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30 results for “synchrotron tomography”
Synchrotron X-ray Computed Tomography scan of a wasp
<h4>Contents:</h4><ul><li><i>bee_yazeed-20231001T170032.h5</i> - SXCT scan of a wasp performed at beamline <a href="https://www.sesame.org.jo/beamlines/beats">ID10-BEATS</a> of SESAME.</li><li><i>SESAME_wasp_yazeed.avi -</i> 3D video rendering of phase-contrast CT reconstruction of <i>bee_yazeed-20231001T170032</i>. The dataset was reconstructed using <a href="https://github.com/gianthk/alrecon/tree/master">alrecon</a>. The video was created using ORS Dragonfly.</li></ul><h4>H5 dataset information:</h4><ul><li>Raw experimental data (sinogram, flat fields and dark fields) and metadata are stored in a common .H5 file.</li><li>The HDF5 file is organized hierarchically following the <a href="https://dxfile.readthedocs.io/en/latest/">Scientific Data Exchange (DXfile)</a> community standard.</li></ul><h4>How to reconstruct:</h4><ul><li>You can use <a href="http://www.silx.org/">Silx</a> to read and explore the .H5 dataset.</li><li>The file can be read within Python using the <a href="https://dxchange.readthedocs.io/en/latest/">DXChange</a> package.</li><li>See the <a href="https://beats.readthedocs.io/reconstruction.html">ID10-BEATS beamline user guide</a> for a detailed description on how to process and reconstruct the scan.</li></ul>
A Dataset for In-situ synchrotron tomography experiments to investigate anisotropic damage of line pipe steel
<p>In this study, anisotropic ductility and associated damage mechanisms of a grade X100 line pipe steel were investigated using in-situ synchrotron-radiation computed tomography (SRCT) of notched round bars. Line pipe materials have anisotropic mechanical properties, such as tensile strength, ductility and toughness. Specimens were tested for loading along both rolling (L) and transverse (T) directions. The <em>in-situ</em> data collected allowed quantifying both specimen deformation (evolution of the cross section) and microscopic damage parameters such as porosity, void shape and void orientation. The data sets provide here are related to the paper <em>"On the origin of the anisotropic damage of X100 line pipe steel, Part I: in-situ synchrotron tomography experiments"</em> being published in <a href="https://www.springer.com/journal/40192">Integrating Materials and Manufacturing Innovation</a>. For each testing direction, dataset are provided using hdf5 and xdmf standarded exchange format. A compressed file is also provided in connection with the analyses explained in the article.</p>
Advancing Vanadium Redox Flow Battery Analysis: A Deep Learning Framework for High-Throughput 3D Visualization and Bubble Quantification via Synchrotron X-ray Tomography
<p>Dataset and model of UTILE-Redox - Deep Learning based Tool for Autonomous 3D Bubble Analysis of Vanadium Flow Batteries from Synchrotron X-ray Imaging. This project focuses on the deep learning-based automatic analysis of Vanadium Redox Flow Batteries (VRFB) Synchrotron X-ray tomographies. This repository contains the Python implementation of the UTILE-Redox software for automatic volume analysis, feature extraction, and visualization of the results.</p>
Translaminar Fracture in a Mini-Protruded Compact Tension Specimen: A Dataset of Micro-Scale Tomograms of a Thin-Ply Carbon Fibre-Epoxy Composite acquired via Synchrotron Radiation Computed Tomography During In-Situ Loading
<p>In this study, we developed a scaled-down “mini-protruded compact tension specimen” to facilitate in-situ tensile testing coupled with synchrotron radiation computed tomography (SRCT). This innovative design provides valuable insights into in-situ translaminar damage mechanisms, significantly enhancing the accuracy of data used in finite element models.</p> <p>The specimen is made of HS40 carbon fibres and ThinPreg<sup>TM </sup>736LT epoxy resin, with the layup of [90<sub>2</sub>/0/90<sub>2</sub>/0/90<sub>2</sub>/0/90<sub>2</sub>]. The translaminar fracture experiments were conducted under continuous loading and scanning using ultra-fast SRCT at the Swiss Light Source (SLS) TOMCAT beamline (Paul Scherrer Institut in Villigen, Switzerland). A polychromatic beam with an energy of 24 keV was used. The achieved voxel size was 800 <em>nm</em>, and 1000 projections per scan and 2 <em>ms</em> exposure time were acquired per scan. The GigaFRoST camera served as the detector. The scans were reconstructed into 3D volumes using the SLS’s in-house absorption-based algorithm (Gridrec) for critical loading steps during a test—both before and after a load drop (detailed in the accompanying Excel file). The tensile loading was exerted on the specimen at a rate of 0.2 <em>mm/min</em> until failure during scanning with the Deben CT500.</p>
FIGURE 7 in Synchrotron-radiation computed tomography uncovers ecosystem functions of fly larvae in an Eocene forest
FIGURE 7. Diversity of fly larvae in Baltic amber. A, SMF-BE-10652, ventral view; B, same, trunk end, ventral view; C, Heleomyzidae, puparium, Dip-00890, dorsal; D, same, anterior spiracles; E, same, ventral view; F, same, posterior spiracles, dorsal view.
FIGURE 4 in Synchrotron-radiation computed tomography uncovers ecosystem functions of fly larvae in an Eocene forest
FIGURE 4. Representatives of Cyclorrhapha, morphotype 1, AKBS-0030. A, reconstruction of the Baltic amber forest: feces with larvae of Cyclorrhapha, morphotype 1 larvae at the front; the adult fly Gedanoleria eocenica Woźnica, 2019 (Heleomyzidae) at the feces; the early horse Eurohippus messelensis feeding at the background, representing hypothetical herbivores, which may have left feces, preserved as organic mass in the amber piece (Artist: Natalia Jagielska); B, SR-µCT scan render of the full amber piece, organic mass in light-grey and larvae in red; C, surface rendering on the SR-µCT scan, organic mass in violet and larvae in orange; D, surface renders of the individual larvae.
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.
FIGURE 3 in Non-destructive analysis of in situ ammonoid jaws by synchrotron radiation X-ray micro-computed tomography
FIGURE 3. Serial cross-sections of the body chamber portion of the specimen cut from the venter (1) to the dorsum (4), in which sectioned images of the upper jaw are shown. Note that the vertical stripes are due to the separated scanning.
3D video renderings of synchrotron tomography data from the CERIC beamtime proposal 20217193
<p>3D video renderings of corroded roman glass sample from synchrotron X-ray micro Computed Tomography data collected within the CERIC beamtime proposal 20217193.</p> <table> <caption>Uploaded videos</caption> <thead> <tr> <th scope="col">File</th> <th scope="col">Description</th> </tr> </thead> <tbody> <tr> <td>581681_whole_sample.avi</td> <td>Overview of the investigated glass specimen.</td> </tr> <tr> <td>581681_HR_pit.avi</td> <td>High-resolution rendering of glass corrosion pit.</td> </tr> <tr> <td>581681_HR_pit_voids_particles.avi</td> <td>HR video of the corrosion pit highlighting void spaces and secondary corrosion products.</td> </tr> <tr> <td>581681_HR_pit_particles-volume.avi</td> <td>HR video of the corrosion pit highlighting sediment particles and their volume.</td> </tr> </tbody> </table> <p> </p>
Data reduction for in situ synchrotron tomography experiments
<p>This dataset corresponds to a series of phase-enhanced tomographic images recorded during a monotonic mechanical tensile test with a polymer material.<br> <br> Tomographic measurements were performed at the PSICHE beamline, SOLEIL synchrotron. The reconstructed voxel size is 1.3 µm. The reconstruction was performed with pyHST (filtered back-projection) using the paganin filter with a propagation distance of 15 pixels. Each tomography measurement consists of 1000 radiographs of 1024×2048 pixels acquired over 180°. The binary reconstructed volumes are therefore 1024×2048×2048 voxels encoded with a dynamic range of 32 bits (floating-point).<br> <br> The 44 measurements taken during the mechanical test represent a volume of 700 GB. The reduction strategy used is based on a thresholding of the specimen in each volume and a zeroing of the voxels outside the sample. In the preserved voxels, the binary representation of each value is truncated to have a precision of the order of the experimental uncertainties: the insignificant least significant bits are replaced by 0s which, combined with a transposition of the order of the bits just before compression (bit shuffling), makes it possible to drastically increase the compressibility of the data. The data is arranged in an HDF5 container using block access with on-the-fly compression/decompression. The total size of the dataset is thus reduced with a reduction ratio of 16:1 using Zstandard level 1. The mask used as well as even smaller volumes (pixel binning 2×2 and 4×4, dynamic range reduction on 4 or 8 bits) are added to allow fast access to very small data if needed, in the same fashion as the thumbnail used in some 2D image formats.<br> <br> The footprint of the reduced version as described is 47 GB. The format is self-described and contains additional metadata.</p>
Data from U and Th zonation in apatite observed by synchrotron X–ray fluorescence tomography and implications for the (U–Th)/He system Sousa et al 2024
<p>Data from </p> <p><span>U and Th zonation in apatite observed by synchrotron X–ray fluorescence tomography and implications for the (U–Th)/He system</span></p> <p><span>Sousa et al</span></p> <p><span>Geochronology</span></p>
Segmented primary phases of Al-alloy EN AW-2618A in the T61 state using synchrotron computed tomography
<p><span>This video shows the primary phases of the aluminum alloy EN AW-2618A in the T61 state measured by synchrotron computed tomography. </span></p> <p><span>Further information is provided in the file content.pdf. </span></p>
Figure 9. Synchrotron radiation X in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 9. Synchrotron radiation X-ray phase-contrast micro-tomography (A, B) and scanning electron microscopy (C–F) of gnathopods of Orchomenella rinamontiae. Paratypes, ♂♂, 11.3 mm (A, B) and 11.3 and 15.4 mm (C–F). A, lateral view of right gnathopod 2. B, medial view of right gnathopod 2. C, lateral view of less gnathopod 1. D, medial view of right gnathopod 1. E, lateral view of less gnathopod 2. F, medial view of right gnathopod 2. Abbreviations: a, gnathopod 1 lateral spine; b, gnathopod 1 medial spine; c, gnathopod 2 tip of dactyl. Scale bars: 200 µm.
Figure 1. Synchrotron radiation X in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 1. Synchrotron radiation X-ray phase-contrast micro-tomography of Orchomenella rinamontiae. Paratype, ♂, 11.3 mm. Volume renderings of lateral less view (A) and ventral view (B). Abbreviations: A1, antenna 1; A2, antenna 2; Gn1, gnathopod 1; Gn2, gnathopod 2. Scale bar: 4.0 mm.
Figure 4. Synchrotron radiation X in A new Antarctic species of Orchomenella G.O. Sars, 1890 (Amphipoda: Lysianassoidea: Tryphosidae): is phase-contrast micro-tomography a mature technique for digital holotypes?
Figure 4. Synchrotron radiation X-ray phase-contrast micro-tomography of Orchomenella rinamontiae. Paratype, ♂, 11.3 mm. Volume renderings of the mouth in ventral view (A), higher magnification of the right mouthparts in ventral view (B), right mouthparts in median view (C), and mouth in dorsal view with the observation point inside the animal (D). Abbreviations: a, outer plate maxilliped; b, inner plate maxilliped; c, outer plate maxilla 2; d, inner plate maxilla 2; e, palp maxilla 1; f, outer plate maxilla 1; g, inner plate maxilla 1. Scale bars: 200 µm.
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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.