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The Scanning Electron Microscope (SEM) as 2D imaging instrument has been widely used in biological, mechanical, and materials sciences to determine the surface attributes (e.g., compositions or geometries) of microscopic specimens. A SEM offers an excellent capability to overcome the limitation of human eyes by achieving increased magnification, contrast, and resolution greater than 1 nanometer. However, SEM micrographs still remain two-dimensional (2D). Having truly three-dimensional (3D) shapes from SEM micrographs would provide anatomic surfaces allowing for quantitative measurements and informative visualization of the objects being investigated. In biology, for example, 3D SEM surface reconstructions would enable researchers to investigate surface characteristics and recognize roughness, flatness, and waviness of a biological structure. There are also various applications in material and mechanical engineering in which 3D representations of material properties would allow us to accurately measure a fractal dimension and surface roughness and design a micro article which needs to fit into a tiny appliance. 3D SEM surface reconstruction employs several computational technologies, such as multi-view geometry, computer vision, optimization strategies, and machine learning to tackle the inverse problem going from 2D to 3D. In this contribution, an attempt is made to provide a 3D microscopy dataset along with the underlying algorithms publicly and freely available at http://selibcv.org/3dsem/ for the research community. (2015-12-09)

Acknowledgements

https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/HVBW0Q - Publication - Tafti, A.P., Kirkpatrick, A.B., Holz, J.D., Owen, H.A. and Yu, Z., 2015. 3DSEM: A 3D Microscopy Dataset. Data in Brief. doi: 10.1016/j.dib.2015.11.018

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The Scanning Electron Microscope (SEM) as 2D imaging instrument has been widely used in biology and material sciences to determine the surface attributes of microscopic specimens. However the SEM micrographs still remain 2D images. To effectively measure and visualize the surface properties, we need to restore the shape model from the SEM images. Having 3D surfaces from SEM images would provide true anatomic shape of microscopic objects which allow for quantitative measurements and informative visualization of the system being investigated.The 3D Microscopy Dataset which is provided here includes both 2D images and 3D reconstructed surfaces of several biological material samples. To get the data and know about "Term Of Usage", please visit http://selibcv.org/3dsem/

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.

3D ultrastructure of myelinated and unmyelinated axons in a rat pelvic nerve visualized by serial block-face scanning electron microscopy (SBF-SEM)

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

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.

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 steady growth, projected to reach a value of $1638.9 million in 2025 and maintain a Compound Annual Growth Rate (CAGR) of 4.2% from 2025 to 2033. This growth is fueled by increasing demand across diverse sectors, including semiconductor manufacturing, materials science research, and life sciences. Advancements in FIB-SEM technology, such as improved resolution, faster imaging speeds, and enhanced automation, are key drivers. The ability to perform high-precision 3D imaging and micro-fabrication makes FIB-SEMs indispensable for applications requiring detailed nanoscale analysis. The market is segmented by application (e.g., semiconductor failure analysis, materials characterization, biological sample imaging), and by geographic region, with North America and Europe currently dominating due to strong research infrastructure and a high concentration of leading companies such as Thermo Fisher Scientific, Hitachi High-Technologies Corporation, JEOL Ltd., Carl Zeiss, and Tescan Group. Competition is intense, with companies focusing on innovation and strategic partnerships to expand their market share. Despite the positive outlook, challenges remain. The high cost of FIB-SEM systems is a significant barrier to entry, particularly for smaller research institutions and companies in developing economies. Furthermore, the need for specialized expertise to operate and maintain these complex instruments presents a limitation. However, ongoing technological advancements, alongside the increasing availability of financing options and service contracts, are expected to mitigate these restraints gradually. The market is expected to witness considerable innovation in areas such as automation, higher throughput, and user-friendly software, leading to wider adoption and accessibility. The increasing adoption of advanced analytical techniques combined with the growing need for higher resolution imaging will contribute to the market's expansion.

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

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.

Discover the booming Cryo-FIB-SEM market! This analysis reveals key trends, growth drivers (materials science, life sciences), leading companies (JEOL, Carl Zeiss, Thermo Fisher), and future projections to 2033. Learn how advancements in cryogenic microscopy are shaping this high-resolution imaging sector.

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 diverse sectors. The compound annual growth rate (CAGR) of 4.5% from 2025 to 2033 indicates a significant expansion, fueled primarily by advancements in SEM technology, leading to enhanced resolution, faster imaging speeds, and broader applications. Key drivers include the rising adoption of SEMs in life sciences for detailed cellular and sub-cellular analysis, material sciences for characterizing material properties at the nanoscale, and semiconductor industries for quality control and defect analysis. The increasing prevalence of nanotechnology research and development further fuels market growth. Furthermore, the continuous innovation in FIB-SEM technology, offering 3D imaging capabilities, expands the scope of applications across various research and industrial domains. Competition among leading manufacturers like Thermo Fisher Scientific, Hitachi High-Technologies Corporation, and Jeol Ltd. drives technological advancements and market expansion. Segmentation by application (Life Sciences, Material Sciences) and type (W-SEM, FEG-SEM, FIB-SEM) highlights distinct growth trajectories, with the FIB-SEM segment expected to witness faster expansion owing to its superior capabilities. Regional variations in market growth are anticipated, with North America and Asia Pacific (particularly China) expected to dominate the market due to high research spending and technological adoption. However, challenges such as high initial investment costs and the need for skilled personnel could potentially restrain market growth to some extent. The forecast period from 2025 to 2033 anticipates substantial market expansion based on the projected CAGR and ongoing technological developments. Continued miniaturization and improved sensitivity of SEMs are anticipated to further broaden their applications in fields like medical diagnostics, environmental monitoring, and forensic science. The integration of advanced analytical techniques with SEMs, such as energy-dispersive X-ray spectroscopy (EDS), will also contribute to market growth. Despite potential challenges, the overall market outlook for SEMs remains highly positive, driven by the intrinsic value of detailed nanoscale imaging across numerous scientific and industrial applications. Growth is expected across all regions, with particular strength in established markets and emerging economies showing increasing investment in research and development.

Raw Scanning electron micoroscope (SEM) Images for publication Sikora P., Skibicki S., Chougan M., Szewczyk P., Cendrowski K., Federowicz K., El-Khayatt A.M., Saudi H.A., Strzałkowski J., Abd Elrahman M., Techman M., Sibera D., Chung S.Y. Silica-coated admixtures of bismuth and gadolinium oxides for 3D printed concrete applications: Rheology, hydration, strength, microstructure, and radiation shielding perspective. Construction and Building Materials (2025) 470, 140563, https://doi.org/10.1016/j.conbuildmat.2025.140563

Synapses have been identified, segmented and quantified in the CA1 field of the human hippocampus with 3D electron microscopy (FIB-SEM). Superficial pyramidal layer and stratum radiatum have been studied. 3 cases have been used (AB1, AB2, AB3) to achieve a total of 18 valid images stacks. Data include the number of asymmetric and symmetric synapses, their sizes and their spatial distribution.

Synapses have been identified, segmented and quantified in the human neocortex (trans entorhinal cortex, TEC) with 3D electron microscopy (FIB-SEM). Layer II of the TEC has been studied. 5 cases have been used (AB1, AB2, IF10, M16 and M17) to achieve a total of 15 valid images stacks. Data obtained include the number of asymmetric and symmetric synapses, their sizes and their spatial distribution. The distribution of their post-synaptic targets has also been determined.

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.

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.

In this project I work on developing ways to use a FIB-SEM to create a 3D model of biological samples. The method can be used in several projects with Grøn Dyst angles and I here report on my work on imaging malaria infected blood cells which is essential for a deeper understanding of how the parasite might be targeted by medicine, and algae samples that are essential for ecotoxicologial studies and later will be used for algae species used in biomass and biofuel production.