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209 results for “scanning electron microscopy”
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 03
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 03 comprises an image 3D model of a <em>Giardia lamblia</em> cell adhered to the plastic substrate of a culture dish. The model was generated by segmentation of the entire cell, the cell nuclei (red) and the ventral disc cytoskeleton (yellow) in an image series of 276 images which was recorded by SBF SEM (see dataset 01). Section interval was 50 nm and pixel size 10 nm. The data folder contains the model-file (Imaris-format) and a 360° rotation of the model as video file (mp4-format).</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 02
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 02 comprises an image series of 1462 images recorded of a <em>Giardia lamblia</em> cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.5 mbar). Original pixel size was 5 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 09
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 09 comprises an image series of 400 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 08
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 08 comprises an image series of 299 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 3 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 04
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 04 comprises an image series of 120 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the T1 detector of the SEM at high vacuum. Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 07
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 07 comprises an image series of 318 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 8 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 06
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 06 comprises an image series of 215 images recorded of a HeLa cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 10 nm using the DBS detector of the SEM at low vacuum (0.4 mbar). Original pixel size was 10 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Serial block-face scanning electron microscopy of adherent cells on thin plastic substrate – Data set 01
<p>Serial block-face (SBF) scanning electron microscopy (SEM) is used for imaging the entire internal ultrastructure of cells, tissue samples or small organisms. We developed a workflow for SBF SEM of adherent cells, such as <em>Giardia</em> parasites and HeLa cells, attached to the surface of a plastic culture dish, which preserves the interface between cells and plastic substrate. Cells were embedded <em>in situ</em> on their substrate using silicone microwells and were mounted for cross-sectioning which allowed SBF imaging of large volumes and many cells. In total we provide 10 data sets with image series from SBF SEM of <em>Giardia</em> and HeLa cells prepared with protocol variants to improve the workflow. A detailed description of the methods and the data set is provided in the download container.</p> <p>Data set 01 comprises an image series of 276 images recorded of a <em>Giardia lamblia</em> cell adhered to the plastic substrate of a culture dish. SBF SEM was done at a section interval of 50 nm using the DBS detector of the SEM at low vacuum (0.5 mbar). Original pixel size was 4 nm. The data folder contains the raw image files, processed image files (see data set description for details of the processing), a video file of a processed image file series.</p>
Scanning electron microscopy datasets -- Emiliania huxleyi strains from naturally high and low CO2 waters responding to high and low CO2 in the lab
<p>Study question: How do Emiliania huxleyi strains isolated from naturally high CO2 waters or low CO2 waters respond to exposure to high and low CO2 levels?</p> <p> </p> <p>Associated article:<br> Peter von Dassow, Francisco Díaz-Rosas, El Mahdi Bendif, Juan-Diego Gaitán-Espitia, Daniella Mella-Flores, Sebastian Rokitta, Uwe John, and Rodrigo Torres. 2018. Over-calcified forms of the coccolithophore <em>Emiliania huxleyi </em>in high-CO2 waters are not preadapted to ocean acidification. Biogeosciences. <a href="https://doi.org/10.5194/bg-15-1-2018">https://doi.org/10.5194/bg-15-1-2018</a></p> <p> </p> <p>Technical notes:</p> <p>Three electron microscopes were used:</p> <ol> <li>TM3000 (Hitachi High-Technologies, Tokyo, Japan) in the Unidad de Microscopía Avanzada of the Facultad de Ciencias Biológicas, Pontificia Univesidad Católica de Chile. The Hitachi microscope is not of high quality, and, when available, other electron microscopes were used.</li> <li>Quanta 250 (FEI, Hillsboro, Oregon, USA) in the Facultad de Geología, Universidad de Chile</li> <li>Quanta FEG 250 (FEI, Hillsboro, Oregon, USA) in the laboratory CIEN-UC, Facultad de Física, Pontificia Universidad Católica de Chile.</li> </ol> <p> </p> <p>Data set 1: Data-sharing-SEM_Calfuco-CO2 experiment.zip</p> <p>Scanning electron microscopy images of E. huxleyi strains after bubbling with 1200 µatm CO2 and 400 µatm CO2 air/CO2 mixes.</p> <p> </p> <p>Data set 2: Field-SEM-2011-2013.zip</p> <p>Scanning electron microscope images of filters of plankton samples taken during field campaigns. See article for methodology. For the samples from ElQuisco_2012 and JuanFernandez_2011, note that the last two digits in the sample name refer to the depth from which the sample was obtained (ej., “FQ.01.01.05D” is from 5 m and “FQ.01.01.15D” is from 15 m). Tables are provided to associate counts and taxonomic identifications to environmental variables from the samples for which data was used in statistical analysis. Note also that images do not correspond to all counts reported, as sometimes counts were made without capturing images due to time pressure for microscope use. </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>
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>
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>
Dataset for Interlacing in atomic resolution scanning transmission electron microscopy
<p>Dataset for the publication: Interlacing in atomic resolution scanning transmission electron microscopy</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>
Data from: The complex synaptic pathways onto a looming-detector neuron revealed using serial block-face scanning electron microscopy (SBEM)
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Data from: Crustacean photoreceptor damage and recovery: Applying a novel scanning electronic microscopy protocol in artificial light at night studies
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Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part I: Data Acquisition, Live Processing and Storage
<p>Scanning transmission electron microscopy data related to paper "Fast Pixelated Detectors in Scanning Transmission Electron Microscopy. Part I: Data Acquisition, Live Processing, and Storage": <a href="https://doi.org/10.1017/S1431927620001713">https://doi.org/10.1017/S1431927620001713</a></p>
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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.