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48 results for “fib”
FIB-SEM tomograms of the steel-concrete interface of mortar and concrete specimens
<p>This datasets contains tomograms showing the steel-concrete interface of mortar (files starting with NCI) and concrete (files starting with CI) specimens. They were acquired by a FIB-SEM (focused ion beam-scanning electron microscope).</p> <p>There are five datasets:</p> <ol> <li>NCI-1, with a voxel size of 30 nm</li> <li>NCI-2, with a voxel size of 50 nm</li> <li>NCI-3, with a voxel size of 50 nm, consisting of four microscopy sessions (A, B, C, D)</li> <li>NCI-4, with a voxel size of 30 nm, consisting of four microscopy sessions (A, B, C, D)</li> <li>CI, with a voxel size of 30 nm, consisting of six microscopy sessions (A, B, C, D, E, F)</li> </ol> <p>More information can be found here: (TBD)</p> <p> </p> <p> </p>
Deep learning segmentation projects of FIB-SEM dataset of U2-OS cell
<p>This submission includes ground truth datasets that were used to segment the nuclear envelope (NE), mitochondria, endoplasmic reticulum (ER) and Golgi from a human bone osteosarcoma epithelial cell (U2-OS) imaged using focused-ion beam scanning electron microscopy (FIB-SEM).</p><p>The full FIB-SEM dataset is deposited to EMPIAR (<a href="https://www.ebi.ac.uk/empiar">https://www.ebi.ac.uk/empiar</a>, EMPIAR-11746). </p>
Benchmark FIB SEM and Airyscan data of HeLa cells
<p>Sample volume electron microscopy dataset cropped from EMPIAR-10819 and fluorescence dataset from BioImage Archive S-BSST707 for the CLEM-Reg paper.</p>
FIB cleaned and reshaped Electrostatic electron vortex beam generators - dataset2
<p>Here is a second set of SEM images of Electrostatic electron vortex beam generators fabricated at the CNR-IMM in Bologna and FIB cleaned and reshaped at the CNR-NANO in Modena. The difference between this batch of devices and the first one is in the thickness of the electrode (the z-dimension), this batch has a electrode thickness of 30um, while the first batch is 10um thick.</p>
FIB cleaned an reshaped Electrostatic Electron Vortex Beam Generators
<p>Here are collected the SEM images (top-view and tilted-view) of the Electrostatic Electron Vortex Beam Generators fabricated at the CNR-IMM in Bologna and then cleaned and reshaped by FIB milling at the CNR-NANO in Modena. Different shapes of the main paired needles have been fabricated to try to optimize the reproduction the ideal phase profile as reported in https://doi.org/10.1103/PhysRevResearch.2.013185</p>
Human Population-Averaged dMRI Templates (FIB Files, NIFTI Files)
<p>The templates were constructed by DSI Studio using q-space diffeomorphic reconstruction.</p> <p>Methods and Data Source: https://brain.labsolver.org/hcp_template.html</p> <p> </p> <p> </p>
FIB-SEM tomography datasets of entire single-cell human monocyte derived macrophages
<p>FIB-SEM tomography was used to determine the absolute number of internalized gold nanoparticles in GM-CSF and M-CSF human monocyte-derived macrophages at the single-cell level. All experiments were performed using a Thermo Scientific Scios 2 Dual Beam microscope (Thermo Fisher Scientific, Waltham, MA, USA). A selected cell was protected with a platinum (Pt) layer of 1 µm thickness (30 kV and current of 1 nA). Then, a trench of 5 µm in depth was milled on the front face and each side of the cell of interest using the ion beam at 7 nA current. Finally, the front face of the volume of interest was polished with an ion beam current of 1 nA until the beginning of the cell was visible to optimize the focus and contrast. FIB-SEM tomography of the whole cell was performed using the FEI Slice and View software (Thermo Fisher Scientific, Waltham, MA, USA, version 4.1). The electron beam acceleration voltage was set to 5 kV, the current to 0.4 nA, the resolution to 1536 × 1024 pixels, and the dwell time to 30 µs. Images were acquired in immersion mode with the backscattered electron detector, yielding clear signals from AuNPs due to the detector's sensitivity to backscattered electrons, which correlates with the atomic number of Au (Z = 79). The ion beam operating with a current of 1 nA current at 30 kV was used to slice through the cell of interest at an interval of 18 nm and a depth of 5 µm. The datasets available on the repository have been aligned and cropped.</p>
Three‐dimensional reconstruction of porous polymer films from FIB‐SEM nanotomography data using random forests
<p>Dataset and code used in M. Röding, et al, "Three-dimensional reconstruction of porous polymer films from FIB-SEM nanotomography data using random forests", published in Journal of Microscopy, 2020. In this work, we develop a segmentation method for focused ion beam scanning electron microscopy (FIB-SEM) data acquired by volumetric imaging of porous polymer films made from ethyl cellulose and hydroxypropyl cellulose (EC/HPC) polymer blends. This type of polymer films are used for controlled release applications. Based on manual segmentation of a fraction of the data, a random forest classifier is trained and applied to the full data set. Here, raw data, manual segmentations, and the Matlab code used for all steps in the analysis are supplied.</p>
FIB-tomography data of Ni-YSZ anodes for Solid Oxide Fuel Cells (SOFC): Comparison of pristine and degraded materials (before/after redox cycling)
<p><em>Contents: </em></p> <p>This dataset contains 3D image stacks acquired with FIB-tomography from Ni-YSZ cermet anodes for Solid Oxide Fuel Cells (SOFC).</p> <p>The data was collected from three different Ni-YSZ anodes (fine-, medium- and coarse-grained). Each of these anodes was investigated first in pristine state (after sintering and reduction) and then also in degraded state (after exposure to 8 redox cycles).</p> <p>The 6 tomographs are then presented as stacks of 2D-tiff-images in 2 different versions: as gray-scale images (raw data) and as segmented images (Ni=white, YSZ=gray and pores=black). In total this gives 12 image stacks.</p> <p><strong>Further details</strong>, such as the voxel resolutions and image window sizes are listed in the downloadable excel file (<strong>2_3D_Data_Info.xlsx</strong>).</p> <p> </p> <p><em>Scientific Context: </em></p> <p>The microstructures of the cermet anodes were investigated for the purpose of optimizing the anode performance, which depends on effective transport properties (i.e. conductivity of ions in YSZ and of electrons in Ni, as well as diffusivity of fuel/gas in the pores). Furthermore the anode performance also depends on the catalytic/electrochemical activity (i.e. Ni-surface area and three phase boundary length TPBL). The microstructure characteristics have a strong influence on effective properties, electrochemical activity and associated anode performance. Furthermore, microstructure degradation (e.g. by Ni-coarsening) may lead to performance loss over time.</p> <p>Hence, the investigations focus on a fundamental, quentitative understanding of the relationships between microstructure characteristics and effective properties. The study reveals quantitative descriptions of all relevant microstructure characteristics (porosity, tortuosity, constrictivity, surface/interface areas, TPBL) and of the corresponding effective transport porperties (electric and ionic.conductivities). The corresponding anode performance was characterized by impedance spectroscopy.</p> <p>The quantitative <strong>results of the microstructure investigation were published</strong> in:</p> <p><strong>Pecho et al</strong> 2015a (doi:10.3390/ma8095265),</p> <p><strong>Pecho et al</strong> 2015b (doi:10.3390/ma8105370),</p> <p><strong>Holzer et al</strong> 2013 (doi: 10.1016/j.jpowsour.2013.05.047),</p> <p><strong>Holzer et al</strong> 2011a (doi: 10.1016/j.jpowsour.2010.08.017) and</p> <p><strong>Holzer et al</strong> 2011b (doi: 10.1016/j.jpowsour.2010.08.006).</p>
Kinesin-1 activity recorded in living cells with a precipitating dye FIB-SEM data 1
<p>Kinesin-1 activity recorded in living cells with a precipitating dye</p> <p>FIB-SEM dataset 1 - QPDTf precipitating dye with HeLa cells</p> <p> </p>
3DED data of FIB milled lysozyme crystals
<p>This repository contains 3DED data from FIB milled lysozyme crystals. The directory contains the following data files:</p> <p><strong>FIB_Lysozyme_Data</strong></p> <ul> <li>argon <ul> <li>Ar_final.pdb</li> <li>Ar_merged.mtz</li> </ul> </li> <li>xenon <ul> <li>Xe_final.pdb</li> <li>Xe_merged.mtz</li> </ul> </li> <li>gallium <ul> <li>Ga_final.pdb</li> <li>Ga_merged.mtz</li> </ul> </li> </ul> <p>For each FIB source, the *_merged.mtz file contains the merged reflection intensities from multiple datasets milled using that source. The corresponding *_final.pdb file is the final refined model.</p>
FIB-tomography data of porous Zr-oxide fabricated with varying sintering conditions
<p>This dataset contains 3D data acquired with FIB-tomography from porous Zr-oxide. The pore structures of the ceramic materials were investigated in context with optimization of transport properties (aimed for low viscous flow/permeability and high electric conduction via liquid electrolyte in the pores), so that the Zr-oxide is suitable for application as liquid junction (diaphragm) in pH-sensors. Further details on the scientific background are given in Holzer et al., 2016, Materials & Design, 99, 314–327. (http://doi.org/10.1016/j.matdes.2016.03.034).</p> <p> </p> <p>The tomographs represent 9 ceramic materials that were produced with different sintering temperatures (1250, 1300, 1325 and 1350°C) and different sintering times (1, 2 and 3 hours). The study includes quantitative descriptions of relevant microstructure characteristics (porosity, tortuosity, constrictivity, hydraulic radius) and corresponding effective transport prorperties (permeability, conductivity).</p> <p> </p> <p>Each tomograph is presented as stack of 2D-tiff-images in two different versions: as gray-scale images (raw data) and as binarized images (segmented, with solid=black and pores=white). The voxel resolution is 10x10x10 nm for all 18 image stacks.</p> <p> </p> <p>More details on the image data (e.g. voxel nr, image window size, data size) are given in the downloadable file '2_3D_Data_Info.xlsx'.</p>
Kinesin-1 activity recorded in living cells with a precipitating dye_FIB-SEM_data_2_part1
<p>Kinesin-1 activity recorded in living cells with a precipitating dye_FIB-SEM_data_2_part1</p>
Kinesin-1 activity recorded in living cells with a precipitating dye_FIB-SEM_data_2_part2
<p>Kinesin-1 activity recorded in living cells with a precipitating dye_FIB-SEM_data_2_part2</p>
FIB-SEM Dataset (Obara + Nixon-Abell et al., 2023)
<p>Analyzed portions of FIB-SEM volumes used for analysis in Obara + Nixon-Abell et al., 2023. Full datasets are available upon request from authors, they are just too large to easily store in this medium. Email Jennifer Lippincott-Schwartz at jlippincottschwartz@janelia.hhmi.org or Christopher Obara at cjobara@gmail.com for full dataset requests.</p><p> </p>
Tomogram of T. kivui FIB-milled cells with HDCR filaments
<p>This entry contains the <em>T. kivui</em> tomogram (MRC format) and associated reconstruction files used in the ICE-TIDE <a href="https://doi.org/10.48550/arXiv.2403.02182">manuscript</a> and <a href="https://github.com/swing-research/Implicit-Cryo-Electron-Tomography">tutorial</a>.</p> <p>For the raw data and more details, please see the <a href="https://doi.org/10.6019/EMPIAR-11058">EMPIAR-11058</a> deposition.</p> <p>These data were originally published in:<br><br>Dietrich, H.M., Righetto, R.D., Kumar, A. <em>et al.</em> Membrane-anchored HDCR nanowires drive hydrogen-powered CO<sub>2</sub> fixation. <em>Nature</em> <strong>607</strong>, 823–830 (2022). <a href="https://doi.org/10.1038/s41586-022-04971-z">https://doi.org/10.1038/s41586-022-04971-z</a></p>
HCP-YA 1065 Subjects dMRI Data (2mm FIB Files)
<p>The minimally-preprocessed data (Glasser et al., 2013) from Human Connectome Projects (Q1-Q4 release, 2015) were acquired by Washington University in Saint Louis and University of Minnesota (Van Essen et al., 2012). The diffusion MRI scan was conducted on a Siemens 3T Skyra scanner using a 2D spin-echo single-shot multiband EPI sequence with a multi-band factor of 3 and monopolar gradient pulse. The spatial resolution was 1.25 mm isotropic. TR = 5500 ms, TE = 89.50 ms. The b-values were 1000, 2000, and 3000 s/mm2. The total number of diffusion sampling directions was 90, 90, and 90 for each of the shells in addition to 6 b0 images. The preprocessed data were corrected for eddy current and susceptibility artifact. The accuracy of b-table orientation was examined by comparing fiber orientations with those of a population-averaged template (Yeh et al. Neuroimage, 2018). The restricted diffusion was quantified using restricted diffusion imaging (Yeh et al., MRM, 77:603–612 (2017)). The diffusion data were reconstructed using generalized q-sampling imaging (Yeh et al., IEEE TMI, ;29(9):1626-35, 2010) with a diffusion sampling length ratio of 1.7.</p>
text-fig. 46. Segisaurus halli, UCMP V 338; stereophotographs of the left femur, tibia and fibula, illustrating state 1 of character 209. Abbreviations: fe, femur; fib, fibula; tib, tibia. Scale bar represents 10 mm. in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 46. Segisaurus halli, UCMP V 338; stereophotographs of the left femur, tibia and fibula, illustrating state 1 of character 209. Abbreviations: fe, femur; fib, fibula; tib, tibia. Scale bar represents 10 mm.
text-fig. 49. Theropod astragali and calcanei, illustrating several tarsal characters, a-b, Lilienstemus lilienstemi\ MB R. 2175; left astragalo-calcaneum; anterior view and proximal view (reversed). c-D, Allosaurus fragilis: MOR 693; stereophotographs of left astragalo-calcaneum in anterior and proximal view. E, Deinonychus antirrhopus; YPM 5226; left astragalo-calcaneum; anterior view (stereophotographs). Abbreviations: asc proc, ascending process of the astragalus; ast, astragalus; calc, calcanéum; fib, facet for fibula; tib, facet for tibia. Scale bars represent 10 mm. in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 49. Theropod astragali and calcanei, illustrating several tarsal characters, a-b, Lilienstemus lilienstemi\ MB R. 2175; left astragalo-calcaneum; anterior view and proximal view (reversed). c-D, Allosaurus fragilis: MOR 693; stereophotographs of left astragalo-calcaneum in anterior and proximal view. E, Deinonychus antirrhopus; YPM 5226; left astragalo-calcaneum; anterior view (stereophotographs). Abbreviations: asc proc, ascending process of the astragalus; ast, astragalus; calc, calcanéum; fib, facet for fibula; tib, facet for tibia. Scale bars represent 10 mm.
text-fig. 55. Left distal tibia, fibula, and proximal tarsals of a, Syntarsus rhodesiensis (QG 1) and B, Lilienstemus lilienstemi (MB R. 2175) in anterior view, showing differences in the development of the distal end of the fibula and its connection with the ascending process of the astragalus. Abbreviations: asc proc, ascending process of the astragalus; astr, astragalus; calc, calcanéum; fib, fibula; tib, tibia. Scale bars represent 10 mm. in The interrelationships and evolution of basal theropod dinosaurs
text-fig. 55. Left distal tibia, fibula, and proximal tarsals of a, Syntarsus rhodesiensis (QG 1) and B, Lilienstemus lilienstemi (MB R. 2175) in anterior view, showing differences in the development of the distal end of the fibula and its connection with the ascending process of the astragalus. Abbreviations: asc proc, ascending process of the astragalus; astr, astragalus; calc, calcanéum; fib, fibula; tib, tibia. Scale bars represent 10 mm.
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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)
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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.