaging">https://www.cwi.nl/research/groups/computational-imaging</a><br><a href="https://www.greefa.com/nl/">https://www.greefa.com/nl/</a></p><p><strong>Contact details</strong><br>dirk [dot] schut [at] cwi [dot] nl</p><p><strong>Acknowledgments</strong><br>This work was funded by the Dutch Research Council (NWO) through the UTOPIA project (ENWSS.2018.003). The authors also acknowledge TESCAN-XRE NV for their collaboration and support of the FleX-ray laboratory.</p>
Fig. 14 in A new species of Copionodon representing a relictual occurrence of the Copionodontinae (Siluriformes: Trichomycteridae), with a CT-scan imaging survey of key subfamilial features
Fig. 14. Copionodon exotatos, holotype, MZUSP 120631, CT-scan image of posterior part of skull and Weberian capsule, dorsal view. Abbreviations: FR1, First Ray 1; CC, complex centrum; WC, Weberian capsule; VC, vertebrae centrum; PR, pleural ribs.
Fig. 15 in A new species of Copionodon representing a relictual occurrence of the Copionodontinae (Siluriformes: Trichomycteridae), with a CT-scan imaging survey of key subfamilial features
Fig. 15. Copionodon exotatos, holotype, MZUSP 120631, CT-scan images of left palatine and associated entopterygoid: a. dorsal view, b. ventral view, c. with entopterygoid removed. Abbreviations: PAL, palatine; EN, entopterygoid.
Fig. 13 in A new species of Copionodon representing a relictual occurrence of the Copionodontinae (Siluriformes: Trichomycteridae), with a CT-scan imaging survey of key subfamilial features
Fig. 13. Copionodon exotatos, holotype, MZUSP 120631, CT-scan image of opercle and interopercle, right side. Abbreviations: VOD, vestigial odontodes; OP, opercle; INT, interopercle. Lateral view.
Fig. 9 in A new species of Copionodon representing a relictual occurrence of the Copionodontinae (Siluriformes: Trichomycteridae), with a CT-scan imaging survey of key subfamilial features
Fig. 9. Copionodon exotatos, holotype, MZUSP 120631, CT-scan image of anterior portion of skull, dorsal view. Abbreviations: PMX, premaxilla; MX, maxilla; QUA, quadrate; PO, preopercle; ME, mesethmoid; AF, anterior fontanel; FR, frontal; DEN, dentary; PAL, palatine; AA, anguloarticular; LE, lateral ethmoid; HYO, hyomandibula.
Fig. 8 in A new species of Copionodon representing a relictual occurrence of the Copionodontinae (Siluriformes: Trichomycteridae), with a CT-scan imaging survey of key subfamilial features
Fig. 8. Collection site of Copionodon exotatos, right-hand branch of Riacho do Mosquito (trib. to rio Santo Antônio, rio Paraguaçu drainage), immediately upstream from Cachoeira do Mosquito (12º21'59.51"S, 41 ºS 22"19.37"W) at exit of rock-enclosed sector.
Fig. 5 in A new species of Copionodon representing a relictual occurrence of the Copionodontinae (Siluriformes: Trichomycteridae), with a CT-scan imaging survey of key subfamilial features
Fig. 5. Copionodon exotatos, paratype, MZUSP 121656, basibranchials and hypobranchials, dorsal view. Grey areas represent cartilage. Abbreviations: BB2-4, basibranchials 2 to 4; HB1-3, hypobranchials 1 to 3. Scale bar = 1 mm.
Fig. 4 in A new species of Copionodon representing a relictual occurrence of the Copionodontinae (Siluriformes: Trichomycteridae), with a CT-scan imaging survey of key subfamilial features
Fig. 4. Copionodon exotatos, paratype, MZUSP 121656, opercle and interopercle, right side, lateral view. Abbreviations: OPOD, opercular odontodes; OP, opercle; INT, interopercle. Scale bar = 1 mm.
Figure 14 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 14. – Schematic illustrations of the occipital process and part of posterior cranial fontanel in species of Mastiglanis. A: Mastiglanis durantoni, MZUSP 118119, paratype; B-G: M. asopos, B: MZUSP 93307 (Rio Negro basin), C: MZUSP 81411 (Rio Negro basin), D: MZUSP 86958 (Rio Preto da Eva basin), E-G: MZUSP 97150 (Rio Xingu basin). Scale bars = 1 mm.
Figure 13 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 13. – CT scan image of posterior portion of skull and anterior part of vertebral column of Mastiglanis durantoni, MZUSP 118118, paratype, ventral view. Anterior to top. Abbreviations: bo, basioccipital; ex, exoccipital; fr, frontal; pa, parasphenoid; par, parapophysis; plr, pleural rib; pro, prootic; pt, pterotic; ptr, pterosphenoid; pts, posttemporo-supracleithrum; sph, sphenotic; tp4a, anterior ramus of transverse process of vertebra 4; tp4p, posterior ramus of transverse process of vertebra 4; tp5, transverse process of vertebra 5; tr, tripus; trs, transscapular process; vc5-7, vertebral centra 5 to 7.
Figure 12 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 12. – CT scan image of suspensorium of Mastiglanis durantoni, MZUSP 118118, paratype, lateral view. Anterior to left. Abbreviations: ent, entopterygoid; hy, hyomandibula; io, interopercle; mt, metapterygoid; op, opercle; po, preopercle; qu, quadrate; sbpo, subpreopercle; spo, suprapreopercle.
Figure 9 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 9. – Live specimen of Mastiglanis durantoni n. sp, lateral view, French Guiana (photo by P.Y. Le Bail). Specimen not preserved.
Figure 6 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 6. – CT scan image of premaxilla of Mastiglanis durantoni, MZUSP 118118, paratype. A: Dorsal view; B: Ventral view. Anterior to top.
Figure 7 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 7. – CT scan image of lower jaw of Mastiglanis durantoni, MZUSP 118118, paratype, lateral view, left side, anterior to left. Abbreviations: aa, anguloarticular; den, dentary; lsp, opening for latero-sensory pore; tr, trabeculae.
Figure 5 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 5. – CT scan image of anterior portion of neurocranium of Mastiglanis durantoni, MZUSP 118118, paratype, dorsal view. Abbreviations: fr, frontal; le, lateral ethmoid; me, mesethmoid.
Figure 3 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 3. – Heads in ventral view, showing difference in upper-jaw lengths. A: Mastiglanis durantoni, n. sp., paratype, MZUSP 118118, 46.9 mm SL; B: Mastiglanis asopos, paratype, MZUSP 7446, 43.9 mm SL.
Figure 2 in Mastiglanis durantoni from French Guyana, a second species in the genus (Siluriformes: Heptapteridae), with a CT scan survey of phylogenetically-relevant characters
Figure 2. – Mastiglanis durantoni, n. sp., holotype, MNHN 2015- 244, 63.7 mm SL. (A) Dorsal and (B) ventral views of head.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.