As told by Shanklin, 2016, 2D SEM images can be turned into 3D object models. “3D surface modeling that can be created using scanning electron microscope absolutely lead to significant understanding of attributes of microscopic surfaces, such as fracture toughness, crack growth and propagation or fracture resistance” (Shanklin, 2016). I considered SEM images, turned them into .ppm format. The .ppm file has been read by a Fortran program to create the 3D mesh, by means of vertices and faces, saved in .obj file format (see please the folder in the dataset). Here I show some cases: Honeycomb, Pores of freeze-dried solutions, Microcellular plastic, Biochar, Wood pores, 'Hexagon' detail of Corbaea scandens, Pollen, Worms, that is a pair of Schistosoma mansoni, and a 'Bassorilievo' and a rendering of Turin Shroud, to show that is it possible to obtain a 3D mesh from pictures. Details and references are given in the .pdf file. Visualizations of .obj files have been obtained by means of https://3dviewer.net/ and GIMP software.

Focused ion beam (FIB) tomography is a destructive technique used to collect three-dimensional (3D) structural information at a resolution of a few nanometers. For FIB tomography, a material sample is degraded by layer-wise milling. After each layer, the current surface is imaged by a scanning electron microscope (SEM), providing a consecutive series of cross-sections of the three-dimensional material sample. Especially for nanoporous materials, the reconstruction of the 3D microstructure of the material, from the information collected during FIB tomography, is impaired by the so-called shine-through effect. This effect prevents a unique mapping between voxel intensity values and material phase (e.g., solid or void). It often substantially reduces the accuracy of conventional methods for image segmentation. Here we demonstrate how machine learning can be used to tackle this problem. A bottleneck in doing so is the availability of sufficient training data. To overcome this problem, we present a novel approach to generate synthetic training data in the form of FIB-SEM images generated by Monte Carlo simulations. Based on this approach, we compare the performance of different machine learning architectures for segmenting FIB tomography data of nanoporous materials. We demonstrate that two-dimensional (2D) convolutional neural network (CNN) architectures processing a group of adjacent slices as input data as well as 3D CNN perform best and can enhance the segmentation performance significantly.

The Cryo-Focused Ion Beam Scanning Electron Microscope (Cryo-FIB-SEM) market is experiencing robust growth, driven by advancements in cryo-electron microscopy (cryo-EM) and the increasing need for high-resolution 3D imaging in diverse scientific fields. The market, estimated at $250 million in 2025, is projected to exhibit a Compound Annual Growth Rate (CAGR) of 15% from 2025 to 2033, reaching approximately $800 million by 2033. This expansion is fueled by the capabilities of Cryo-FIB-SEM to visualize and analyze intricate cellular structures and macromolecular complexes at unprecedented detail, particularly crucial in structural biology, materials science, and nanotechnology. Key drivers include the rising demand for advanced imaging techniques in drug discovery, the growing adoption of cryo-EM in academic research, and the continuous technological improvements in instrument sensitivity and automation. Leading players like JEOL, Carl Zeiss, and Thermo Fisher Scientific are at the forefront of innovation, driving market competition and pushing the boundaries of resolution and imaging speed. However, the market faces certain restraints. The high cost of Cryo-FIB-SEM systems limits accessibility, primarily for smaller research institutions and laboratories. Furthermore, the specialized expertise required for operation and data analysis presents a barrier to entry. Nevertheless, the increasing availability of grants and funding for advanced research, along with the development of user-friendly software and streamlined workflows, is gradually mitigating these challenges. Market segmentation reveals a strong presence in North America and Europe, reflecting the concentration of leading research institutions and high technological adoption rates in these regions. The ongoing development of correlative microscopy techniques, integrating Cryo-FIB-SEM with other imaging modalities, promises to further enhance its applications and market potential, accelerating growth in the coming years.

The dataset consists of scanning electron microscope (SEM) images of 3D-imprinted microneedles from fabricated conductive, UV-cured hydrogels composites Financing: Miniatura 7, DEC-2023/07/X/ST5/01377.

A single Nickel nanowire has been characterised using 3 experimental techniques.Scanning electron microscope (SEM) data folder contains a single .TIFF image of a fallen Nickel nanowire, where the title refers to the name of the sample.Atomic and magnetic force micrscope (AFM and MFM) data folder contains raw output data where titles refer to the name of the sample (181017JA) and the magnetic field applied (eg 0mT), from software Nanoscope 5, these can be opened in any AFM processing software such as Gwyddion or WSxM. Each file contains data regarding the height (corresponding to AFM) and the phase (corresponding to the MFM).Simulation data folder contains .VTS files where the titles correspond to the appropriate field applied to the simulated wire. The file type .VTS can be opened and viewed within a 3D visualisation program such as Paraview. Research results based upon these data are published at https://doi.org/10.3390/nano10030429

We used Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) to perform a 3D analysis of the synapses in the layer III neuropils of the Brodmann areas 3b (somatosensory), 4 (motor), and 17 (visual primary) from human brain samples. 3 human brain autopsies cases have been used to achieve a total of 22 FIB/SEM valid image stacks: 4 stacks in BA17 from a single case (AB7); 9 stacks in BA3b (three stacks per case, AB2, AB3, and AB7); and 9 stacks in BA4 (three stacks per case, AB2, AB3, and AB7). Specifically, we studied synaptic junctions, 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 dataset constitutes a detailed description of the synaptic characteristics of the human cortex, which is a necessary step to better understand the organization of the cortex.

The Focused Ion Beam-Scanning Electron Microscope (FIB-SEM) market is experiencing robust growth, driven by advancements in nanotechnology, materials science, and semiconductor research. The increasing demand for high-resolution imaging and precise material manipulation at the nanoscale is fueling market expansion across diverse sectors, including academia, research institutions, and the semiconductor industry. Applications range from failure analysis in electronics to advanced materials characterization and 3D reconstruction of biological samples. Considering a conservative estimate based on typical growth in specialized scientific equipment markets, let's assume a 2025 market size of $500 million with a Compound Annual Growth Rate (CAGR) of 7% projected through 2033. This CAGR reflects both the ongoing technological advancements within FIB-SEM technology and the consistent expansion of its applications in various fields. The market segmentation indicates strong demand across both double-beam and multibeam systems, with university and research institutions representing significant customer bases. Leading manufacturers such as Hitachi, Thermo Fisher, JEOL, Zeiss, and Raith GmbH are competing in this dynamic market through continuous innovation and strategic partnerships. The continued development of sophisticated software for data analysis and 3D reconstruction will be a key factor driving future growth. Furthermore, the increasing need for advanced characterization techniques in fields like life sciences and energy research will contribute significantly to market expansion. However, high capital costs associated with FIB-SEM systems and the requirement for specialized expertise in operation and maintenance could potentially restrain market growth, particularly in smaller research labs or developing regions. Nevertheless, the advantages provided by FIB-SEM technology in terms of precision, resolution, and analytical capabilities are expected to outweigh these challenges, ensuring continued market growth throughout the forecast period. The Asia-Pacific region, with its burgeoning technological advancements and growing research investments, is expected to witness significant growth in the coming years.

Different methods for three-dimensional visualization of biological structures have been developed and extensively applied by different research groups. In the field of electron microscopy, a new technique that has emerged is the use of a focused ion beam and scanning electron microscopy for 3D reconstruction at nanoscale resolution. The higher extent of volume that can be reconstructed with this instrument represent one of the main benefits of this technique, which can provide statistically relevant 3D morphometrical data. As the life cycle of Plasmodium species is a process that involves several structurally complex developmental stages that are responsible for a series of modifications in the erythrocyte surface and cytoplasm, a high number of features within the parasites and the host cells has to be sampled for the correct interpretation of their 3D organization. Here, we used FIB-SEM to visualize the 3D architecture of multiple erythrocytes infected with Plasmodium chabaudi and analyzed their morphometrical parameters in a 3D space. We analyzed and quantified alterations on the host cells, such as the variety of shapes and sizes of their membrane profiles and parasite internal structures such as a polymorphic organization of hemoglobin-filled tubules. The results show the complex 3D organization of Plasmodium and infected erythrocyte, and demonstrate the contribution of FIB-SEM for the obtainment of statistical data for an accurate interpretation of complex biological structures.

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

The entorhinal cortex (EC) is a brain region located on the anterior part of the medial temporal lobe which has been shown to be essential for memory functions and spatial navigation. Mapping the EC connectivity may contribute to the understanding of its structural design. One possible approach to decipher EC connectivity is its analysis at the ultrastructural level, using electron microscopy, to map synaptic contacts (synapses). Thus, a detailed ultrastructural analysis to map true synaptic contacts (or synapses) using 3D electron microscopy could contribute to a better understanding of the human cerebral cortex organization. We used Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) to perform a 3D analysis of the synapses in the neuropil in layers 1, 2 (subdivisions 2-is and 2-ni) and 3 of the medial Entorhinal Cortex (MEC). 3 human brain autopsies cases (AB2, AB7, and M16) have been used to obtain a total of 36 FIB/SEM valid image stacks. Specifically, we studied synaptic junctions, 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. Present data are intended to complete a detailed description of the synaptic organization of the human medial Entorhinal Cortex to better understand its functional organization.

The global Scanning Electron Microscope (SEM) market, valued at $3.718 billion in 2025, is projected to experience robust growth, driven by increasing demand across life sciences, materials science, and nanotechnology research. The compound annual growth rate (CAGR) of 4.5% from 2025 to 2033 indicates a steady expansion, fueled by advancements in SEM technology, such as improved resolution, faster imaging speeds, and enhanced analytical capabilities. The life sciences sector, particularly in drug discovery and development, is a significant driver, leveraging SEM for high-resolution imaging of biological samples. Materials science applications, including semiconductor analysis and material characterization, also contribute substantially to market growth. The increasing adoption of FIB-SEM (Focused Ion Beam Scanning Electron Microscope) systems, offering superior 3D imaging and micro-machining capabilities, further propels market expansion. While competitive pricing pressures and the high initial investment cost of SEMs can pose challenges, the overall market outlook remains positive, driven by continued technological innovation and growing research funding across various sectors. The market segmentation reveals a strong presence of established players such as Thermo Fisher Scientific, Hitachi High-Technologies Corporation, and JEOL Ltd., indicating a competitive landscape. However, emerging companies are also contributing with innovative solutions and niche applications. Regional market analysis suggests a strong concentration in North America and Europe, reflecting advanced research infrastructure and high adoption rates. However, the Asia-Pacific region is expected to demonstrate considerable growth potential due to rising investments in research and development and the increasing manufacturing activity in emerging economies such as China and India. The continued integration of SEMs with other analytical techniques and the development of user-friendly software solutions will further enhance the accessibility and application of this crucial technology across diverse research fields.

The global Focused Ion Beam Scanning Electron Microscope (FIB-SEM) system market is experiencing robust growth, projected to reach $578.3 million in 2025 and maintain a Compound Annual Growth Rate (CAGR) of 5.5% from 2025 to 2033. This expansion is driven by several key factors. Advancements in semiconductor technology necessitate higher resolution imaging and precise material modification at the nanoscale, fueling demand for FIB-SEM systems in research and development. The increasing adoption of FIB-SEM in life sciences, particularly for 3D cellular imaging and analysis, further contributes to market growth. Material science applications, such as failure analysis and characterization of new materials, also represent a significant market segment. The market is segmented by ion source type (Ga Ion Source and Non-Ga Ion Source) and application (Material Science, Life Sciences, and Semiconductor). Leading players like Thermo Fisher Scientific, Hitachi, Zeiss, JEOL Ltd, Tescan Group, and Raith are driving innovation and competition within this dynamic market. Geographical distribution reveals a strong presence across North America, Europe, and Asia Pacific, reflecting the concentration of research institutions and advanced manufacturing facilities in these regions. Growth in emerging markets, such as those in Asia Pacific and the Middle East & Africa, is anticipated to be significant in the coming years, driven by increasing investment in scientific research and technological advancement. While the market faces some restraints, such as the high cost of FIB-SEM systems and the need for specialized expertise for operation and maintenance, the overall growth trajectory remains positive, propelled by continuous technological innovations and the expanding applications of FIB-SEM across various scientific disciplines. The market is expected to see significant growth across all segments with the semiconductor industry and life sciences expected to be the most prominent growth drivers in the coming years.

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; }

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.

Human Cytomegalovirus (HCMV) can infect a variety of cell types by using virions of varying glycoprotein compositions. It is still unclear how this diversity is generated, but spatio-temporally separated envelopment and egress pathways might play a role. So far, one egress pathway has been described in which HCMV particles are individually enveloped into small vesicles and are subsequently exocytosed continuously. However, some studies have also found enveloped virus particles inside multivesicular structures but could not link them to productive egress or degradation pathways.We used a novel 3D-CLEM workflow allowing us to investigate these structures in HCMV morphogenesis and egress at high spatio-temporal resolution. We found that multiple envelopment events occurred at individual vesicles leading to multiviral bodies (MViBs), which subsequently traversed the cytoplasm to release virions as intermittent bulk pulses at the plasma membrane to form extracellular virus accumulations (EVA...

In Global 3D Analytical FIB-SEM market Hitachi High-Tech Corporation has introduced the 3D SEM1 CT1000, which is necessary for defect monitoring in the semiconductor sector.

We have processed brain material from transgenic mice expressing the enhanced green fluorescent protein (EGFP) coupled with the synaptic protein PSD95 (EGFP95) in order to accomplish the automated counting process using 3D connected components of fluorescent puncta in stacks of confocal microscope images for the CA1 region of the hippocampal formation. Adjacent brain sections have been processed with 3D electron microscopy using FIB/SEM in order to cross-validate and interpret confocal data with ultrastructural data on the number and size of PSD puncta in different brain regions. Furthermore, we have developed a PSDs volume segmentation and quantification algorithm designed to be executed in a supercomputer in order to obtain results in multiple brain regions in a short time.

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 Giardia 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 in situ 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 Giardia 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.

Data set 03 comprises an image 3D model of a Giardia lamblia 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).

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