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2,001 results for “X-Ray”
Data bundle for "Advancing characterisation with statistics from correlative electron diffraction and X-ray spectroscopy, in the scanning electron microscope"
<p>Prepared by Tom McAuliffe (t.mcauliffe17@imperial.ac.uk)</p> <p>This repository is a release of the raw data and analysis results for: 'Advancing characterisation with statistics from correlative <br> electron diffraction and X-ray spectroscopy, in the scanning electron microscope' <br> https://doi.org/10.1016/j.ultramic.2020.112944</p> <p>The raw data is given as 'RawData.h5' - this contains patterns, spectra, and metadata in the Bruker-exported format.</p> <p>Outputs of our analysis code (which will be made available via AstroEBSD) are contained in 'PCA_Outputs' subfolders. Exported plots and <br> .mat results files are contained within. These are organised by Figure number in the paper.</p> <p>The provided results are divided into two major sections:<br> (1) Variation in the variance tolerance limit (and corresponding numbers of retained components), and the weighting of the PCA in favour of EBSD or EDS information.<br> RCCs are validated by cross-correlation with the corresponding raw data point pattern and/or spectrum. <br> (2) Full outputs of PCA analysis having varied the weighting parameter. This contains IPF maps, quantified chemical maps, PC scores, and label maps. <br> </p>
ds-uct-001: Cast Iron GGG40: X-Ray micro-CT of a nodular cast iron sample class GGG40.
<p><strong>Summary</strong>:<br> .X-Ray micro-computed tomography (micro-CT) of a nodular cast iron sample class GGG40, including both raw projection data and the final reconstructions, for three different resolutions (voxel sizes of 1 μm, 3 μm and 11 μm).<br> .The 3D image was generated with an X-Ray micro-CT Scanner version Xradia Versa 510 from Zeiss performed by A Pereira at the UFF micro-CT Facility.<br> .For use of these data, please remember to cite the DOI of the Zenodo repository and relevant papers.</p> <p><strong>Details</strong>:<br> .Tomo1 (1024) - Voxel size: 1 μm; Sample-source: 26 mm; Sample-detector: 150 mm; Optical magnification: 4.0X; Filter: HE#6; Beam energy: 160 kV; Power: 10 W; Exposure time: 60.0 sec; Projections: 1600.<br> .Tomo2 (1024) - Voxel size: 3 μm; Sample-source: 28 mm; Sample-detector: 35 mm; Optical magnification: 4.0X; Filter: HE#4; Beam energy: 160 kV; Power: 10 W; Exposure time: 10.0 sec; Projections: 3200.<br> .Tomo3 (1024) - Voxel size: 11 μm; Sample-source: 30 mm; Sample-detector: 158 mm; Optical magnification: 0.4X; Filter: HE#4; Beam energy: 160 kV; Power: 10 W; Exposure time: 3.0 sec; Projections: 3200.</p> <p><strong>Contents</strong>:<br> ._info_ds-uct-001.txt<br> .ds-uct-001_cast_iron_ggg40_01um_8bits.zip<br> .ds-uct-001_cast_iron_ggg40_03um_8bits.zip<br> .ds-uct-001_cast_iron_ggg40_11um_8bits.zip<br> .ds-uct-001_cast_iron_ggg40_01um_1600p.txrm<br> .ds-uct-001_cast_iron_ggg40_01um_1600p_Drift.txrm<br> .ds-uct-001_cast_iron_ggg40_01um_1600p_recon.txm<br> .ds-uct-001_cast_iron_ggg40_03um_3200p.txrm<br> .ds-uct-001_cast_iron_ggg40_03um_3200p_Drift.txrm<br> .ds-uct-001_cast_iron_ggg40_03um_3200p_recon.txm<br> .ds-uct-001_cast_iron_ggg40_11um_3200p.txrm<br> .ds-uct-001_cast_iron_ggg40_11um_3200p_Drift.txrm<br> .ds-uct-001_cast_iron_ggg40_11um_3200p_recon.txm</p>
ds-uct-002: Root Canal Strain: X-Ray micro-CT of four teeth before and after root canal procedure.
<p><strong>Summary</strong>:<br> .X-Ray micro-computed tomography (micro-CT) of four teeth before (TomoB) and after (TomoA) simulation of root canal treatment and retreatment procedures instrumented with strain-gauge, including reconstructions, for two different resolutions (TomoB and TomoA with voxel sizes of 20.0 μm and 10.5 μm, respectively).<br> .The 3D image was generated with an X-Ray micro-CT Scanner version Xradia Versa 510 from Zeiss performed by A Pereira at the UFF micro-CT Facility.<br> .For use of these data, please remember to cite the DOI of the Zenodo repository and relevant papers.</p> <p><strong>Details</strong>:<br> .Tomo1B/Tomo2B/Tomo3B/Tomo4B (1024) - Voxel size: 20.0 μm; Sample-source: 45.0 mm; Sample-detector: 110 mm; Optical magnification: 0.4X; Filter: LE#1; Beam energy: 60 kV; Power: 5 W; Exposure time: 2.0 sec; Projections: 1600.<br> .Tomo1A/Tomo2A/Tomo3A/Tomo4A (2048) - Voxel size: 10.5 μm; Sample-source: 48.2 mm; Sample-detector: 110 mm; Optical magnification: 0.4X; Filter: LE#2; Beam energy: 60 kV; Power: 5 W; Exposure time: 7.0 sec; Projections: 1600.</p> <p><strong>Contents</strong>:<br> ._info_ds-uct-002.txt<br> .ds-uct-002_root_canal_strain_tomo1b_20um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo2b_20um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo3b_20um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo4b_20um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo1a_10um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo2a_10um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo3a_10um_8bits.zip<br> .ds-uct-002_root_canal_strain_tomo4a_10um_8bits.zip<br> .PB_PARECER_CONSUBSTANCIADO_CEP_2650528.pdf</p>
ds-uct-007: Asphalt Concrete: X-Ray micro-CT of an asphalt concrete sample.
<p><strong>Summary</strong>:<br> .X-Ray micro-computed tomography (micro-CT) of an asphalt concrete sample, including both raw projection data and the final reconstructions, for one single resolution (voxel size of 7 μm).<br> .The 3D image was generated with an X-Ray micro-CT Scanner version Xradia Versa 510 from Zeiss performed by A Pereira at the UFF micro-CT Facility.<br> .Image data segmented with four different segmentation techniques: DL (Deep Learning), ML (Machine Learning), TH (Thresholding) and WS (Watershed).<br> .For use of these data, please remember to cite the DOI of the Zenodo repository and relevant papers.<br> <strong>Details</strong>:<br> .Tomo - Voxel size: 7 μm; Sample-source: 31 mm; Sample-detector: 274.25 mm; Optical magnification: 0.4X; Filter: LE#6; Beam energy: 100 kV; Power: 9 W; Exposure time: 4.0 sec; Projections: 1600.</p> <p><strong>Contents</strong>:<br> ._info_ds-uct-007.txt<br> .ds-uct-007_asphalt_concrete_07um_16bits.zip<br> .ds-uct-007_asphalt_concrete_07um_1600p.txrm<br> .ds-uct-007_asphalt_concrete_07um_1600p_Drift.txrm<br> .ds-uct-007_asphalt_concrete_07um_1600p_recon.txm<br> .ds-uct-007_asphalt_concrete_07um_DL.zip<br> .ds-uct-007_asphalt_concrete_07um_ML.zip<br> .ds-uct-007_asphalt_concrete_07um_TH32.zip<br> .ds-uct-007_asphalt_concrete_07um_WS.zip</p>
An interactive figure of the 2016 and 2020 X-ray light curves of LMC 1968 as observed by the XRT instrument on Swift
<p>This repository contains all the files necessary to create the interactive figure in the Research Note ov Schwarz, Page, Kuin, & Darnley 2020. The figure was created using the <a href="https://aas-timeseries.readthedocs.io/en/latest/">aas-timeseries</a> package of the <a href="https://www.astropy.org">astropy</a> project. The file lmc68.py is the underlying python code while the two lmcrel*.csv are the input files for the 2016 and 2020 eruptions of the recurrent nova LMC 1968 as observed by the XRT instrument on board the Neil Gehrels Swift observatory. A Jupyter notebook is required to preview the interactive figure. The output from the code is saved in the interactive.tar.gz package. It consists of four files:</p> <ul> <li>index.html</li> <li>figure.json</li> <li>data_75e74aca-09f1-4846-966e-9e33c7acc8d3.csv</li> <li>data_5402e718-01cf-4ad7-92a5-7679d4076ed5.csv</li> </ul> <p>The first file, index.html, is the html framework that houses the interactive figure. figure.json contains the interactive figure commands while the two data*csv files are the underlying data. The interactive figure can be viewed if this package is opened on a web server. A copy of this interactive figure is available <a href="https://authortools.aas.org/LMC1968/">here</a> so you can try it out.</p>
X-ray light-field - Small branch - 1 deg angular range
<p>X-ray light-field of a small branch, taken with the FleX-ray scanner, in the Computational Imaging group of CWI (Amsterdam).</p> <p>Angular range is ~1 degree, panel pixel size ~150 um.</p> <p>This bundle includes:</p> <ul> <li> <pre><code>light-field_corrected.vox</code></pre> Light-field in the VOX v0 data format (based on HDF5). Any HDF5 reader can open it. Native support is available here: <a href="https://github.com/cicwi/plenoptomos">https://github.com/cicwi/plenoptomos</a>. The image floating point precision is FP32.</li> <li> <pre><code>light-field_acquisition_rawdata.tbz </code></pre> <p>Light-field acquisition raw data, archived with Tar and Bzip2. It contains TIF images as projections, dark-field and flat-field. The ini and txt files provide information about the scan (motor positions, etc).</p> </li> <li> <pre><code>tomo_acquisition_rawdata.tbz</code></pre> Tomographic acquisition raw data, archived with Tar and Bzip2. It contains TIF images as projections, dark-field and flat-field. The ini and txt files provide information about the scan (motor positions, angles, etc).</li> <li> <pre><code>tomo_reconstruction_and_segmentation.h5</code></pre> <p>Tomographic reconstruction of the raw data, in HDF5. Any HDF5 reader can open it. It contains two self-descriptive datasets: "volume" and "segmentation".</p> </li> </ul>
X-ray light-field - Gel bubbles - 1 deg angular range
<p>X-ray light-field of bubbles in hair gel, taken with the FleX-ray scanner, in the Computational Imaging group of CWI (Amsterdam).</p> <p>Angular range is ~1 degree, panel pixel size ~150 um.</p> <p>This bundle includes:</p> <ul> <li> <pre><code>light-field_corrected.vox</code></pre> Light-field in the VOX v0 data format (based on HDF5). Any HDF5 reader can open it. Native support is available here: <a href="https://github.com/cicwi/plenoptomos">https://github.com/cicwi/plenoptomos</a>. The image floating point precision is FP32. The images have been back-ground subtracted.</li> <li> <pre><code>light-field_acquisition_rawdata.tbz </code></pre> <p>Light-field acquisition raw data, archived with Tar and Bzip2. It contains TIF images as projections, dark-field and flat-field. The ini and txt files provide information about the scan (motor positions, etc).</p> </li> <li> <pre><code>tomo_acquisition_rawdata.tbz</code></pre> Tomographic acquisition raw data, archived with Tar and Bzip2. It contains TIF images as projections, dark-field and flat-field. The ini and txt files provide information about the scan (motor positions, angles, etc).</li> <li> <pre><code>tomo_reconstruction_and_segmentation.h5</code></pre> <p>Tomographic reconstruction of the raw data, in HDF5. Any HDF5 reader can open it. It contains two self-descriptive datasets: "volume" and "segmentation".</p> </li> </ul>
Raw data for article "In Situ Synchrotron X-Ray Diffraction Characterization of Corrosion Products of a Ti-Based Metallic Glass for Implant Applications" Gostin et al 2018
<p>This repository contains raw data for the article "In Situ Synchrotron X-Ray Diffraction Characterization of Corrosion Products of a Ti-Based Metallic Glass for Implant Applications" by Gostin et al. 2018 in Advanced Healthcare Materials, 7, 1800338 (https://doi.org/10.1002/adhm.201800338).</p> <p>Most data comes from one beamtime at the Diamond synchrotron in the UK in May 2016. It consists of X-ray diffraction images taken in situ in artificial corrosion pits on a Ti-based metallic glass.</p> <p>Please see the README file for more details.</p>
Hyperspectral X-ray CT data set of mineralised ore sample with Au and Pb deposits
<p><strong>General data description:</strong></p> <p>This is a hyperspectral (energy-resolved) X-ray CT projection data set of a mineralised ore sample with small gold and galena deposits. It was acquired in a laboratory micro-CT scanner with an energy-sensitive HEXITEC detector in the Henry Moseley X-ray Imaging Facility at The University of Manchester.</p> <p>The data included contains all the relevant files required for reconstruction, following a hyperspectral scan of a mineralised ore sample. The sample contains a number of mineral phases, of varying concentration, distributed throughout. Some phases (including gold, and lead-based Galena) produce unique absorption edges, which act as spectral identifiers that can be measured by an energy-sensitive detector.</p> <p><strong>File descriptions:</strong></p> <p>The data set consists of one .txt file and three .mat (MATLAB) data files.</p> <p>Au_rock_scan_geometry.txt gives a breakdown of the full sample and detector geometry used when acquiring the raw projections. The number of horizontal detector pixels accounts for the fact that a set of 5 tiled scans of the sample were collected and later stitched together.</p> <p>Au_rock_sinogram_full.mat contains the full 4D sinogram constructed following flat-field normalisation of the raw projection data. The data matrix contains the total number of energy channels acquired during scanning, as well as the conventional elements of vertical/horizontal detector pixel number and total projection angles.</p> <p>commonX.mat provides a direct conversion between the energy channels, and the energies (in keV) that they correspond to, following a calibration procedure prior to scanning.</p> <p>FF.mat contains the 4D flatfield data acquired when no sample was present. This data was used to normalise the projection datasets, as the sinogram was constructed.</p>
X-ray diffraction images of bovine trypsin crystals recorded at the FemtoMAX beamline of Max IV synchrotron facility
<p>The deposition concerns bovine trypsin diffraction images in two wedges. Each image is recorded on a still crystal and separated by 0.1 deg rotation. The x4.tar.gz archive contains summed intensities from individual snapshots at the same orientation, whereas x4_single.tar.gz archive contains single snapshots/orientation. </p>
X-ray diffraction images for PDB 6Z5G: The RSL - sulfonato-calix[8]arene complex, I23 form, citrate pH 4.0, solved by S-SAD
<p>Anomalous diffraction data collected at 5.975 KeV at Swiss Light Source beam line X06DA using a Pilatus 2M-F detector. </p> <p> </p>
Raw X-Ray CT data of CFC-Cu ITER monoblock mock-up
<p>Raw X-Ray CT data for CFC-Cu ITER monoblock mock-up. The monoblock was manufactured at Politecnico di Torino, Italy (Dr Valentina Casalegno) and X-ray tomography scanning was performed at the Manchester X-ray Imaging Facility, University of Manchester, UK (Dr Llion Evans).</p> <p>This data was used for the publication Evans, Ll.M. et al. "Transient Thermal Finite Element Analysis of CFC-Cu ITER Monoblock Using X-ray Tomography Data", Fusion Engineering and Design 2015. DOI: 10.1016/j.fusengdes.2015.04.048</p>
X-ray diffraction images used for refinement of cytochrome cL from Methylobacterium extorquens.
<p>X-ray diffraction images for cytchrome cL from <em>M. extorquens</em> extending to 1.6 Angstroms resolution that were collected at ID14-2 at the ESRF (Grenoble) in April 2001. This dataset was used for high resolution refinement of the structure. </p>
X-ray diffraction images for L-threonine dehydrogenase from Trypanosoma brucei with NAD and pyruvate bound.
<p>X-ray diffraction images which were collected at ESRF (Grenoble) using an ADSC 315r CCD detector on beamline ID29 on 11th November 2009. More details are given in the uploaded notes. </p>
Spatially-localized X-ray scattering and X-ray microtomography measurements on Moso bamboo
<p><strong>Spatially-localized X-ray scattering and X-ray microtomography measurements on Moso bamboo</strong></p> <p> </p> <p>This data set is originally used in:</p> <p>Ahvenainen, P., Dixon, P. G., Kallonen, A., Suhonen, H., Gibson, L. J., & Svedström, K. (2017). Spatially-localized bench-top X-ray scattering reveals tissue-specific microfibril orientation in Moso bamboo. <em>Plant Methods</em>. <strong>13</strong>:5 DOI: 10.1186/s13007-016-0155-1</p> <p>This data set includes measurements on Moso bamboo (<em>Phyllostachys edulis</em>) performed with two separate set-ups at the Department of Physics, University of Helsinki as described in the above open-access publication. The X-ray microtomography (XMT) measurements, X-ray diffraction tomography (XDT) and localized X-ray scattering (LXS) are done with set-up 1. In LXS, the region-of-interest is selected from a tomographic reconstruction slice based on the XMT measurement using a small X-ray beam (diameter: 200 µm). Additional wide-angle X-ray scattering (WAXS) measurements are conducted with set-up 2 using a larger X-ray beam (diameter approx. 1 mm). </p> <p>The two-dimensional scattering patterns (Pilatus 1M hybrid pixel array detector) and tomographic reconstruction slices obtained with set-up 2 are stored as TIFF-images (.tif). The two-dimensional scattering patterns (MAR345 image plate detector) obtained with set-up 2 are stored as 32-bit RAW files (unsigned integers, 2300 columns, 2300 rows). </p> <p>The novel combined WAXS/XMT set up (set-up 1) is first presented in: Suuronen, J.-P., Kallonen, A., Hänninen, V., Blomberg, M., Hämäläinen, K., & Serimaa, R. (2014). Bench-top X-ray microtomography complemented with spatially localized X-ray scattering experiments. <em>Journal of Applied Crystallography</em>, <strong>47</strong>(1), 471–475. doi:10.1107/S1600576713031105</p> <p>Any queries related to the data set or the related Plant Methods article may be directed to the first author by email:</p> <p>Patrik Ahvenainen, PhD; patrik.ahvenainen@alumni.helsinki.fi</p>
X-ray diffraction images for an MDM2/Nutlin-3a complex
<p>This submission includes a zip archive of diffraction images recorded with the MARMOSAIC 225 mm CCD detector at the ESRF beam line ID23-2. Relevant meta data can be found in the headers of those diffraction images or in the Protein Data Bank entry 4HG7.</p>
A high-throughput 3D X-ray histology facility for biomedical research and preclinical applications - Supplementary Data
<p><strong>Videos</strong></p><ul><li><strong>Video 1</strong> A video going through the Z stack in single slices. This is a cross- sectional view of the XRH image stack along the XY plane. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue.</li><li><strong>Video 2 </strong>A video going through the Y stack in single slices. This is a cross- sectional view of the XRH image stack along the XZ plane. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue.</li><li><strong>Video 3 </strong>A video going through the X stack in single slices. This is a cross- sectional view of the XRH image stack along the YZ plane. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue.</li><li><strong>Video 4 </strong>3D X-ray histology (XRH) is a µCT -based workflow tailored to fit seamlessly into current histology workflows in biomedical and pre-clinical research, as well as clinical histopathology. Microanatomical detail can be captured from standard (non-stained) formalin-fixed and paraffin-embedded (FFPE) tissue blocks.</li><li><strong>Video 5</strong> Average Intensity Projection (AIP) of the sample through the Histologically relevant plane. This is a 2D visualisation rendering the Average Intensity of 20x single XY slices along the z-axis of the stack. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue.</li><li><strong>Video 6 </strong>Maximum Intensity Projection (MIP) of the sample through the Histologically relevant plane. This is a 2D visualisation rendering the Maximum Intensity of 20x single XY slices along the z-axis of the stack. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue.</li><li><strong>Video 7 </strong>Standard deviation projection of the sample going through the histologically relevant plane. This is a 2D visualisation rendering the Standard Deviation of 20x single XY slices along the z- axis of the stack. XRH datasets are normally oriented (resliced) in a way that a scroll through the stack along the XY plane emulates the physical histology slicing of the tissue.</li></ul><p><i>* <strong>Videos 5 -7</strong> are also referred to as "thick-slice rolls" </i>- <i>Thick-slice rolling is a 2D thick-slice viewing that allows rolling of a pre-selected number of slices (n) along the z-axis of the 3D data. A single thick-slice roll forwards is accomplished by translating the thick-slice by one single slice forwards; that is moving forward by one (+1) slice from the first and nth element and reapplying the criteria or operations to the new slice sub-stack.</i><br> </p><p><strong>The questionnaire used to collect feedback about the needs of the XRH community.</strong></p><ul><li>Survey.docx</li><li>Survey.pdf</li></ul><p><br><strong>Exemplar report of a semi-automatically generated augmented PDF file</strong> that contain sample information, imaging settings, still images with descriptive figure legends, and links to corresponding online videos</p><ul><li>DEMO02019-FFPE_report_99EbPXG.pdf</li></ul><p> </p><p>= = = = = = = = = = = = = = = = <br><strong>System performance data ZIP</strong><br>= = = = = = = = = = = = = = = = </p><p>This ZIP file contains imaging data collected through different systems and setups at the XRH facility at the μ-VIS X-ray Imaging Centre at the University of Southampton for the purpose of acceptance and/or system performance characterisation. Below is an overview of the folder structure and its contents</p><p>The following files are X-ray imaging data collected on September 28, 2017, using the Med-X system and a Jima phantom at 55 kV peak and 7 Watts. </p><ul><li>20170928_MEDX_1642_JIMA_55kVp7W-2.tif</li><li>20170928_MEDX_1642_JIMA_55kVp7W.tif</li><li>20170928_MEDX_1642_JIMA_55kVp7W.tif.profile.xml</li></ul><p>This PDF document is related to a QRM MicroCT bar pattern phantom, and its specifications</p><ul><li>QRM-MicroCT-Barpattern-Phantom.pdf</li></ul><p>Graphs showing the calculated focal-spot size as a function of the X-ray power (W) for the Molybdenum rotating target calculated using Edge Modulation function testing. The performance is then compared with the performance of the Reflection target across the same range of powers. Raw data can be found in XRH_QRM_Refl-vs-Rot-TargetComparison_SingleReconSlices_5umPixelSize folder. Test performed in July 2021. </p><ul><li>XRH_202107_MoRot-testing_EdgeModFunction-QRMrecons+RotReflCompar.png</li></ul><p> </p><p><i><strong>/ XRH-XT-H-225-ST_FocalSpots</strong></i><br>This directory contains radiographic data collected using the XRH system with a JIMA phantom and MoRt (Molybdenum rotating), TT (Transmission), and Reflection targets.</p><ul><li>20200113_XRH_Jima test MoRT 55kV 15W.tif, 20200113_XRH_Jima test MoRT 55kV 30W.tif, etc.: <br>These files represent radiographs taken on January 13, 2020, using the XRH system, Jima phantom, MoRT target at 55 kVp and varying wattages.</li><li>20200207_XRH_JIMA 80kV TT1a.tif, 20200207_XRH_JIMA 80kV TT1b.tif, etc.<br>Similar to the above, these files are from February 7, 2020, and use 80 kVp with a TT target.</li><li>20231115_XRH_reflW_80kVp6W.tif, 20231115_XRH_reflW_80kVp6W_02.tif, etc.<br>These files are from November 15, 2023, and collected using the XRH system with a Reflection target at 80 kVp and 6 Watts.</li></ul><p><i><strong>/ XRH_QRM_Refl-vs-Rot-TargetComparison_SingleRadioFromCTs_5umPixelSize</strong></i><br>This directory contains single radiographs taken with a pixel size of 5 micrometers using the Molybdenum rotating (MoRt), and the Reflection target using tungsten (W) and Molybdenum (Mo) metals.</p><p><i><strong>/ XRH_QRM_Refl-vs-Rot-TargetComparison_SingleReconSlices_5umPixelSize</strong></i><br>This directory contains sinlge reconstruction slices of the setups mentioned above. Slices are exported from CT volumes and were used for the Edge Modulation function study. </p><p>For interpretation of the filenames in the folders listed above please see below and refer to specific files and folders for detailed information and results related to each imaging session:</p><ul><li><i><xx>kVp or <xx>kV </i>:Imaging at a peak voltage of <xx> kVp.</li><li><i><y>W</i> :Imaging at <y> Watts;<i> </i>"." is represented with "-"; i.e. 20210705_XRH_2766_PJB_TEST03552-EQPMT_W_6-9W is acquired using a power of 6.9 W</li><li><i>MoRt, TT, Refl </i> :Molybdenum, Transmission, and Reflection targets, respectively.</li><li><i>_W_ and _Mo_ </i> :Tungsten and Molybdenum target materials.</li><li><i>_horiz</i> :Reconstruction slices in line with the X-ray beam's propagation direction.</li><li><i>_vert</i> :Reconstruction slices normal to the X-ray beam's propagation direction and parallel to the detector plane.</li></ul>
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>
IODP Expedition 391 Portable X-ray fluorescence (p-XRF)
Energy-Dispersive X-Ray Fluorescence (ED-XRF) is a rapid, non-destructive technique for determining qualitative and quantitative changes in chemical composition. Aboard the JOIDES Resolution, pXRF is used for measuring points on section halves, rock pieces, and sometimes powders. Spots are typically irradiated at multiple conditions to excite and measure a wide range of elements. The peak intensity changes (we do not provide concentrations) are then used to help recognize and define major chemo-stratigraphic units without the need for destructive sampling.
IODP Expedition 391 X-ray diffraction (XRD)
X-ray diffraction (XRD) is used to identify minerals and their proportions in sediment or hard rock sample powders on a Bruker AXS D4 Endeavor X-ray diffractometer. Results are returned as diffractograms in a viewable format (either PDF or PNG).
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.