Understanding the Brain Through Electron Microscopy

The human brain is one of the most complex and fascinating organs in the human body and governs a wide range of functions, from controlling our movements and senses to shaping our thoughts and emotions. As a result, comprehending the brain’s intricate workings has captivated scientists and researchers for centuries. One of the key tools utilized in this pursuit is electron microscopy.

Understanding the Brain Through Electron Microscopy

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What is Electron Microscopy?

Electron microscopy is a technique that uses beams of electrons to create high-resolution images of biological samples at the nanoscale. Unlike traditional light microscopy, which uses visible light to view samples, the electrons used in electron microscopy have much shorter wavelengths than visible light, allowing for much higher magnification and resolution.

There are different types of electron microscopy techniques that have been used to study the brain, including transmission electron microscopy (TEM) and scanning electron microscopy (SEM).

TEM uses beams of electrons to pass through a thin section of tissue, allowing for detailed imaging of cellular and subcellular structures such as synaptic connections, neuronal morphology and organelles with neurons.

SEM uses a beam of electrons to scan the surface of a sample, providing a 3D image of the structure. Therefore, it can be used to study the surface features of neurons and glia, such as dendritic spines and astrocytic processes.

Both of these techniques have their advantages and disadvantages when studying the brain. TEM requires complex sample preparation and imaging in a high vacuum environment, which may not be suitable for all types of brain samples and may introduce artifacts or alter the native state of the tissue.

SEM has a lower resolution than TEM, thus not providing the same level of internal structure information. Both techniques are time-consuming and require specialist expertise, so the choice depends on the specific research questions, sample types and image requirements of the brain study.

Applications of Electron Microscopy in Neuroscience Research

Electron microscopy has been used extensively to study the brain and its components and has significantly advanced our understanding of the most important organ in the human body.

It has allowed researchers to visualize detailed ultrastructural features at the cellular and subcellular levels, revealing the intricate morphology of neurons, the organization of synapses and the distribution of neurotransmitter receptors.

It has facilitated the study of neurodevelopment, neural circuitry and synaptic plasticity, providing insights into the fundamental principles of brain function and contributing to our understanding of various neurological disorders.

One of the major breakthroughs in neuroscience was the discovery of the synapse in the mid-20th century.

Electron microscopy allowed researchers to visualize the ultrastructure of brain tissue at nanoscale resolution, revealing the tiny gaps between nerve cells where synaptic connections occur. This confirmed that synapses are the points of communication between neurons, where neurotransmitters are released and received.

This discovery provided the foundation for our understanding of neural networks and brain function.

Electron microscopy has been used to provide information about the functional properties of neurons and neural circuits by capturing images of synaptic activity. By using techniques such as freeze-fracture replication, researchers can obtain images of the molecular changes that occur during synaptic transmission, providing insights into the mechanisms of underlying neural communication.

Advancements in Electron Microscopy

Recent technological advancements in electron microscopy, such as correlative light-electron microscopy (CLEM) and serial block-face electron microscopy (SBEM), have improved our ability to study the brain at high resolution and in 3D, leading to new insights into brain structure and function.

CLEM is a technique that combines light and electron microscopy to provide high-resolution information about the same sample.

It has allowed researchers to obtain a larger volume of 3D data on cellular and subcellular ultrastructure’s and deepened our understanding of how the brain changes during development.

A 2015 study highlighted the importance of SBEM in the process of circuit reconstruction in neuroscience. Mapping the connections between neurons in the brain is crucial for understanding how the brain works but is challenging due to the complexity of the brain’s microcircuits.

SBEM can provide the necessary resolution and field of view to reconstruct these circuits, as it allows scientists to create a 3D image of a sample by imaging the block face after each section is removed by a microtome.


Like all powerful scientific techniques, electron microscopy has some challenges and limitations. One of the biggest challenges is sample preparation which can be time-consuming and labor-intensive.

The samples must be fixed, dehydrated, and embedded in resin before imaging, which can affect the quality of the image.

Another challenge is data analysis, as the large datasets generated by electron microscopy require specialized tools and expertise for analysis.

There are ongoing efforts to improve sample preparation and data analysis to address these challenges. New sample preparation techniques and tools and software are being developed to help researchers reduce time and effort, leading to more efficient data set analysis.

Future Directions

There are exciting future directions for electron microscopy-based neuroscience research. One potential direction is the development of new imaging techniques that can provide an even higher resolution and a larger field of view.

For example, there are efforts to develop new microscopy techniques that use X-rays or other forms of radiation to image the brain at the atomic level.

In conclusion, electron microscopy is a powerful tool for studying the brain, providing insights into its structural, molecular, and functional aspects. Despite the challenges and limitations in sample preparation and data analysis, current endeavors to resolve these problems are opening up exciting opportunities for new findings in neuroscience research.

Ultimately, the continued development and improvement of electron microscopy-based techniques will be essential for unraveling the complex mysteries of the brain and opening up new avenues for treating and preventing neurological disorders.

References and Further Reading

Hayashi, S., Ohno, N., Knott, G. and Molnár, Z. (2023). Correlative light and volume electron microscopy to study brain development. Microscopy (Oxford, England), p. dfad002. https://academic.oup.com/jmicro/advance-article/doi/10.1093/jmicro/dfad002/6976169

WANNER, A.A., KIRSCHMANN, M.A. and GENOUD, C. (2015). Challenges of microtome-based serial block-face scanning electron microscopy in neuroscience. Journal of Microscopy, 259(2), pp. 137–142. https://onlinelibrary.wiley.com/doi/10.1111/jmi.12244

Zheng, Z., Lauritzen, J.S., Perlman, E., Robinson, C.G., Nichols, M., Milkie, D., Torrens, O., Price, J., Fisher, C.B., Sharifi, N., Calle-Schuler, S.A., Kmecova, L., Ali, I.J., Karsh, B., Trautman, E.T., Bogovic, J.A., Hanslovsky, P., Jefferis, G.S.X.E., Kazhdan, M. and Khairy, K. (2018). A Complete Electron Microscopy Volume of the Brain of Adult Drosophila melanogaster. Cell, 174(3), pp. 730-743.e22. https://www.sciencedirect.com/science/article/pii/S0092867418307876

Last Updated: Jun 7, 2023

Jenna Philpott

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Jenna Philpott

Jenna graduated from Nottingham Trent University in 2022 with a BSc in Biochemistry. She achieved a first in her undergraduate research project which concerned the role of metabolic stress on pancreatic beta cell function, investigating its contribution to the development of type 2-diabetes mellitus (T2DM). The study highlighted the importance of understanding molecular pathways in beta cells for developing prevention measures and new therapeutic options for T2DM.  


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