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342 results for “Electron Microscopy”
Spectrocopic coincidence experiment in transmission electron microscopy
<p>This dataset contains individual EEL and EDX events where for every event (electron or X-ray), their energy and time of arrival is stored. The experiment was performed in a transmission electron microscope (Tecnai Osiris) at 200 keV. The material investigated is an Al-Mg-Si-Cu alloy. The 'full_dataset.mat' contains the full dataset and the 'subset.mat' has the first five frames of the full dataset. The attached 'EELS-EDX.ipynb' is a jupyter notebook file. This file describes the data processing in order to observe the temporal correlation between the electrons and X-rays. </p> <p>The data is part of the following publication 'Spectroscopic coincidence experiments in transmission electron microscopy' See the full article and supplementary (<a href="https://doi.org/10.1063/1.5092945">https://doi.org/10.1063/1.5092945</a>) for experimental details and results derived from this data. Feel free to process this data in alternative ways but please refer to Zenodo doi and the published paper.</p>
Analytical Electron Microscopy of Grain Boundary Segregation: Application to Al-Zn-Mg-Cu (7xxx) Alloys - Supporting Data
<p>Data to reproduce the figures reported in the manuscript Analytical Electron Microscopy of Grain Boundary Segregation: Application to Al-Zn-Mg-Cu (7xxx) Alloys. Published open access in Materials Characterization <a href="https://doi.org/10.1016/j.matchar.2019.06.016">https://doi.org/10.1016/j.matchar.2019.06.016</a></p>
Data from: The complex synaptic pathways onto a looming-detector neuron revealed using serial block-face scanning electron microscopy (SBEM)
<p>The locust's lobula giant movement detector 1 (LGMD1) looming detector pathway is part of the compound eye visual system and enables the animals to reliably detect collisions. Trans-medullary afferent neurons are considered key players in this pathway. Thousands of these neurons connect the second visual neuropile region, or medulla, with the third neuropile region, or lobula complex. In the lobula complex they are in synaptic contact with the LGMD1, which forms a dendritic tree in the outer region of the lobula complex neuropile. In order to describe their anatomy and connectivity patterns with other upstream neurons of the LGMD1, we used serial block-face scanning electron microscopy. We thus produced serial electron micrographs spanning from the dendritic tree in the outer lobula complex to the origin of the trans-medullary afferent neurons in the medulla. Starting from the LGMD1, we segmented and 3D-reconstructed entire trans-medullary afferents, as well as connecting neurons and other trans-medullary neurons nearby. This study was based on two datasets from different locusts of fourth instar. Here we provide the raw data for this study as .tiff stacks.</p>
FIGURE 2 in Scanning Electron Microscopy Vouchers And Genomic Data From An Individual Specimen: Maximizing The Utility Of Delicate And Rare Specimens
FIGURE 2: Image of agarose gel showing bright bands representing positive amplification of COI. A – Erythraeus sp; B – Trichosmaris sp; C – Raoiella indica; - negative control.
FIGURE 3 in Scanning Electron Microscopy Vouchers And Genomic Data From An Individual Specimen: Maximizing The Utility Of Delicate And Rare Specimens
FIGURE 3: Images (40X) of slide mounted Raoiella indica specimen (dorsal view on left, ventral view on right) after LTSEM imaging, DNA extraction, and KOH soak.
X-ray computed tomography and scanning electron microscopy datasets of unidirectional and textured glass fibre composites.
<p>3D x-ray tomography and 2D scanning electron microscopy (SEM) data behind the publications: </p> <p>Salling, F.B, Jeppesen, N., Sonne, M.R., Hattel, J.H., Mikkelsen, L.P. Individual Fibre Inclination Segmentation from X-ray Computed Tomography using Principal Component Analysis, <em>Journal of Composite Materials</em>, <strong>56</strong>, 83-98, <a href="https://doi.org/10.1177%2F00219983211052741">https://doi.org/10.1177/00219983211052741</a>, 2022.</p> <p>to where the reference should be given if used. </p> <p>Details on the data-set is given in the supplementary document found together with the data</p> <p>The data-files is given for the two material case called Mock and UD. For each material case, the data is given as:</p> <ul> <li>.txm-files: 3D reconstructed x-ray scan files <ul> <li>FoV 2mm binning 2 (analyzed in the paper)</li> <li>FoV 4mm binning 1 (additional data-set)</li> </ul> </li> <li>2Dtif.zip-files: 2D tif-stack version of the 3D reconstructed data-set</li> <li>.tif-files: stitched SEM scanning file used for fiber volume fraction determination</li> <li>.hdr-files: meta-data ASCII file behind the SEM scan</li> <li>tif.zip-files: The individual images behind the stitched SEM scanning file</li> <li>fig-files: digital form of the fibre trajectories colored according to their individual mean inclination used in figure xx in reference yy</li> <li>m-files: Matlab-script for calculating the fibre volume fraction (Vf) from the SEM image</li> <li>mat-files: Mat-file with the segmented part in the SEM image used for the Vf calculation</li> </ul>
Electron microscopy files (SBFSEM & TEM) for "Syncytial nerve net in a ctenophore sheds new light on the early evolution of nervous systems"
<p>4 electron microscopy datasets:</p> <p>1) SBFSEM data of 1-day old ctenophore <em>Mnemiopsis leidyi</em> (animal 1)</p> <p>2) SBFSEM data of 1-day old ctenophore <em>Mnemiopsis leidyi</em> (animal 2)</p> <p>3) SBFSEM data of 1-day old ctenophore <em>Mnemiopsis leidyi</em> (animal 3)</p> <p>4) TEM data of nerve net of 1-day old ctenophore <em>Mnemiopsis leidyi </em></p>
Investigation via Electron Microscopy and Electrochemical Impedance Spectroscopy of the Effect of Aqueous Zinc Ions on Passivity and the Surface Films of Alloy 600 in PWR PW at 320 C
<p>This upload includes the raw EDS data in Bruker Esprit format and the raw EIS data in excel dat format that is presented in the manuscript published in Corrosion and Materials Degradation entitled <em>Investigation via Electron Microscopy and Electrochemical Impedance Spectroscopy of the Effect of Aqueous Zinc Ions on Passivity and the Surface Films of Alloy 600 in PWR PW at 320 C.</em></p>
Dataset for scanning electron microscopy based local fiber volume fraction analysis of non-crimp fabric glass fiber reinforced composites
<p>SEM data sets, Matlab codes, and output from the local fiber volume fraction analysis from the publications:</p> <p>Mortensen, U.A., Rasmussen, S., Mikkelsen, L.P., Fraisse, A., Andersen, T.L. The impact of the fibre volume fraction on the fatigue performance of glass fiber composites used in the wind turbine industry, <em>Composites Part A</em>, submitted Dec 2022.</p> <p>Mikkelsen, Lars P., Fæster, S., Dahl, V.A. Dataset for scanning electron microscopy based local fiber volume fraction analysis of non-crimp fabric glass fiber reinforced composites. <em>Data in Brief</em>, Submitted, 2023.</p> <p>to where a reference should be given. </p> <p>The files are structured in the following way.</p> <ul> </ul> <p>L1, L2: Low FVF cases 1 and 2; see the publication.<br> H1, H2: High FVF case 1 and 2; see the publication.</p> <p>SEM images:</p> <ul> <li>*.bmp: Single SEM scan</li> <li>*.bmp.hdr: settings for single SEM scan</li> <li>*.tif: Stitched SEM scan</li> <li>*.tif.hdr: settings for stitched SEM scan</li> </ul> <p>*_BundleAnalysis.m: Script for manual segmentation of the individual bundles.</p> <ul> <li>*.zip files: Functions used by the ..._BundleAnalysis.m scripts</li> <li>*-CURVES_AND_AREAS.mat: Matlab saving of bundle definitions used by the ...BUndlesAnalysis.m script</li> <li>*BWbundles.mat: Output from the _BundleAnalysis.m script</li> </ul> <p>*.m: Local fiber volume fraction analysis script of SEM-scan based on output from BundleAnalysis tool</p> <ul> <li>Figxx.png: Reference to specific figures in the publications shown for all 4 cases</li> <li>Fig7.m: Matlab script for plotting figure 7</li> </ul> <p> </p> <p> </p> <p> </p> <p> </p>
Data for manuscript "Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting"
<p>The tar file contains the input files for RADICAL augmented MDFF implementation (R-MDFF) for two protein systems, Adenylate Kinase (ADK) and Carbon Monoxide Dehydrogenase (CODH). These examples demonstrate the implementation of R-MDFF using RADICAL-Cybertools to flexibly fit biomolecules in cryo-EM density maps with on-the-fly decision making.</p> <p>All molecular simulations were performed using CUDA enabled NAMD 2.14 installed on OLCF Summit HPC resource. The CHARMM36 force field parameters were used for the proteins. Synthetic density maps were prepared at 1.8, 3 and 5 Å for ADK and 1.8 and 3 Å for CODH using VMD 1.9.3 software installed on OLCF Summit HPC resource. During the analysis stage, the cross correlation coefficients between density maps and atomic model were computed using VMD 1.9.3 on Summit HPC as part of the R-MDFF workflow.</p> <p>The source code is publicly available on GitHub: <a href="https://github.com/radical-collaboration/MDFF-EnTK">https://github.com/radical-collaboration/MDFF-EnTK </a></p> <p>The preprint of this research is submitted on bioRxiv, doi: <a href="https://doi.org/10.1101/2021.12.07.471672">https://doi.org/10.1101/2021.12.07.471672 </a></p> <p>To obtain maximum compression of the data, the tar command used to generate this tarball was:</p> <pre><code class="language-bash">GZIP=-9 tar --exclude='last.pdb' --exclude='*last_from_prev_iter.pdb' --exclude='*old' --exclude='*log' --exclude='*coor' --exclude='*vel' --exclude='*xsc' --exclude='*dcd' --exclude='lastframepdbs_fix' --exclude='*out' --exclude='*sl' --exclude='*rs' --exclude='*prof' --exclude='*err' --exclude='*dx' --exclude='*grid.pdb' --exclude='*txt' -cvzf rmdffv2.tar.gz rmdff-zenodo/</code></pre> <p> </p>
SEM imaging data used in "Investigation of the porosity of L/LL4 ordinary chondrite Bjurböle using synchrotron radiation microtomography and scanning electron microscopy: Implications for parent body evolution"
<p>SEM imaging data used in ”Investigation of the porosity of L/LL4 ordinary chondrite Bjurböle using synchrotron radiation microtomography and scanning electron microscopy: Implications for parent body evolution” contains images of a polished section of a 0.35 cm<sup>3</sup> sample of Bjurböle obtained using scanning electron microscopy (SEM) in backscattered electron mode (pixel size 0.55 µm), as well as elemental maps of some details of the sample obtained by an energy dispersive spectrometer, as zip archives. Folder SEM contains the images covering the entire polished section. Bulk porosity of the sample was determined to be 21.9 vol% using a gas pycnometer. </p>
German NFDI, FAIRmat-NFDI, NOMAD, NOMAD OASIS, pynxtools, example datasets for atom probe microscopy and electron microscopy
<p>The following repository contains a collection of data and metadata files in different vendor formats which were collected in the fields of atom probe microscopy (LEAP instruments) and electron microscopy (Nion instruments). These files are meant for development and testing purposes of the nomad north-remote-tools-hub and the related nomad-nexus-parser software tools within the FAIRmat project.FAIRmat is a consortium lead by the Humboldt-Universität zu Berlin. FAIRmat is a member of the German Research Data Infrastructure (NFDI) initiative.</p> <p>A detailed description of the background and content of the individual files follows:</p> <p><strong>ger_berlin_haas_nionswift_multimodal.zip</strong><br> This is a dataset for testing how to load entire data and metadata from compressed NionSwift project files directly.<br> This is a dataset for testing the em_nion reader which handles files from Nion microscopes and NionSwift software.<br> The data were collected by Benedikt Haas from Humboldt-Universität zu Berlin. The parser was developed together<br> with Sherjeel Shabih also from Humboldt-Universität zu Berlin. Both work in the group of Prof. Christoph Koch.<br> EM.STEM.Nion.Dataset.1.zip is a dataset we used for an earlier version of this parser</p> <p><strong>APM.LEAP.Datasets.*.zip:</strong><br> This is a collection of two datasets for testing the generic nx_apm reader which handles commercial and community file formats for reconstructed ion position and ranging data from atom probe microscopy experiments. The datasets were collected by different authors.<br> <br> <strong>APM.LEAP.Datasets.1.zip:</strong><br> <em>R31_06365-v02.pos</em>, was shared by Jing Wang and Daniel Schreiber (both at PNNL). Details to the dataset are available<br> under the following DOIs:<br> https://doi.org/10.1017/S1431927618015386<br> https://doi.org/10.1017/S1431927621012241<br> <em>70_50_50.apt</em>, was a shared by Xuyang Zhou at his time with the Max-Planck-Institut für Eisenforschung GmbH as a open-source test data to the publication he lead on machine-learning-based techniques for composition profiling.<br> The dataset and publication is available via the following DOI and resources:<br> https://doi.org/10.1016/j.actamat.2022.117633<br> The dataset specifically is also available here:<br> https://github.com/RhettZhou/APT_GB/tree/main/example/Cropped_70_50_50<br> The range files <em>*.rng </em>and<em> *.rrng</em> range serve as examples to develop tools for parsing them and handle the formatting of range files. The scientific content of the range files was inspired by experiments but is not related to the above-mentioned atom probe datasets<br> and should not be used to analyze these test data for more than pure development purposes.<br> Use instead your own data and matching range files for scientific analyses.</p> <p><strong>APM.LEAP.Datasets.2.zip</strong><br> <em>R18_53222_W_18K-v01.epos</em>, was shared with Markus Kühbach by Andrew Breen<br> during their time at the Max-Planck-Institut für Eisenforschung GmbH.<br> <br> We would like to invite the community to use the nomad infrastructure and support us with<br> sharing data and dataset which we can then use to improve the file format parsing, the reading capabilities,<br> and analyses services of the nomad infrastructure so that the community can profit again from these developments.</p> <p><strong>aut_leoben_leitner.zip</strong><br> is the dataset associated to the grain boundary solute segregation case study discussed in https://arxiv.org/abs/2205.13510</p> <p><strong>usa_portland_wang.zip</strong><br> is the dataset associated with the ODS steel specimen dataset, which is a good example for testing and learning iso-surface<br> based analyses with the paraprobe-toolbox. This dataset was mentioned as one of the test cases in https://arxiv.org/abs/2205.13510</p> <p><strong>ger_erlangen_felfer_ck10.zip</strong><br> is the Ck10 for fundamentals dataset from the atom-probe-toolbox<br> https://github.com/peterfelfer/Atom-Probe-Toolbox/tree/master/test%20data/Ck%2010%20steel%20for%20fundamentals</p> <p><strong>usa_denton_smith_apav_gbco.zip</strong><br> is the GBCO-type dataset from J. Smith and M. Young discussed in their following publications:<br> https://doi.org/10.1017/S1431927621012794 and https://github.com/openjournals/joss-reviews/issues/4862<br> <br> <strong>usa_denton_smith_apav_si.zip</strong><br> is a very small dataset in POS, ePOS, APT, RNG, and RRNG for development and testing purposes.<br> The dataset is a part of APAV mentioned here<br> https://gitlab.com/jesseds/apav/-/tree/JOSS/apav/tests</p>
Dataset for Interlacing in atomic resolution scanning transmission electron microscopy
<p>Dataset for the publication: Interlacing in atomic resolution scanning transmission electron microscopy</p>
Supplementary Information for "Analytical electron microscopy study of the composition of BaHfO₃ nanoparticles in REBCO films: The influence of rare-earth ionic radii and REBCO composition"
<p>Supplementary information containing image and spectroscopy data, and data-processing notebooks for the article "<strong>Analytical electron microscopy study of the composition of BaHfO<sub>3</sub> nanoparticles in REBCO films: The influence of rare-earth ionic radii and REBCO composition</strong>".</p> <p>Article (open access): <a href="https://doi.org/10.1039/D3MA00447C">https://doi.org/10.1039/D3MA00447C</a></p> <p>The data is sorted in folders for each figure, and the <em>Notes.pdf</em> file contains additional information about the different file formats and processing steps.</p> <p>If you have questions, you can contact Lukas Grünewald at the E-Mail listed on the ORCID page: <a href="https://orcid.org/0000-0002-5898-0713">https://orcid.org/0000-0002-5898-0713</a></p>
Electron microscopy data for Hopfion rings in a cubic chiral magnet
<p>Raw data for Figures shown in the main text and Extended Data Figs 1-4 are provided here. Data is provided in *.dm4 format, which can be opened by Gatan Microscopy Suite (GMS) software 3.4. </p>
Scanning gate microscopy of non-retracing electron-hole trajectories in a normal-superconductor junction - code
<p>We theoretically study the Scanning Gate Microscopy (SGM) of the electron and hole trajectories in a Normal-Superconductor (NS) interface where a Quantum Point Contact (QPC) is embedded. In the zero bias case, electrons after getting Andreev reflected as a hole from the NS interface, have a similar wave vector, which causes the self-interference pattern in the SGM conductance plots. For the nonzero bias case, electrons and holes have different wave vectors. As a result, a disturbed and branched flow SGM conductance map is observed. Also by plotting the probability currents, we can clearly see the difference in two cases. The code contains all of these calculations.</p>
Fluctuation electron microscopy data from amorphous Tb-Co and SiNx
<p>These datasets were used for fluctuation electron microscopy (FEM) analysis of amorphous Tb<sub>17</sub>Co<sub>83</sub>. The Tb<sub>17</sub>Co<sub>83</sub> is 30 nm thick. The deposited Ta is sandwiched between two layers of amorphous 10 nm-thick SiN<sub>x</sub>. Data are also provided for SiN<sub>x</sub> deposited on SiN<sub>x</sub>. Samples include: (1) Tb<sub>17</sub>Co<sub>83 </sub>deposited at 20<sup>o</sup>C, (2) Tb<sub>17</sub>Co<sub>83 </sub>deposited at 200<sup>o</sup>C, (3) Tb<sub>17</sub>Co<sub>83 </sub>deposited at 300<sup>o</sup>C, (4) Tb<sub>17</sub>Co<sub>83 </sub>deposited at 20<sup>o</sup>C and annealed at 200<sup>o</sup>C, and (5) Tb<sub>17</sub>Co<sub>83 </sub>deposited at 20<sup>o</sup>C and annealed at 300<sup>o</sup>C.</p> <p>FEM patterns were collected in a FEI TitanX operated at 200 kV with a convergence angle of 0.51 mrad and a camera length of 300 mm. </p> <p>Samples (1) Tb<sub>17</sub>Co<sub>83 </sub>deposited at 20<sup>o</sup>C and (3) Tb<sub>17</sub>Co<sub>83 </sub>deposited at 300<sup>o</sup>C were tilted between 0<sup>o</sup> and 40<sup>o</sup> in 5<sup>o</sup> increments. The tilted FEM data is also included.</p> <p><strong>File types</strong></p> <p>.dm4 (Gatan DigitalMicrograph) files are provided with the raw scanning nanodiffraction data for each sample. Each sample has multiple associated .dm4 files because measurements were repeated for statistical purposes.</p> <p><strong>Data processing</strong></p> <p>For the steps involved in FEM data processing, please visit: https://github.com/ScottLabUCB/FEM</p> <p><strong>File name format</strong></p> <p>Using "gRTa200_t00_200kV_cl300_ca0p51_exp0p3_spot9_ss5nm_04.dm4" as an example, the naming format is:</p> <p>"sample descriptor _ tilt angle _ TEM voltage_camera length [mm] _ convergence angle [mrad] _exposure [sec] _spot size _ step size between probe positions [nm]_ data set number.dm4"</p> <p>Data are from Tb<sub>17</sub>Co<sub>83 </sub>capped with SiN<sub>x</sub> unless only "SiN" is stated in the descriptor, in which case the data are from SiN<sub>x</sub>.</p> <p>For the tilted data, the naming format is:</p> <p>"sample descriptor _ tilt angle _ spot size _ exposure [sec] convergence angle [mrad]_ bin factor _camera length _ TEM voltage _ data set number.dm4"</p> <p>For all data, the step size is 5 nm, the spot size is 9, the exposure is 0.3 seconds, the convergence angle is 0.51 mrad, the camera length in 300 mm, and the TEM extraction voltage is 200 kV.</p> <p> </p>
Data from: The complex synaptic pathways onto a looming-detector neuron revealed using serial block-face scanning electron microscopy (SBEM)
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Simulations of cochlear nucleus bushy cells reconstructed from serial blockface electron microscopy (V1.3)
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Data from: Correction of preferred-orientation induced distortion in cryo-electron microscopy maps
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DANDI Archive for NWB datasets
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International Brain Laboratory public data
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OpenNeuro
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