Search
Cell Electron Microscopy
Electron microscopy provides unprecedented, ultra-resolution images of cellular structures that continue to reshape our understanding of cell biology. The impact of electron microscopy on cell biology is broad, ranging from the first identification of the cell’s internal membranes to the observation of mitochondrial, cytoskeletal, and nuclear pore structures. The enhanced structural clarity of electron microscopy deepens our understanding of cellular functions, disease mechanisms, and molecular interactions.
Today, electron microscopes offer access to multi-scale structural data, ranging from molecular-resolution views of proteins and complexes to nanometer-resolution, 3D volumes of whole cells and microorganisms. These advanced imaging capabilities allow researchers to explore cellular architecture in unprecedented detail, providing insights that are crucial for advancing cell biology.
Explore just some of the uses of electron microscopy across different areas of cell biology and find the right technology to drive your research.
Cytoskeleton and centrosomes
The cytoskeleton provides mechanical support, enables cell movement, and facilitates intracellular transport. Centrosomes serve as the main microtubule-organizing centers in animal cells, coordinating the formation of the mitotic spindle during cell division. Together, these structures maintain cellular integrity, ensure accurate chromosome segregation, and support various cellular processes critical for growth and development. Electron microscopy provides the resolution required to visualize cytoskeletal components ranging from 7–25 nm, as well as the internal structures and architecture of centrosomes.
Cryo-ET of centrosome molecular architecture
Cryo-electron tomography (cryo-ET) reveals centrosome molecular architectures across the cell cycle of C. elegans embryonic cells.
Adapted from Figure 1 of Tollervey F, et al. Molecular architectures of centrosomes in C. elegans embryos visualized by cryo-electron tomography. Developmental Cell 60:6 (2025).
TEM micrograph of microtubule organization
Transmission electron microscopy of microtubule organization after treatment with a drug candidate for myeloid malignancies.
Adapted from Figure 4 of Su M, et al. Targeting SRSF2 mutations in leukemia with RKI-1447: A strategy to impair cellular division and nuclear structure. iScience 27:4 (2024).
Nucleus and nuclear structures
The nucleus and its associated structures house and regulate the cell’s genetic material, controlling virtually all aspects of cellular function and identity. From the nuclear envelope and pores to chromatin, the nucleolus, nuclear matrix, and lamina, electron microscopy provides the resolution required to understand the intricate architecture of these cellular components, providing insights into how cells respond to developmental cues, environmental stresses, and disease states.
Cryo-ET of nuclear pore complex and basket
An example of a nuclear pore complex and nuclear basket revealed by cryo-electron tomography.
Adapted from Figure 4 of Singh D, et al. The molecular architecture of the nuclear basket. Cell 187:19 (2024).
TEM micrograph of chromatin fibers in sperm
Organization of chromatin fibers during spermatid development in Gryllus bimaculatus, imaged by transmission electron microscopy.
Adapted from Figure 6 of Orsi GA, et al. Biophysical ordering transitions underlie genome 3D re-organization during cricket spermiogenesis. Nature Communications 14:1 (2023).
Mitochondria
Mitochondria not only generate ATP but also play a critical role in regulating cell growth, signaling, and death. Electron microscopy reveals the fine details of mitochondria, from their outer and inner membranes, to the delicate folds of the cristae, the structure of the intermembrane space, and the components inside the matrix.
3D model of the mitochondrial network in muscle
The mitochondrial network in 365 μm3 of muscle tissue, visualized with volume electron microscopy using a focused ion beam scanning electron microscope (FIB-SEM).
Adapted from Figure 2 of Gineste C, et al. Enzymatically dissociated muscle fibers display rapid dedifferentiation and impaired mitochondrial calcium control. iScience 25:12 (2022).
Cryo-ET of mitochondria morphology
Mitochondrial morphology of S. cerevisiae, obtained with cryo-electron tomography, in respiratory and fermentation conditions.
Adapted from Figure 2 of Singh MK, et al. A constricted mitochondrial morphology formed during respiration. Nature Communications 16:1 (2025).
The endoplasmic reticulum and Golgi apparatus
The endoplasmic reticulum (ER) and Golgi apparatus play central roles in the synthesis, processing, and trafficking of proteins and lipids. The endoplasmic reticulum serves as the entry point for newly synthesized proteins destined for secretion or membrane insertion, while also maintaining lipid homeostasis and calcium storage. Electron microscopy can provide visualization of rough (ribosome-studded) and smooth ER membranes as well as the ER lumen (the location of protein folding and calcium storage). Proteins are then transported to the Golgi apparatus, where they undergo further modification, sorting, and packaging for delivery to their final destinations. Electron microscopy can image the cisternae stacks, vesicles, and provide structural insights on the cis- and trans- faces of the Golgi. Understanding the structure and dynamics of these organelles provides critical insights into how cells maintain internal organization, respond to stress, and regulate processes like secretion, signaling, and immune responses.
Endoplasmic reticulum imaged with SEM
Scanning electron microscopy of a basal neuron, packed with cubic endoplasmic reticulum membranes.
Adapted from Figure 8 of Devakinandan GVS, et al. Single-cell transcriptomics of vomeronasal neuroepithelium reveals a differential endoplasmic reticulum environment amongst neuronal subtypes. eLife 13:RP98250 (2024).
doi: 10.7554/elife.98250
TEM tomography of the Golgi apparatus
3D visualization of the Golgi apparatus, obtained with TEM tomography, revealing organizational differences in wild type and knockout cell lines.
Adapted from Figure 3 of Parchure A, et al. TUG protein acts through a disordered region to organize the early secretory pathway. Nature Communications 16:5518 (2025).
Endosomes, lysosomes, and other vesicles
The vesicular and endomembrane system, which includes endosomes, lysosomes, peroxisomes, and secretory vesicles, governs intracellular trafficking, degradation, and compartmentalized biochemical reactions. These organelles coordinate the uptake, sorting, and recycling of membrane proteins and nutrients, while also managing waste breakdown, oxidative detoxification, and the targeted release of cellular products. Disruption to these pathways is linked to numerous diseases, including lysosomal storage disorders, neurodegeneration, and cancer. Understanding the structure and function of these compartments is essential for unraveling how cells maintain homeostasis, communicate, and adapt to their environment.
Cryo-ET of lysosome interactions
Cryo-electron tomography of membrane contacts between lysosomes and the endoplasmic reticulum.
Adapted from Figure 3 of Cai S, et al. In situ architecture of the lipid transport protein VPS13C at ER–lysosome membrane contacts. Proc Natl Acad Sci USA 119:29 (2022).
SEM of cytoplasmic fragments and lysosomes
Scanning electron micrograph of cytoplasmic chromatin fragments (shown in light red) and their interaction with lysosomes (blue).
Adapted from Figure 5 of Freyter BM, et al. Nuclear Fragility in Radiation-Induced Senescence: Blebs and Tubes Visualized by 3D Electron Microscopy. Cells 11:2 (2022).
Electron microscopy solutions for cell biology research
Electron microscopy provides high-resolution visualization of cellular structures far beyond the limits of light microscopy. Techniques such as transmission and scanning electron microscopy allow researchers to study organelles, membranes, cytoskeletal elements, and macromolecular complexes in fine detail, and can be correlated with data from fluorescence microscopy (CLEM). 3D EM techniques like TEM tomography, FIB-SEM, and serial block-face SEM (SBF-SEM) can explore the spatial organization of cells and cellular structures. Cryo-electron tomography can even capture 3D ultrastructure at molecular resolution, and is especially valuable for visualizing dynamic or transient structures such as membrane contact sites, cytoskeletal arrangements, and large protein complexes in situ. Together, electron microscopy techniques provide multi-scale data for structural insights into fundamental cell biology, disease mechanisms, and genetic models.
Transmission electron microscopy
Transmission electron microscopy (TEM) enables large area imaging of cell and tissue samples, tomography for 3D visualization, and more, all at nanometer resolution.
Cryo-electron tomography
Cryo-electron tomography (Cryo-ET) provides molecular-level 3D imaging within the cellular context provides unique opportunities to understand cell biology at sub-nanometer resolution.
Scanning electron microscopy
Scanning electron microscopy (SEM) can capture cell morphology, topography, and subcellular organization, while also enabling intricate reconstruction in 2D/3D.
Volume electron microscopy
Volume electron microscopy (vEM) provides the opportunity to image in 3D at the nanometer lengthscale to provide detailed volumetric structural insights into cells and tissues.
Header image courtesy of Benjamin Engel, Biozentrum, University of Basel.
For Research Use Only. Not for use in diagnostic procedures.