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.

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.

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; }

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

Here we provide a Fortran file to create a 3D mesh (.obj file format) from a 2D grey-scale image, for instance, a SEM (Scanning Electron Microscope) image. The zipped folder contains some examples of 3D reconstructions, as .obj files, that can be visualized on-line by means of https://3dviewer.net/ .

A set of serial-section electron backscatter diffraction (EBSD) data files and a 3D reconstruction of a model Zircaloy-4 with 7 wt.% Nb addition alloy following hot-rolling.

The 3D data set contains measurements of the material rolled at 725C to 75% reduction. The measurements include indexing of both the alpha and the beta phases in 441 sequential slices, each of 0.1 μm, through a small section of the material, taken using the dual beam Thermo Scientific Helios Xe+ plasma focused ion-beam scanning electron microscope (PFIB-SEM). The 3D EBSD data set includes EBSD measurements in the form of ctf files, binary data files, an Aztec project file, and accompanying images for each slice.

A 3D volume was reconstructed from the 3D EBSD data set using a customised pipeline within the DREAM.3D software. The results of this analysis are included in the 'dream3d' folder, which includes a description of the pipeline, the final fully reconstructed dream3d data file, an xdmf file used for visualising the data in ParaView, a h5ebsd file containing results for the reconstruction, and grain averaged data for each of the identified features.

Please see our accompanying paper for analysis of the 3D reconstruction - as well as analysis of the 2D measurements from 10.5281/zenodo.3784460 - and for interpretation of the coupled crystallographic texture evolution;

C.S. Daniel, A. Garner, P.D. Honniball, L. Bradley, M. Preuss, P.B. Prangnell, J. Quinta da Fonseca, Co-deformation and dynamic annealing effects on the texture development during alpha–beta processing of a model Zr-Nb alloy, Acta Materialia 205 (2021) 116538. 10.1016/j.actamat.2020.116538

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.

Synapses have been identified, segmented and quantified in the adult mouse somatosensory cortex with 3D electron microscopy (FIB-SEM). Three animals have been used (ID5, ID24 and ID25). The six layers of the somatosensory cortex have been studied. Data obtained include the number of asymmetric and symmetric synapses, their sizes and their spatial distribution.

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 (EVAs). Our data support the existence of a novel bona fide HCMV egress pathway, which opens the gate to evaluate divergent egress pathways in generating virion diversity.

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.

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.

Microsporidia are obligate intracellular pathogens that infect a wide range of invertebrate and vertebrate hosts, including humans. In humans, microsporidia most often infect the gastrointestinal tract and cause diarrheal diseases, but in immunocompromised patients, infections can be fatal. Previous knowledge of microsporidian intracellular development was based on 2D transmission electron microscopy images and light microscopy. This study used serial block-face scanning electron microscopy (SBF-SEM) to capture 3D snapshots of the human-infecting species, Encephalitozoon intestinalis, within host cells. The dataset includes SBF-SEM, live-cell imaging, and light microscopy data. SBF-SEM analysis shows changes in mitochondrial morphology in infected cells, and live-cell imaging provides insights into mitochondrial dynamics during infection.

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

HIV-1-containing internal compartments are readily detected in images of thin sections from infected cells using conventional transmission electron microscopy, but the origin, connectivity, and 3D distribution of these compartments has remained controversial. Here, we report the 3D distribution of viruses in HIV-1-infected primary human macrophages using cryo-electron tomography and ion-abrasion scanning electron microscopy (IA-SEM), a recently developed approach for nanoscale 3D imaging of whole cells. Using IA-SEM, we show the presence of an extensive network of HIV-1-containing tubular compartments in infected macrophages, with diameters of ∼150–200 nm, and lengths of up to ∼5 µm that extend to the cell surface from vesicular compartments that contain assembling HIV-1 virions. These types of surface-connected tubular compartments are not observed in T cells infected with the 29/31 KE Gag-matrix mutant where the virus is targeted to multi-vesicular bodies and released into the extracellular medium. IA-SEM imaging also allows visualization of large sheet-like structures that extend outward from the surfaces of macrophages, which may bend and fold back to allow continual creation of viral compartments and virion-lined channels. This potential mechanism for efficient virus trafficking between the cell surface and interior may represent a subversion of pre-existing vesicular machinery for antigen capture, processing, sequestration, and presentation.

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.

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

Sample: Double-innervated Meissner corpuscle from the forepaw of a 3-week-old C57BL/6J WT mouseSample Description: Across mammalian skin, structurally complex and diverse mechanosensory end organs respond to mechanical stimuli and enable our perception of dynamic, light touch. How forces act on morphologically dissimilar mechanosensory end organs of the skin to gate the requisite mechanotransduction channel Piezo2 and excite mechanosensory neurons is not understood. Here, we report high-resolution reconstructions of the hair follicle lanceolate complex, Meissner corpuscle, and Pacinian corpuscle and the subcellular distribution of Piezo2 within them. Across all three end organs, Piezo2 is restricted to the sensory axon membrane, including axon protrusions that extend from the axon body. These protrusions, which are numerous and elaborate extensively within the end organs, tether the axon to resident non-neuronal cells via adherens junctions. These findings support a unified model for dynamic touch in which mechanical stimuli stretch hundreds to thousands of axon protrusions across an end organ, opening proximal, axonal Piezo2 channels and exciting the neuron.This dataset contains manually proofread automatic segmentation of the FIB-SEM dataset in jrc_mus-meissner-corpuscle-2.Protocol: Samples were dissected and drop fixed in glutaraldehyde and paraformaldehyde, and then osmicated with osmium tetroxide and potassium ferrocyanide, followed by osmium tetroxide only. Samples were subsequently stained with uranyl acetate and samarium chloride. Samples were dehydrated with an ethanol series followed by anhydrous acetone, infiltrated with Durcupan resin, and cured at 60°C.Contributions: Sample provided by Annie Handler (Harvard Medical School/HHMI) and Qiyu Zhang (Harvard Medical School/HHMI), prepared for imaging by Song Pang (HHMI/Janelia, currently at Yale School of Medicine), imaged by Song Pang and C. Shan Xu (HHMI/Janelia, currently at Yale School of Medicine), post data registration by C. Shan Xu, global image alignment and processing by Annie Handler and Qiyu Zhang, automatic segmentation by Tri M. Nguyen (Harvard Medical School) under the supervision of Wei-Chung Allen Lee (Harvard Medical School), ground truth annotation by Rebecca Plumb, Brianna Sanchez, Karyl Ashjian, Aria Shotland, Bartianna Brown, Madiha Kabeer, Nusrat Africawala, Stuart Cattel, Annie Handler, and Qiyu Zhang (all Harvard Medical School/HHMI), and segmentation proofreading by Annie Handler, Qiyu Zhang, and Michael Nolan-Tamariz (Harvard Medical School/HHMI).Acquisition ID: jrc_mus-meissner-corpuscle-2Voxel size (nm): 6 x 6 x 6 (x, y, z)Data dimensions (µm): 74.1 x 55.1 x 69.6 (x, y, z)Scanning speed (MHz): 1Dataset URL (Redirect): https://data.janelia.org/gTkdEEM DOI: https://doi.org/10.25378/janelia.23969106Visualization Website: https://openorganelle.janelia.org/datasets/jrc_mus-meissner-corpuscle-2Publication: Handler et al., 2023

Sample: Pacinian corpuscle from the fibular periosteum membrane of a 16-week-old mixed background Plp1-EGFP mouseSample Description: Across mammalian skin, structurally complex and diverse mechanosensory end organs respond to mechanical stimuli and enable our perception of dynamic, light touch. How forces act on morphologically dissimilar mechanosensory end organs of the skin to gate the requisite mechanotransduction channel Piezo2 and excite mechanosensory neurons is not understood. Here, we report high-resolution reconstructions of the hair follicle lanceolate complex, Meissner corpuscle, and Pacinian corpuscle and the subcellular distribution of Piezo2 within them. Across all three end organs, Piezo2 is restricted to the sensory axon membrane, including axon protrusions that extend from the axon body. These protrusions, which are numerous and elaborate extensively within the end organs, tether the axon to resident non-neuronal cells via adherens junctions. These findings support a unified model for dynamic touch in which mechanical stimuli stretch hundreds to thousands of axon protrusions across an end organ, opening proximal, axonal Piezo2 channels and exciting the neuron.This dataset contains the FIB-SEM data of a Pacinian corpuscle from the fibular periosteum membrane of a 16-week-old mixed background mouse.Protocol: Samples were dissected and drop fixed in glutaraldehyde and paraformaldehyde, and then osmicated with osmium tetroxide and potassium ferrocyanide, followed by osmium tetroxide only. Samples were subsequently stained with uranyl acetate and samarium chloride. Samples were dehydrated with an ethanol series followed by anhydrous acetone, infiltrated with Durcupan resin, and cured at 60°C.Contributions: Sample provided by Annie Handler (Harvard Medical School/HHMI) and Qiyu Zhang (Harvard Medical School/HHMI), prepared for imaging by Song Pang (HHMI/Janelia, currently at Yale School of Medicine), imaged by Song Pang and C. Shan Xu (HHMI/Janelia, currently at Yale School of Medicine), post data registration by C. Shan Xu, global image alignment and processing by Annie Handler and Qiyu Zhang, automatic segmentation by Tri M. Nguyen (Harvard Medical School) under the supervision of Wei-Chung Allen Lee (Harvard Medical School), ground truth annotation by Rebecca Plumb, Brianna Sanchez, Karyl Ashjian, Aria Shotland, Bartianna Brown, Madiha Kabeer, Nusrat Africawala, Stuart Cattel, Annie Handler, and Qiyu Zhang (all Harvard Medical School/HHMI), and segmentation proofreading by Annie Handler, Qiyu Zhang, and Michael Nolan-Tamariz (Harvard Medical School/HHMI).Acquisition ID: jrc_mus-pacinian-corpuscleVoxel size (nm): 6 x 6 x 6 (x, y, z)Data dimensions (µm): 58.0 x 62.5 x 291.1 (x, y, z)Scanning speed (MHz): 3,2,1Dataset URL (Redirect): https://data.janelia.org/zzlhQVisualization Website: https://openorganelle.janelia.org/datasets/jrc_mus-pacinian-corpusclePublication: Handler et al., 2023