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167 results for “x-ray imaging”
Raw Data: Gold Coated ZnO Microstructures by Bragg Coherent X-Ray Diffraction Imaging
<p>Two sets of raw data from gold coated ZnO microstructure (rod) investigated by Bragg coherent X-ray diffraction imaging used in publication: "Visualizing Intrinsic 3D-Strain Distribution in Gold Coated ZnO Microstructures by Bragg Coherent X-Ray Diffraction Imaging and Transmission Electron Microscopy with Respect to Piezotronic Applications" (<a href="https://doi.org/10.1002/aelm.202100546">https://doi.org/10.1002/aelm.202100546</a>)</p> <p>Included is data from two different spatial positions along the c-axis of the ZnO rod. Futher on called position 1 (P1) and position 2 (P2). For each position there is a .nxs file of a rocking scan around the {10-10} Bragg reflection, collected by a 2D detector and other recorded values, e.g. motor positions, counter values. </p>
X-ray Fluorescence Ghost Imaging - CuSn mask - Three Wires (Fe & Cu)
<p>X-ray Fluorescence Ghost Imaging (XRF-GI) dataset of three wires (one Fe, and two Cu) in a plastic capillary. The capillary contains trace elements like Zn, Zr, etc.</p> <p>The GI scan is presented in the following article <a title="Synchrotron-based x ray fluorescence ghost imaging" href="https://doi.org/10.1364/OL.499046">10.1364/OL.499046</a>. A total of 896 GI realizations were taken, organized into 16 vertical translations and 56 horizontal translations of the structuring element (CuSn mask).<br>The dataset contains both the sample transmission images and the masks plus sample transmission images. No images of the masks are provided (they need to be computed).</p> <p>The data is organized in an HDF5 file, under the following structure:</p> <pre><code>dataset_CuSn-mask_3wires.h5 │ ├data │ ├flat_panel │ │ ├dark [float32: 16 × 170 × 350] │ │ ├empty_beam [float32: 170 × 350] │ │ ├sample [float32: 16 × 170 × 350] │ │ └sample_and_masks [float32: 16 × 56 × 170 × 350] │ └xrf [float32: 16 × 56 × 4096] │ └metadata └xrf ├bias_keV [float64: scalar] ├gain_keV [float64: scalar] └ranges ├Ca [int64: 2] ├Cu [int64: 2] ├Fe [int64: 2] ├Si [int64: 2] ├Ti [int64: 2] ├Zn [int64: 2] └Zr [int64: 2] </code></pre> <p>The meaning of the paths is:</p> <ul> <li><code>/data/xrf</code> contains the XRF spectra for each GI realization</li> <li><code>/data/flat_panel/dark</code> contains the dark images of each scan line (no beam)</li> <li><code>/data/flat_panel/empty_beam</code> contains the empty beam (no sample & no masks) intensity distribution</li> <li><code>/data/flat_panel/sample</code> contains the transmission images of the sample at each scan line</li> <li><code>/data/flat_panel/sample</code>_and_masks contains the transmission images of the sample and masks at each GI realization</li> <li><code>/metadata/xrf/bias_keV</code> contains the bias in keV of the XRF spectrum</li> <li><code>/metadata/xrf/gain_keV</code> contains the gain in keV of each XRF energy bin</li> <li><code>/metadata/xrf/ranges/</code> contains the bin ranges for interesting K<sub>alpha</sub> elemental emission lines in the XRF spectrum</li> </ul> <p>For further information we refer to the associated publication.</p> <p>The data can be processed with structured illumination routines of the code at: <a href="https://github.com/cicwi/PyCorrectedEmissionCT">https://github.com/cicwi/PyCorrectedEmissionCT</a>.</p>
PTX-498: A multi-center pneumothorax segmentation chest X-ray image dataset
<p>Pneumothorax is a common medical emergency defined as the abnormal collection of air in the pleural space between the lung and chest wall. Its typical symptoms include chest pain and dyspnea, leading to oxygen deficiency or even life-threatening in severe cases. Therefore, an efficient and automatic pneumothorax diagnosis algorithm would be useful in many clinical scenarios. Recently, deep learning methods have achieved impressive progress in medical image segmentation tasks. However, a large-scale dataset is one of the critical components for the success of deep learning. On the other hand, there are few public chest X-ray images with pneumothorax.</p> <p>To stimulate the researchers' interest in the pneumothorax diagnosis algorithm, <strong>we released a new data set PTX-498 here. It contains 498 chest X-ray images of pneumothorax collected from three hospitals, and each image contains pixel-level annotations.</strong> All images were resized to 1024×1024. The raw image intensity was clipped according to the window width and level inside the dicom tag and then normalized to 0 to 255. The contours of the pneumothorax area were labelled by two senior radiologists using ITK-SNAP. The dataset was anonymized and every record related to patients' privacy was removed. Only the image data and the corresponding labels were included in PTX-498.</p> <p><strong>Please use the latest v2-fix version which removes duplicate images and uses the window width and level from the original dicom tag for normalization.</strong></p> <p><strong>Citation: If you are interested in this dataset and applying it in your research, please cite the following article.</strong><br> Paper link: https://doi.org/10.1016/j.neucom.2021.05.029<br> Cite this article as Yunpeng Wang, Kang Wang, Xueqing Peng, Lili Shi, Jing Sun, Shibao Zheng, Fei Shan, Weiya Shi, Lei Liu*. DeepSDM: Boundary-aware pneumothorax segmentation in chest X-ray images [J]. Neurocomputing, 2021, 454: 201-211.</p> <div> <div class="gtx-trans-icon"> </div> </div>
Supplementary Materials for "Simultaneous single-shot radiographic imaging using a laser-driven x-ray and proton micro-source"
<p>Simulation Data Repository, please read the contained README file in the contained simulation/ directory.</p> <p>This directory contains a copy of the used PIConGPU source code, version 0.5.0-dev-60ad9eb85 and analysis scripts.</p> <p>The PIConGPU source code is archived including its complete git history (git version 2.17.1) in source/picongpu.tar.gz with the input parameter template inside in share/picongpu/examples/Wneedle .</p> <p>Generally, PIConGPU source code is available via <a href="https://doi.org/10.5281/zenodo.591746">https://doi.org/10.5281/zenodo.591746</a> with its public git repository being maintained on <a href="https://github.com/ComputationalRadiationPhysics/picongpu">https://github.com/ComputationalRadiationPhysics/picongpu</a> .</p> <p>The two simulations’ exact input is modified accordingly in the directory input/ inside: 2D_a0-45_Z-10_ppc-20_002_light.tar.gz (p-polarized; along X) 2D_a0-45_Z-10_ppc-20_003_light.tar.gz (s-polarized; along Z).</p> <p>“Heavy” simulation data (checkpoints in simOutput/checkpoints/, full-resolution field and particle output in simOutput/bp/ ) has been stripped from this archive and are archived on NERSC’s HPSS tape archive.</p> <p>Analysis scripts are provided as Jupyter notebooks (DensityPlot_polX.ipynb and DensityPlot_polZ.ipynb) and depend on the following software:</p> <p>- adios 1.13.1 python bindings with enabled c-blosc transformations<br> - numpy 1.17.1<br> - matplotlib 3.1.1<br> - PIConGPU post-processing helper modules located in each simulation root directory under “input/lib/python/”<br> <br> The detailed conda environment can be found in the README.</p>
Nanoscale Imaging of High-Field Magnetic Hysteresis in Meteoritic Metal Using X-Ray Holography
<p>Data of magnetisation (two datasets) of the cloudy zone of Tazewell IIICD iron meteorite. Data was obtained using X-ray holography. Magnetization data is a 3D matrix containing magnetisation data in form of data[x location][y location][applied field], applied field values is provided in a separate file.</p> <p>Further details about this dataset and conditions of measurements can be found in Blukis et al., 2020 submitted to Geochemistry, Geophysics, Geosystems</p>
X-ray diffraction images for human recombinant 5-aminolevulinic acid dehydratase (ALAD).
<p>X-ray diffraction images for recominant human 5-aminolevulinic acid dehydratase (ALAD) collected at ESRF (Grenoble) beam line ID14-2 using an ADSC Quantum 4 detector to a resolution of 2.8 Å. A series of 1 ̊ oscillation images were recorded with an exposure time of 10 seconds per image. More details are given with the scanned notes and the log file. </p>
X-ray diffraction images for human native 5-aminolevulinic acid dehydratase (ALAD).
<p>X-ray diffraction images of human native ALAD collected at station 9.5 at synchrotron radiation source (SRS) Daresbury, UK, with a Marresearch 345 image plate detector on Sunday 26th April 1998. More details of the data collection are given in the files suffixed SUMMARY.</p>
Original X-ray diffraction images for 5-aminolevulinic acid dehydratase (ALAD) from E. coli complexed with porphobilinogen.
<p>The diffraction images which allowed the original 2.1 Angstrom resolution structure determination of <em>Escherichia coli</em> ALAD co-crystallised with a non-covalently bound moiety of the product, porphobilinogen (PBG), are presented. </p>
Atomic resolution X-ray diffraction images for methanol dehydrogenase from Methylobacterium extorquens.
<p>Atomic resolution X-ray diffraction images for methanol dehydrogenase from <em>Methylobacterium extorquens</em> collected at ESRF (Grenoble, France) using beamline ID29 in May 2002 with an ADSC detector. The diffraction resolution for the first pass is approximately 1.1 - 1.2 Angstroms and a second pass was collected to recoup the reflections that were overloaded in the first pass. More details of the data collection are in the included scanned notes and log files. </p>
X-ray diffraction images for cytochrome cL from the methylotrophic bacterium Methylobacterium extorquens.
<p>X-ray diffraction images for cytochrome c<sub>L</sub> from <em>Methylobacterium extorquens</em> collected at the ESRF beamline ID14-2 using an ADSC detector in Feb 2001. The diffraction data extend to around 2.0 Angstroms resolution and were used for the initial structure determination of this protein. Further details in the log files and the notes. </p>
Atomic resolution X-ray diffraction images of native endothiapepsin.
<p>X-ray diffraction images that were collected at DESY (Hamburg) to a resolution of 0.9 Angstroms from native endothiapepsin. The data were collected using a MAR345 detector at beamline BW7B in June 1999. More details are in the included notes. </p>
Atomic resolution X-ray diffraction images for endothiapepsin complexed with the inhibitor H261.
<p>X-ray diffraction images for a complex of endothiapepsin with the hydroxyethylene renin inhibitor H261 which were collected at DESY (Hamburg) in June 1998 using the beamline BW7B with a Mar image plate detector in two passes. The data extend to a resolution of almost 1.1 Angstroms. More details are given in the accompanying notes. </p>
X-ray diffraction images for 5-aminolevulinic acid dehydratase with a putative reaction intermediate resembling the product porphobilinogen bound.
<p>X-ray diffraction images for yeast 5-aminolevulinic acid dehydratase co-crystallised with the substrate 5-aminolevulinic acid. The structure demonstrated a putative product-like intermediate bound covalently to Lys 263 with an amino side chain ligated to the active-site zinc ion in a position normally occupied by a catalytic hydroxide ion. The data were collected in two passes using the ESRF beamline ID29 in Feb 2002 and extend to approximately 1.6 Å resolution. </p>
X-ray diffraction images for yeast 5-aminolevulinic acid dehydratase complexed with 4-oxosebacic acid.
<p>X-ray diffraction images for yeast 5-aminolaevulinic acid dehydratase complexed with 4-oxosebacic acid which were collected using beamline ID14-2 at the ESRF (Grenoble) in Feb 2001. </p>
X-ray diffraction images for the H145E mutant of the iron-dependent superoxide dismutase from Mycobacterium tuberculosis.
<p>X-ray diffraction images of the H145E mutant (prefixed h145e) which were collected in October 1995 using a graphite-monochromated copper K-alpha rotating anode source (wavelength 1.5418 Å) with a Marresearch 90 cm image plate detector at a distance of 120 mm from the crystal. The data were collected at room temperature in two passes, each consisting of 100 one degree rotations of the crystal. Each image had an exposure time of 20 minutes. The crystal was rotated in the capillary tube prior to collection of the second pass in order to record the 'blind' region of the diffraction pattern and this set of images is prefixed h145eb. </p>
X-ray diffraction images for the H145Q mutant of the iron-dependent superoxide dismutase from Mycobacterium tuberculosis.
<p>X-ray diffraction images collected from one crystal at room temperature using a rotating anode copper source (wavelength 1.5418 Å) and a 30 cm Marresearch image plate detector. The crystal-to-detector distance was 150 mm and a 90 mm image plate scan radius was used. Each of the 60 images had an exposure time of 20 minutes and corresponds to a 3 degree phi-rotation of the crystal. Diffraction extends to about 3.3 Å resolution. </p>
X-ray diffraction images for bovine inositol monophosphatase.
<p>X-ray diffraction images for bovine inositol monophosphatase which were collected using the ESRF beamline ID14-4 to a resolution of around 1.4 Å. The data were collected in two passes, the second for measuring intensities that were overloaded in the first. More details are given in the included notes. </p>
X-ray diffraction images for 5-aminolevulinic acid dehydratase (ALAD) from E. coli.
<p>X-ray diffraction images for <em>Escherichia coli</em> 5-aminolevulinic acid dehydratase (ALAD) which was crystallised in the presence of the inhibitor levulinic acid (15 mM) and bismuth nitrate (1 mM). The data were collected at beamline 9.6 at the SRS Daresbury Laboratory (UK) on 10th March 1994 using a 30 cm Marresearch image plate detector, a crystal temperature of 100 K, a wavelength of 0.88 Å and a crystal-to-detector distance was 300 mm. The oscillation angle was 2.5 degrees and 21 images were collected at constant dose in the time available. A wax image for determining the direct beam position was taken with the detector at a distance of 400 mm.</p>
X-ray diffraction images for yeast 5-aminolevulinic acid dehydratase complexed with 4-keto-5-aminohexanoic acid.
<p>X-ray diffraction images which were collected at the EMBL beamline BW7B, DESY (Hamburg) on 28th June 1999 using a Marresearch 345 image plate detector. The data were collected in three passes, images in the first main one having file prefix hykah, the second being a low-resolution run (lr) and, the last, a very high resolution (vhr) pass. More details are given in the notebook pages. </p>
X-ray diffraction images for yeast 5-aminolevulinic acid dehydratase complexed with succinylacetone.
<p>X-ray diffraction images which were collected on 28th March 1999 at the EMBL beamline BW7B at DESY (Hamburg) using a Marresearch 345 image plate detector. More information in the notes. </p>
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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.