This dataset includes 3D scanning electron microscopy (SEM) images of a female mouse corpus callosum and MATLAB code for random walker (RaW) segmentations of myelinated axons. The code additionally characterizes inner axonal diameters and fiber orientation dispersion within segments of the intra-axonal spaces and myelin sheaths.

In the study, a female 8-week-old C57BL/6 mouse was perfused trans-cardiacally using a fixative solution. The genu of corpus callosum was later excised from the midsagittal slice of the dissected brain, and the tissue was sampled from the central region of the genu and was fixed in the same fixative solution. The tissue was then stained and an En Bloc lead staining was performed to enhance membrane contrast. The brain sample was dehydrated in alcohol and acetone, and embedded in Durcupan ACM resin. Then, the tissue sample was analyzed with SEM.

The SEM dataset includes 4 files:

• datac.nii (a stack of SEM data, 200 slices; resolution: 24nm by 24nm by 100nm; volume: 36μm by 48μm by 20μm)
• maskc.nii (foreground mask)
• myelin_mask.nii (myelin mask generated by pixel-wise classifier in ilastik)
• fibers.nii (intra-axonal space segmented by using random-walker-based approach)

Scanning electron microscopy (SEM) has an important application in the petroleum field, which is often used to analyze the microstructure of reservoir rocks, etc. Most of these analyses are based on two-dimensional images. In fact, SEM can carry out micro-nano scale three-dimensional measurement, and three-dimensional models can provide more accurate information than two-dimensional images. Among the commonly used SEM 3D reconstruction methods, parallax depth mapping is the most commonly used method. Multiple SEM images can be obtained by continuously tilting the sample table at a certain Angle, and multiple point clouds can be generated according to the parallax depth mapping method, and a more complete point clouds recovery can be achieved by combining the point clouds registration. However, the root mean square error of the point clouds generated by this method is relatively large and unstable after participating in point clouds registration. Therefore, this paper proposes a new method for generating point clouds. Firstly, the sample stage is rotated by a certain angle to obtain two SEM images. This operation makes the rotation matrix a known quantity. Then, based on the imaging model, an equation system is constructed to estimate the unknown translation parameters, and finally, triangulation is used to obtain the point clouds. The method proposed in this paper was tested on a publicly available 3D SEM image set, and the results showed that compared to the disparity depth mapping method, the point clouds generated by our method showed a significant reduction in root mean square error and relative rotation error in point clouds registration.

Dataset of raw and image processed 3D Cryo-FIB SEM data recorded from Mallomonas cells.

Materials qualification of reactor structural materials is a critical step in rapid implementation of advanced nuclear reactor technologies, particularly to assess the corrosion performance in these designs. Accelerated qualification of reactor structural materials requires incorporating powerful computational toolsets, such as phase field modelling in the Multiphysics Object-Oriented Simulation Environment (MOOSE) framework, to predict the evolution of structural materials due to corrosion. Accordingly, computational toolsets will require experimental data generated at appropriate length scales to validate accuracy. Focused ion beam (FIB) provides a high degree of control over manipulation of materials for analytical purposes, including capturing data on the evolution in the microstructure and elemental composition of materials at the mesoscale, an appropriate length scale for phase field modelling of intergranular diffusion phenomena using the MOOSE framework. For instance, the FEI Helios G4 UX dual beam plasma FIB microscope at the Irradiated Materials Characterization Laboratory (IMCL) is capable of backscatter diffraction (EBSD) and energy-dispersive x-ray spectroscopy (EDS) documenting the evolution in the microstructure and elemental composition, respectively. The Helios can perform EDS and EBSD three-dimensionally (3D) using tomography, which is then combined using different software packages to visualize 3D volumes correlating elemental composition to microstructural data. The purpose of this investigation was to develop a streamlined characterization and data processing workflow for 3D tomography studies on the FEI Helios G4 plasma FIB. The investigation is segmented into three parts: 1) Optimizing the data collection workflow, 2) identifying appropriate data processing and visualization software (i.e. DREAM.3D, MIPAR, and VGStudioMax), and 3) establishing an infrastructure for public release. The optimization of the data collection workflow is in collaboration with members of the U220 department to setup formal training on the tomography operation of the G4, through ThermoFisher Scientific, and exploring DREAM.3D, MIPAR, and VGStudioMax data processing/visualization software packages. VGStudioMax currently demonstrates the most promise for future use. Optimization of the data collection and processing workflow is still ongoing. A collaboration with INL High Performance Computing (HPC) established an open-source license for expediting the public release of FIB tomography datasets through HPC. FIB tomography data generated by the G4 will provide comprehensive data for validating 3D phase field mesoscale modelling tools within the MOOSE framework for accelerated qualification of reactor structural materials. label::after { content: "" !important; }

Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations inasmuch as they only visualize a single slice or a relatively small volume of the cell, respectively. Here, we overcome these limitations by long-term imaging whole cells and tissues via the enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) platform in high resolution mode with month-long acquisition duration. We use this approach to generate reference 3D image data sets at 4-nm isotropic voxels. Together with subsequent segmentation, we hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents, thus addressing questions related to cell identities, cell morphologies, cell-cell interactions, as well as intracellular organelle organization and structure. Fan-shaped body, the largest substructure of the central complex controls various behaviors of insects. To understand brain functions, knowing neuron connectivity at synapse level is critical. High-resolution FIB-SEM images with large volume provide significant values in both identifying synaptic structures and tracing fine neuronal profiles. The detailed examination of synapses and unique intracellular features could add important insights to the understanding of the types of synaptic vesicles, synaptic polarity and neuron’s property.Sample: Fan-shaped body of a 5 day-old adult male Drosophila (Genome type: iso Canton S G1 x w1118 iso 5905).Protocol: Chemical Fixation, ORTO-Lead-EPTA staining via progressive lowering of temperature and low temperature staining (PLT-LTS) heavy metal enhancement protocol.Contributions: Sample provided by Zhiyuan Lu (HHMI/Janelia), prepared, imaged and post-processed by Song Pang (HHMI/Janelia), with post-processing by C. Shan Xu (HHMI/Janelia).Dataset ID: jrc_fly-fsb-1Final voxel size (nm): 4.00 x 4.00 x 4.00 (X, Y, Z)Dimensions (µm): 45 x 56 x 45 (X, Y, Z)Acquisition date: 2019-09-14Dataset URL: https://data.janelia.org/TrW8bVisualization Website: https://openorganelle.janelia.org/datasets/jrc_fly-fsb-1Publication: “Isotropic 3D electron microscopy reference library of whole cells and tissues” by C. Shan Xu et al. (in preparation)

The platelet-em dataset contains two 3D scanning electron microscope (EM) images of human platelets, as well as instance and semantic segmentations of those two image volumes. This data has been reviewed by NIBIB, contains no PII or PHI, and is cleared for public release. All files use a multipage uint16 TIF format. A 3D image with size [Z, X, Y] is saved as Z pages of size [X, Y]. Image voxels are approximately 40x10x10 nm

This data article presents a data set comprised of 2048 synthetic scanning electron microscope (SEM) images of powder materials and descriptions of the corresponding 3D structures that they represent. These images were created using Blender, an open source computer graphics suite, and the generating scripts are included with the data set. Eight particle size distributions are represented with 256 independent images from each. The particle size distributions are relatively similar to each other, so that the dataset offers a useful benchmark to assess the fidelity of image analysis techniques.

The data are in the proprietary dm4 format as saved by the acquisition software. However, they can be easily opened and converted in Fiji/ImageJ with the Bioformats importer. We recommend alignment of the stack and binning of 2x2 for working with the data.

Synapses have been identified, segmented and quantified in the adult mouse hippocampus with 3D electron microscopy (FIB-SEM). Three animals have been used (ID2, ID4 and ID28). Three layers of the CA1 area have been studied: stratum oriens, stratum radiatum and stratum lacunosum-moleculare. Data obtained include the number of asymmetric and symmetric synapses, their sizes and their spatial distribution.

Two separate files are included in this dataset. They are a compilation of multiple cross-sectional SEM inclusion analyses of the same area, for 2 samples. Both samples are from the same heat, one from the lade metallurgy furnace (LMF) and the other from the tundish. The SEM analysis was carried out at Carnegie Mellon University using a Thermo Fisher / FEI Aspex Explorer, at 10 kV accelerating voltage. The data is filtered to remove non-inclusions (pores and erroneous readings). For each sample, a specified area was marked and analyzed in the SEM. Then the surface was polished to remove several micrometers and reanalyzed again in the SEM. This process was reiterated to obtain multiple serial sections (i.e. 3D inclusion distribution). Five serial sections were analyzed for the LMF sample, and six for the tundish sample. Inclusions' z coordinate was calculated based on the amount of material removed between sections.

O tamanho do mercado de TV 3D sem vidro é categorizado com base em Tipo (TV 3D ativa, TV 3D passiva) e Aplicação (doméstica, comercial) e regiões geográficas (Norte). América, Europa, Ásia-Pacífico, América do Sul e Oriente Médio e África).

O relatório fornecido apresenta o tamanho do mercado e previsões para o valor do mercado de TV 3D sem vidro, medido em milhões de dólares, em todo o mencionado segmentos.

Research data that supports the findings presented in the manuscript "Stochastic 3D modeling of nanostructured NVP/C active material particles for sodium-ion batteries" published in Batteries & Supercaps (https://doi.org/10.1002/batt.202300409).

This includes

1) Experimental image data obtained by focused ion beam scanning electron microscopy (FIB-SEM), high-resolution SEM (HR-SEM), transmission electron microscopy (TEM), and enery-dispersive X-ray spectoscropy (EDX). Imaging is described in Section 2.3.

2) Segmented image data of FIB-SEM stack and HR-SEM images, which build the basis for calibrating the stochastic model in Section 3.2. The segmentation has been performed as described in Section 2.4.

3) Virtual nanostructures generated by the stochastic model in order to study structure-property relationships in Section 4.2.

For this dataset synapses have been identified, segmented and quantified in the deep part of the pyramidal layer, the stratum oriens and the stratum lacunosum-moleculare of the CA1 field of the human hippocampus with 3D electron microscopy (FIB-SEM). 5 human autopsies have been used to achieve a total of 15 valid images stacks (3 stacks per case) per investigated region. Data include the number and density per volume of asymmetric and symmetric synapses, their sizes and their 3D spatial position. The distribution of their post-synaptic targets has also been determined.

This acquisition is part of the CellMap 2024 Segmentation ChallengeChallenge DOI: https://doi.org/10.25378/janelia.c.7456966Challenge Website: https://cellmapchallenge.janelia.org/Sample: Wild-type, interphase HeLa cell.Sample description: Understanding cellular architecture is essential for understanding biology. Electron microscopy (EM) uniquely visualizes cellular structure with nanometer resolution. However, traditional methods, such as thin-section EM or EM tomography, have limitations inasmuch as they only visualize a single slice or a relatively small volume of the cell, respectively. Here, we overcome these limitations by long-term imaging whole cells and tissues via the enhanced Focus Ion Beam Scanning Electron Microscopy (FIB-SEM) platform in high resolution mode with month-long acquisition duration. We use this approach to generate reference 3D image data sets at 4-nm isotropic voxels. Together with subsequent segmentation, we hope to create a reference library to explore comprehensive quantification of whole cells and all their constituents, thus addressing questions related to cell identities, cell morphologies, cell-cell interactions, as well as intracellular organelle organization and structure.HeLa cells, human cervical cancer cells that are the oldest and most commonly used cell line, are easily cultured and widely used in cell biology labs as a basic model to test diverse hypotheses. Having such cells imaged in their entirety can provide a reference to which perturbations in growth, genetic, environment, etc. can be compared. Here we present a typical 3D data set on the example of the entire HeLa cell. The mitochondrial network is clearly identified, as well as 2D cross-sections of standard cellular organelles, such as centrosome, Golgi apparatus, and nuclear envelope. Notably, every example illustrates the advantages of isotropic 3D imaging for cell biology. No single 2D cross-section allows visualizing all centriole sub-distal appendages, however quick segmentation of 3D data set characterizes them easily. Stereotypical 2D images of the Golgi stacks do not reveal the fenestration details and long thin tubular extensions, that can only be seen in 3D. Polyribosomal chains on the nuclear envelope are mostly hidden in 2D cross-sections but easily resolved and detailed in 3D. The unique ability of enhanced FIB-SEM to image whole cells and tissues at 4-nm isotropic voxels over large volumes makes it an ideal tool to map in toto the 3D ultrastructural relationship in living systems.Protocol: High pressure freezing, freeze-substitution resin embedding with 2% OsO4 0.1% UA 3% H2O in acetone; resin embedding in Eponate 12.Contributions: Sample provided by Aubrey Weigel (HHMI/Janelia), prepared for imaging by Gleb Shtengel (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Acquisition ID: jrc_hela-3Final voxel size (nm): 4.0 x 4.0 x 3.24 (X, Y, Z)Dimensions (µm): 50 x 4 x 39 (X, Y, Z)Imaging start date: 2017-08-09Imaging duration (days): 31Landing energy (eV): 1000Imaging current (nA): .25Scanning speed (MHz): .2Dataset URL: s3://janelia-cosem-datasets/jrc_hela-3/jrc_hela-3.zarr/recon-1/em/EM DOI: https://doi.org/10.25378/janelia.13114244Visualization Website: https://openorganelle.janelia.org/datasets/jrc_hela-3Publication: Xu et al., 2021, Heinrich et al., 2021

Image datasets from the publication : LimeSeg: A coarse-grained lipid membrane simulation for 3D image segmentation

• Vesicles.tif: spinning-disc confocal images of giant unilamellar vesicles
• HelaCell-FIBSEM.tif: a 3D Electron Microscopy (EM) dataset of nearly isotropic sections of a Hela cell, acquired with a focused ion beam scanning electron microscope (FIB-SEM). Sections are aligned with TrackEm2 (doi: ), without additional preprocessing.
• DrosophilaEggChamber.tif: point scanning confocal images of a Drosophila egg chamber. Channel 1: cell nuclei stained with DAPI. Channel 2: cell membranes visualized with fused membrane proteins Nrg::GFP and Bsg::GFP.

Image metadata contains extra information including voxel sizes.

We used Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) to perform a 3D analysis of the synapses in the neuropil in layer III of the Brodmann's areas 24 and 38 of the human brain. 3 human brain autopsies cases have been used to achieve a total of 27 FIB/SEM valid images stacks. Specifically, we studied synaptic structural characteristics, which were fully reconstructed in 3D. We analyzed the synaptic density, 3D spatial distribution, and type (excitatory and inhibitory), as well as the shape and size of each synaptic junction. Moreover, their postsynaptic targets were determined. The present work constitutes a detailed description of the synaptic organization of the human cortex, which is a necessary step to better understand the functional organization of the cortex in both health and disease.

Pancreatic islets (or Islets of Langerhans) are micro-organs consisting mainly of beta, alpha, delta, polypeptide cells and endothelial cells. Beta cells are the majority of the islet cells. They secrete insulin, which is stored in secretory granules (SGs), in order to maintain blood glucose homeostasis. Beta cells within the islet are heterogeneous in their response to glucose. Furthermore, not all insulin SGs within beta cells have the same likelihood of being released. Large-scale high-resolution FIB-SEM enables biologists to investigate the ultrastructural differences between beta cells within an islet as well as features that require higher resolution such as ribosomes and the cytoskeleton. Sample: Wild-type mouse pancreatic islets treated with low glucose.Protocol: High-pressure freezing and freeze-substitution with 1% OsO₄ and 0.1% UA in acetone additionally containing 1% H2O for membrane contrast. Samples were immersed in the cocktail for 5 hours at −90 °C followed by raising the temperature to 0 °C over a time course of 18 hours. Then, samples were washed twice in 100% dry acetone for 1 hour and the temperature was raised to room temperature followed by embedding in Durcupan.Contributions: Sample provided by Andreas Mueller and Michele Solimena (Paul Langerhans Institute, Dresden), prepared for imaging by Song Pang (HHMI/Janelia), with imaging and post-processing by C. Shan Xu (HHMI/Janelia).Dataset ID: jrc_mus-pancreas-3Final voxel size (nm): 4.00 x 4.00 x 4.00 (X, Y, Z)Dimensions (µm): 20 x 20 x 8 (X, Y, Z)Acquisition date: 2018-07-07Dataset URL: Visualization Website: https://openorganelle.janelia.org/datasets/jrc_mus-pancreas-3

Volume correlative light and electron microscopy (CLEM) image data of (i) 9 serial sections of rat pancreas tissue and (ii) 63 serial sections of zebrafish pancreas tissue. Datasets were acquired via integrated array tomography, a nanoscale imaging technique for the 3D reconstruction of biological material. See https://doi.org/10.3389/fmolb.2021.822232 for details.

O tamanho do mercado de scanner 3D sem fio é categorizado com base em Tipo (Laser, Luz Estruturada) e Aplicação (Engenharia de Construção, Automotiva, Saúde, Outros) e regiões geográficas ( América do Norte, Europa, Ásia-Pacífico, América do Sul e Oriente Médio e África).

O relatório fornecido apresenta tamanho de mercado e previsões para o valor do mercado de scanners 3D sem fio, medido em milhões de dólares, em todo o segmentos mencionados.