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2,001 results for “x-rays”
Hyperspectral X-ray CT Voxelized TV reconstruction of a single, iodine-stained lizard head sample
<p><strong>Dataset description</strong></p> <p>These datasets are voxel based reconstructions of hyperspectral CT data using the Core Imaging Library (CIL). They are stored as NeXus files (derived from hdf5) which can be read in, visualised and manipulated using CIL.</p> <p> - PDHG_TV_1000_Sp_alpha_0.004.nxs</p> <p>Is the solution after 1000 iterations of PDHG with TV applied in the spatial domain. </p> <p> - PDHG_TV_1000_SpCh_alpha_0.003_beta_0.5.nxs</p> <p>Is the solution after 1000 iterations of PDHG with TV applied both in the spatial domain, and in the energy (channel) domain. </p> <p> </p> <p><strong>Dataset intended use</strong></p> <p>These datasets are used in the CIL training notebook:</p> <p>https://github.com/TomographicImaging/CIL-Demos/blob/main/examples/3_Multichannel/03_Hyperspectral_reconstruction.ipynb</p> <p>They can be imported using CIL, with the following code snippet:</p> <pre><code class="language-python">from cil.io import NEXUSDataReader reader = NEXUSDataReader(file_name='path/to/data/PDHG_TV_1000_Sp_alpha_0.004.nxs') data = reader.read()</code></pre> <p> </p>
Supplemental Material to Journal Article "Determination of as-built properties of fiber reinforced polymers in a wind turbine blade using scanning electron and high-resolution X-ray microscopy"
<p>This set supplements the figure data to the article "Determination of as-built properties of fiber reinforced polymers in a wind turbine blade using scanning electron and high-resolution X-ray microscopy", DOI: <a href="https://doi.org/10.1016/j.jcomc.2022.100310">https://doi.org/10.1016/j.jcomc.2022.100310</a></p>
X-ray diffraction patterns of the effects of dATP on permeabilized porcine myocardium
<p>X-ray and mechanical experiments were performed using permeabilized porcine left ventricle wall muscle. The frozen muscle was thawed in skinning solution at room temperature before dissection into smaller strips and skinned at room temperature for 3 hours. Permeabilized fiber bundles were further dissected into preparations with a length of 4 mm with a diameter of 200 µm prior to attachment of aluminum T-clips to both ends for X-ray experiments. X-ray diffraction patterns were collected at BioCAT beamline on a MarCCD 165 detector (Rayonix Inc., Evanston IL) with a 1 s exposure time as a function of five increasing dATP compositions (0%, 2%, 10%, 25%, and 100%) with the total NTP concentration (dATP + ATP) remaining constant at 2.5 mM after 10 min incubation in each solution.</p>
Single crystal X-ray diffraction data of Th-TCPE and Ce-TCPE
<p><span>Two new </span><span>MOFs (Th/ Ce </span><span>-TCPE) based on 1,2,4,5-tetrakis(4-carboxyphenyl)ethylene (H4TCPE) were obtained using a straightforward reaction under moderate conditions. Th and Ce form</span><span>ed</span><span> the central units of this MOF in the mononuclear and in the unusual trinuclear cluster configurations, respectively. The resulting MOFs were analyzed by fluorescence spectroscopy to understand their luminescence. The obtained data revealed that benzene's electron cloud density and torsion angle on the ligand were affected by the acetic acid molecule and Th(IV), which caused Th-TCPE to irradiate stronger blue emission, but Ce-TCPE showed no fluorescence due to the self-quenching. Such unique luminescence property could be used for fluorescence or radiopharmaceutical sensing.</span></p>
Sensor data for "Influence of X-Ray Radiation on Historical Paper"
<p>This is the raw and processed data used in the paper "Influence of X-Ray Radiation on Historical Paper". It consists of the following:</p> <ol> <li>all images in the CR3 format, taken before, during, and after irradiation of the paper,</li> <li>the images converted to JPEG, as well as crops of the relevant parts stored as nupy arrays</li> </ol>
ODP Site 1249, ODP Site 1252, and IODP Site U1325: X-ray fluoresence core scanning, laser diffraction grain size, CNS elemental/isotopic, environmental magnetism, and age model data
<p>We present data used as part of an integrative early diagenesis study (submitted September 2022 to Marine Geology) focused on identifying zones of magnetite dissolution and pyrite precipitation in which magnetic susceptibility records are altered in gas-hydrate bearing sediments on the Cascadia Margin using archived cores from the Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP). We analyzed the upper 85 to 100 m below seafloor (mbsf) from ODP Sites 1249 and 1252, and IODP Site U1325. ODP 1249 is at the summit of Hydrate Ridge in an area of active methane seepage and massive gas hydrate accumulations and ODP 1252 is in a nearby slope basin with little occurrence of hydrate. IODP Site U1325 is on the northern Cascadia Margin in a slope basin, with turbidite-hosted gas hydrate. We also include XRF data from the upper sections of ODP Site 1251, IODP U1327, and U1328.</p> <p>We measured X-ray fluorescence using an Avaatech core scanner at the IODP Gulf Coast Repository at Texas A&M University. We measured total carbon, total organic carbon (TOC), total nitrogen, and total sulfur using a Perkin Elmer 2400 Series CHNS/O Analyzer at the university of New Hampshire (ODP Site 1249 and 1252 only). A subset was analyzed for δ<sup>13</sup>C-TOC using a Costech ECS 4010 elemental analyzer interfaced with a Thermo Finnegan Delta Plus XP continuous flow isotope ratio mass spectrometer at Washington State University. Grain size was measured with a Malvern Mastersizer 2000 laser diffraction particle size analyzer and Hydro 2000G dispersal unit at the University of New Hampshire. Mass frequency-dependent magnetic susceptibility was measured using a Bartington MS2 Magnetic Susceptibility Meter and Bartington MS2B dual frequency sensor (Site U1325 only). Isothermal remanent magnetization and thermal demagnetization curves were measured using a HSM2 SQUID-based Spinner Magnetometer with an ASC Scientific IM-10-30 Impulse Magnetizer and ASC Scientific TD-48SC magnetically-shielded oven (Site U1325 only). Radiocarbon was measured on mixed planktic foraminifers at the Radiocarbon was measured at National Ocean Sciences Accelerator Mass Spectrometry (NOSAMS) facility at Woods Hole Oceanographic Institution (ODP Site 1252 and IODP Site U1325).. Radiocarbon ages were calibrated to calendar ages using CALIB 8.2 and the Marine20 calibration curve. For ODP Site 1252 we used a reservoir correction of 230 ± 50 years (Yaquina Bay, Oregon, USA) and for IODP Site U1325 we used a reservoir correction of 202 ± 50 years (Amphitrite Point, British Columbia, Canada). δ<sup>18</sup>O was measured on benthic foraminifer <em>Uvigerina peregrina</em> tests using a Finnegan MAT 252 isotope ratio mass spectrometer with Kiel III device at the Oregon State University Stable Isotope Laboratory (ODP 1252) and a Finnegan MAT 253 isotope ratio mass spectrometer with Kiel IV device at the University of Michigan Stable Isotope Laboratory (ODP Site 1249 and IODP Site U1325).</p>
X-ray diffraction data of twinned gamma-form of o-nitroaniline
<p>The diffraction data are of the gamma-form of o-Nitroaniline, C<sub>6</sub>H<sub>6</sub>N<sub>2</sub>O<sub>3</sub>. This compound is known to be polymorphic; the alpha-form is probably amorphous, while the beta- and gamma-forms are crystalline. Difficulties with the unit-cell determination of the gamma-form were reported as a consequence of twinning. These newly recorded diffraction data are of a twinned crystal.</p> <p>The raw data and processing with EVAL are described in details in IUCrData as a Raw Data Letter [Lutz & Kroon-Batenburg, IUCrData (2022].</p> <p>The data were recorded on a Bruker ApexII diffractometer and stored as .sfrm files. They were also converted with Bruker imagesum.py script as part of the APEXII software to full .cbf files.</p>
Data for publication: Nanomechanical and Structural Study of Au38 Nanocluster Langmuir-Blodgett Films Using Bimodal Atomic Force Microscopy and X-Ray Reflectivity
<p>Original data of Figures published in:</p> <p><strong>Nanomechanical and Structural Study of Au<sub>38</sub> Nanocluster Langmuir-Blodgett Films Using Bimodal Atomic Force Microscopy and X-Ray Reflectivity</strong></p> <p>Journal of Colloid and Interface Science, 2022, Michal Swierczewski<sup>,</sup> Alexis Chenneviere, Lay-Theng Lee, Plinio Maroni and Thomas Bürgi*<sup>[</sup></p> <p> </p>
Scanning x-ray diffraction data on cardiac tissue
<p>Dataset used in conjunction with the article "Scanning X-ray Diffraction on Cardiac Tissue: Automatized Data Analysis and Processing" published in Journal of Synchrotron Radiation (2017). </p> <p>An example script to analyze the data is available within the toolbox described in the above mentioned article. The toolbox is available on https://irpgoe.github.io/nanodiffraction/.</p> <p> </p> <p> </p>
X-Ray Diffraction Data Cubic Insulin and Thaumatin SSX for RIP phasing
<p>Diffraction images collected on dectris Pilatus. Format of images in *.cbf.</p> <p>Images collected with Mesh and Collect strategy at ESRF.</p> <p>Thaumatin : contain 6 sets of exposure reflecting 6 increasing Dose (from 1 to 6)</p> <p>Cubic Insulin : contain 3 sets of sub-data sets : Before_1 and Before_2 (means before UV irradiation). and After : (after UV irradiation).</p> <p>For full information refer to material and method in : (<em>submit, will be update</em>)</p>
X-ray flux data
<p>This dataset contains X-ray flux data from March 1, 2001 through October 18, 2017. The source of this data is the National Oceanic and Atmospheric Administration (NOAA - https://www.ngdc.noaa.gov/stp/spaceweather.html) or, more specifically, at https://satdat-vip.ngdc.noaa.gov/sem/goes/data/new_full</p> <p>The samples are generated every 2 or 3 seconds. Each tuple has the following information separated by a comma:</p> <ul> <li>time_tag: Date and time for each observation in the format YYYY-mm-dd hh:mm:ss.SSS UTC"</li> <li>xs: X-ray short wavelength channel irradiance (0.5 - 0.3 nm);</li> <li>xl: X-ray long wavelength channel irradiance (0.1 - 0.8 nm);</li> <li>"-99999" indicates missing values.</li> </ul> <p>The scripts used to obtain this data from the NOAA website are available in the repository https://gradvohl.github.io/xrayflux</p> <p>The file is compressed with tar and gunzip.</p>
0.48 Angstrom 3,5-dinitrobenzoic acid (3,5-DNBA) C2/c polymorph single crystal X-ray diffraction data set recorded at Diamond Light Source I19-1
<p>Data set from 3,5-dinitrobenzoic acid (3,5-DNBA) C2/c polymorph recorded during in house research (DLS proposal: NR18193). Each run is saved as a single compressed tar file for convenience, runs 1, 2, 3 correspond to 3 x 170 degree omega scans at phi 0, 120, 240 degrees with 2-theta of 30 degrees, run 4 phi scan at 2-theta 0, runs 5-8 omega scans at 2-theta 55 degrees, giving data to 0.48A.</p> <p> </p> <p>Now including scale factor graph & report from processing</p>
Compounds with multi-target activity from X-ray structures, corresponding analog series, and associated scaffolds
<p>A total of 702 crystallographic ligands with activity against multiple targets from different protein families (multi-family ligands) were extracted from the Protein Data Bank (PDB). These ligands are made available as aromatic non-stereo SMILES strings together with their target information. A subset of these ligands were also found in the ChEMBL database yielding additional target annotations. Target and family assignments were made following the UniProt classification scheme. In addition, 133 analog-series-based (ASB) scaffolds were derived from series of PDB ligands and structural analogs identified in ChEMBL, which are also made available. For each ASB scaffold, the number of analogs, targets, and target families is provided (union of PDB and ChEMBL annotations).</p>
Data and example reconstruction code for "Investigating the missing wedge problem in small-angle x-ray scattering tensor tomography across real and reciprocal space"
<p>Data sets and example code for the paper "Investigating the missing wedge problem in small-angle x-ray scattering tensor tomography across real and reciprocal space".</p> <p> </p> <p>Requires the software Mumott, see: https://doi.org/10.5281/zenodo.7798530</p>
Radiographic data of a wooden block with metal markers at the J. Paul Getty Museum X-ray facility
<p><strong>Summary</strong></p> <p>This submission contains radiographic data containing metal markers of a small wooden block. </p> <p>The data is made available as part of [Bossema et al., 2024].</p> <p><em> </em></p> <p><strong>Apparatus</strong></p> <p>The dataset is acquired using the X-ray facility located at the J. Paul Getty Museum, Los Angeles. Full details can be found in [Bossema et al., 2024].</p> <p><em> </em></p> <p><strong>List of Contents</strong></p> <p>The content of the submission is given below. All raw data (i.e. no corrections) is made available in .tif format.</p> <p>The folder contains:</p> <ul> <li>darks: folder containing darkfield images, IMG<em>*.dicom</em></li> <li>flats: folder containing flatfield images, IMG<em>*.dicom</em></li> <li>data1: raw (unprocessed or uncorrected) projection data, IMG<em>*.dicom</em></li> <li>data2: raw (unprocessed or uncorrected) projection data, IMG<em>*.dicom</em></li> </ul> <p> </p> <p><strong>Additional Links</strong></p> <p>Accompanying code can be found here.</p> <p><em> </em></p> <p><strong>Contact Details</strong></p> <p>For more information or guidance in using these datasets, please get in touch with </p> <ul> <li>bossema [at] cwi.nl</li> </ul> <p><strong>References</strong></p> <p><a href="https://www.nature.com/articles/s41467-024-48102-w">Bossema, F.G., Palenstijn, W.J., Heginbotham, A. <em>et al.</em> Enabling 3D CT-scanning of cultural heritage objects using only in-house 2D X-ray equipment in museums. <em>Nat Commun</em> <strong>15</strong>, 3939 (2024). https://doi.org/10.1038/s41467-024-48102-w</a></p> <p><em> </em></p> <p> </p>
Radiographic data of a wooden block with metal markers at the Rijksmuseum X-ray facility
<p><strong>Summary</strong></p> <p>This submission contains radiographic data containing metal markers of a small wooden block. </p> <p>The data is made available as part of [Bossema et al., 2024].</p> <p><em> </em></p> <p><strong>Apparatus</strong></p> <p>The dataset is acquired using the X-ray facility located at the Rijksmuseum, Amsterdam. Full details can be found in [Bossema et al., 2024].</p> <p><em> </em></p> <p><strong>List of Contents</strong></p> <p>The content of the submission is given below. All raw data (i.e. no corrections) is made available in .tif format.</p> <p>The folder contains:</p> <ul> <li>darks_flats: folder containing darkfield and flatfield images, <em>frame*.tif</em></li> <li>data: raw (unprocessed or uncorrected) projection data, <em>frame*.tif</em></li> </ul> <p> </p> <p><strong>Additional Links</strong></p> <p>These datasets are produced by the <a>Computational Imaging group</a> at Centrum Wiskunde & Informatica (CI-CWI). Accompanying code can be found here.</p> <p><em> </em></p> <p><strong>Contact Details</strong></p> <p>For more information or guidance in using these datasets, please get in touch with </p> <ul> <li>bossema [at] cwi.nl</li> </ul> <p><strong>References</strong></p> <p><a href="https://www.nature.com/articles/s41467-024-48102-w">Bossema, F.G., Palenstijn, W.J., Heginbotham, A. <em>et al.</em> Enabling 3D CT-scanning of cultural heritage objects using only in-house 2D X-ray equipment in museums. <em>Nat Commun</em> <strong>15</strong>, 3939 (2024). https://doi.org/10.1038/s41467-024-48102-w</a></p>
X-ray radiation damage cycle of solvated inorganic ions
<p>Data set pertaining to the manuscript "X-ray radiation damage cycle of solvated inorganic ions", accepted for publication at Nature Communication.</p> <p>The manuscript describes results on the low-energy electron emission in a cascade of the decay of core ionized states, explored experimentally by liquid jet multi-electron coincidence spectra compared to theoretical predictions. Here we provide the underlying experimental data including metadata.</p> <p>Files with extension .h5 are hdf5-files structured according to the NeXus standard v2024.02, see<br>https://www.nexusformat.org/<br>https://fairmat-experimental.github.io/nexus-fairmat-proposal/50433d9039b3f33299bab338998acb5335cd8951/mpes-structure.html<br>NeXus data files can be opened with any software capable of opening hdf5-structured files. The following viewers are adapted to the specifics of the NeXus data format:<br>* nexpy (distributed with python)<br>* https://h5web.panosc.eu/h5wasm (web-based NeXus viewer maintained by the European Photon and Neutron Open Science Cloud-consortium)<br>Additionally, some properties of our liquid jet sample environment are described by extensions to standard NeXus explained in a notes-section in each file.</p> <p> </p> <p>In each NeXus file-entry, two types of data are present:<br>1. An energy-calibrated single electron spectra as histogram of the single electron events in events/eV ('data').<br>2. Energy-calibrated single, double and triple electron events ('raw').</p> <p> </p> <p>The following files are provided: Electron emission coincidence data pertaining to Mg<sup>2+</sup> and Al<sup>3+</sup> measurements mg_ee_coinc.h5 (Mg<sup>2+</sup> data recorded at BESSY II) mg_petra_ee_coinc.h5 (Mg<sup>2+</sup> data recorded at PETRA III) al_ee_coinc.h5 (Al<sup>3+</sup> data recorded at PETRA III)</p> <p> </p> <p>Contact: Dana Bloß (dana.bloss@uni-kassel.de) Andreas Hans (hans@physik.uni-kassel.de) </p> <p> </p> <p> </p> <p> </p>
Cellular-resolution X-ray microtomography of an entire mouse brain: supporting data, scripts and parameters
<h2><strong>Abstract </strong></h2> <p><strong>Purpose:</strong> Histology is the gold standard for sub-cellular visualization of the mouse brain. It offers excellent in-plane resolution, but a comparably low out-of-plane resolution due to physical sectioning. X-ray microtomography does not require this trade-off. Tomographic imaging of the entire mouse brain with isotropic cellular resolution produces datasets of multiple terabytes in size. These data must be processed and made accessible to domain experts who may have only limited image processing knowledge.</p> <p><strong>Approach:</strong> Extended-field X-ray microtomography covering an entire mouse brain was performed. The 4,495 projections from 8 × 8 offset acquisitions were stitched to reconstruct a 15,000^3 voxel volume. The microtomography volume was non-rigidly registered to the Allen Mouse Brain Common Coordinate Framework v3 based on a combination of image intensity and landmark pairs.</p> <p><strong>Results: </strong>We present a 3.3 teravoxel dataset covering a full mouse brain with 0.65 μm voxel size. The data were block-wise transformed to a common coordinate system then stored in a public repository with a hierarchical format for navigation and overlay with anatomical annotations in online viewers such as Neuroglancer or siibra-explorer.</p> <p><strong>Conclusions:</strong> This study demonstrates X-ray imaging and data processing for a full mouse brain, augmenting current atlases by improving resolution in the third dimension by an order of magnitude. The data are publicly available and easily accessible for domain experts via browser-based viewers.</p> <h2>Data</h2> <p>File <code>b32_atlas_registration.zip</code> contains the input data, parameter files and output data of affine and non-rigid registration of the 32 x 32 x 32 voxels downsampled microtomography image to the Allen Mouse Brain Common Coordinate Framework v3.</p> <p>File <code>create_sharded_Neuroglacer_format.pdf</code> will provide instructions how to create gZip-compressed, sharded, pre-computed Neuroglancer format via the open source software <a href="https://github.com/seung-lab/igneous">igneous</a>. This is currently still missing.</p> <h2>Processing</h2> <p>Reconstruction of extended field microtomography images mit projection stitching in horizontal and vertical direction was achieved with our software pipeline <a href="https://github.com/unibas-bmc/mosaicreconstruction">mosaicreconstruction</a>.</p> <p>The 32 x 32 x 32 voxels downsampled microtomography image was registered with the open source software <a href="https://elastix.lumc.nl/">elastix (and transformix)</a>. The <code>elastix.log</code> file states the used command line options. Directory names require adapting for reproducing the results. </p> <p>As terabyte large images and the non-rigid transformation parmeters do not fit into memory, we developed a distributed hierarchical approach with sub-volume transformations for the high resolution level, see <a href="https://github.com/unibas-bmc/LargeVolumeTransformix">LargeVolumeTransformix</a>. The high resolution tomography volume (moving volume) was warped to the atlas (fixed volume) by dividing the fixed space into 12 × 12 × 12 target subregions, such that the axes-aligned extended moving image subregion, the moving image transformed subregion, and the transformation parameters all fit in memory for an isotropic target voxel resolution of 0.65 μm.</p>
X-ray Diffraction Data for PDB ID 8VWR. Steroid Hydratase from Comamonas testosteroni
<p>X-ray diffraction data used for the structrual determination of steroid hydratase from Comamonas testosteroni, deposited in the PDB with the ID 8VWR.</p>
Database of simulated pulse profiles from X-ray accreting pulsar
<p>This database is a parquet file that stores a list of dictionary with the simulated pulse profiles from an X-ray accreting pulsar. Every dictionary contains 7 paframeters defining the pulsar and the associated pulse profile. It is highly recommended to check the GitHub repository containing instructions on how to read and use the data stored. </p> <p><a href="https://github.com/SimoneGalla/X-ray-accreting-pulsar/tree/main/pulse-Profile-X-ray-pulsars">X-ray-accreting-pulsar/pulse-Profile-X-ray-pulsars at main · SimoneGalla/X-ray-accreting-pulsar (github.com)</a></p>
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.