Automated Serial Electron Microscopy

Automated Serial Electron Microscopy: Revolutionizing High-Throughput Imaging

Electron microscopy has long been a cornerstone in scientific research, enabling scientists to explore the intricate details of biological and material structures at the nanoscale. Traditional electron microscopy techniques, while powerful, have limitations in terms of throughput and efficiency. In recent years, a groundbreaking advancement has emerged—Automated Serial Electron Microscopy (ASEM). This cutting-edge technology promises to revolutionize the field by providing high-throughput, high-resolution imaging with unprecedented efficiency. In this article by Academic Block, we will delve into the principles, applications, and future prospects of ASEM, exploring how it is reshaping the landscape of microscopy.

I. Basics of Electron Microscopy

Before delving into Automated Serial Electron Microscopy, it is crucial to understand the basics of conventional electron microscopy. Electron microscopes utilize electron beams instead of light to achieve resolutions far beyond the capabilities of optical microscopes. The two primary types of electron microscopes are Transmission Electron Microscopes (TEM) and Scanning Electron Microscopes (SEM).

  1. Transmission Electron Microscopy (TEM)

TEMs operate by transmitting electrons through the specimen, providing detailed internal images of thin sections. Electromagnetic lenses focus the transmitted electrons onto a detector, generating high-resolution images. TEMs are particularly useful for studying internal cellular structures, nanoparticles, and biological tissues at the nanoscale.

  1. Scanning Electron Microscopy (SEM)

SEM, on the other hand, scans the surface of specimens with a focused electron beam. This process generates a three-dimensional topographical image of the specimen’s surface, offering valuable insights into the morphology and structure of materials. SEM is widely applied in various scientific disciplines, including materials science, biology, and geology.

II. The Limitations of Conventional Electron Microscopy

While traditional electron microscopy techniques provide unparalleled resolution, they are not without limitations. Two significant challenges are throughput and sample preservation.

  1. Throughput

TEM and SEM techniques often involve manual sample preparation, limiting the number of specimens that can be processed within a given timeframe. This constraint hampers large-scale studies and high-throughput imaging, hindering the efficiency of electron microscopy in certain applications.

  1. Sample Preservation

Sample preservation is another critical concern, especially when studying delicate biological specimens. The harsh vacuum conditions and electron beam radiation can lead to sample damage, artifacts, and alterations in structure. Preserving the native state of biological samples during imaging is a formidable challenge in electron microscopy.

III. Enter Automated Serial Electron Microscopy (ASEM)

Automated Serial Electron Microscopy addresses the limitations of traditional electron microscopy methods by introducing automation and serial imaging capabilities. ASEM combines the advantages of TEM and SEM while offering unprecedented throughput and sample preservation. Let’s explore the key components and principles that make ASEM a revolutionary technique in the realm of microscopy.

  1. Instrumentation and Workflow

ASEM systems typically consist of an integrated platform with automated sample handling, imaging, and data acquisition components. The workflow begins with sample loading onto specialized carriers or grids, which are then automatically transferred into the microscope chamber. The automated system sequentially captures images of the specimen’s sections, allowing for three-dimensional reconstructions.

  1. Serial Sectioning

One of the defining features of ASEM is serial sectioning, where the specimen is incrementally sliced into ultra-thin sections. These sections are then imaged one after another to reconstruct a three-dimensional representation of the original sample. The ability to examine the internal structures of specimens in a sequential manner distinguishes ASEM from conventional techniques.

  1. Automated Data Acquisition

ASEM systems employ advanced imaging software and hardware to automate the data acquisition process. High-speed cameras, robotic manipulators, and precise stage control mechanisms work in tandem to capture images of each section rapidly. This automation significantly enhances the throughput of the imaging process.

IV. Applications of ASEM

The advent of ASEM has opened up new avenues for research across various scientific disciplines. Its unique capabilities make it particularly valuable in fields where high-throughput, three-dimensional imaging is crucial.

  1. Neuroscience

In neuroscience, ASEM has revolutionized the study of neural circuits and synaptic connections. Researchers can now investigate the three-dimensional morphology of neurons and their intricate connections with unprecedented detail. ASEM has proven instrumental in understanding the structural basis of neural functions, synaptic plasticity, and neurodegenerative disorders.

  1. Cell Biology

ASEM is transforming cell biology by enabling researchers to explore the internal structures of cells in a more comprehensive and efficient manner. The ability to acquire serial sections of cellular specimens allows for the detailed examination of organelles, vesicles, and other cellular components in three dimensions. This is particularly valuable for unraveling complex cellular processes and understanding disease mechanisms.

  1. Materials Science

In materials science, ASEM facilitates the study of materials at the nanoscale with improved efficiency. Researchers can investigate the three-dimensional structure of materials, including nanoparticles, composites, and crystalline structures. This capability is crucial for optimizing material properties and advancing the development of innovative materials for various applications.

  1. Paleontology and Archaeology

ASEM has found applications in paleontology and archaeology by providing detailed insights into the structure and composition of fossils and archaeological specimens. The three-dimensional reconstructions enable scientists to analyze the internal structures of ancient biological specimens, shedding light on evolutionary processes and cultural practices.

V. Mathematical equations behind the Automated Serial Electron Microscopy

The mathematical equations used in Automated Serial Electron Microscopy (ASEM) are diverse and can vary based on the specific algorithms and methods employed. Below are some general concepts and mathematical expressions associated with different aspects of ASEM:

1. Image Acquisition and Reconstruction:
    • Serial Sectioning: Zi = Zi−1 + ΔZi ; where Zi represents the position of the i-th section, and ΔZi is the thickness of the i-th section.
    • Tomographic Reconstruction:
I(x,y,z) = −∞ P(x − s cos⁡θ, y − s sin⁡θ, z − s sin⁡ϕ) ds ;

This represents the Radon transform used in tomographic reconstruction, where I(x,y,z) is the reconstructed 3D image, and P(x,y,z) is the original object function.

2. Image Processing and Analysis:

    • Image Registration: Registration may involve transformation functions such as T(x,y,z) representing translations, rotations, and scaling.Iregistered(x,y,z) = I(x′,y′,z′) ; where (x′,y′,z′) = T(x,y,z) ;
    • Feature Detection: Various algorithms, such as edge detection using gradient information: I=(∂I/∂x, ∂I/∂y, ∂I/∂z) ;

3. Automation Algorithms:

    • Robotic Manipulation: Robot control algorithms involving kinematics and dynamics equations.
    • Stage Control: Equations of motion for precise stage control: F=m⋅a; where F is the force, m is the mass, and a is the acceleration.

4. Data Analysis:

    • Data Mining: Various statistical methods and algorithms may be employed.
    • Quantitative Analysis: Measurements such as volume (V), surface area (A), or distances between points (d):V = ∫ ∫ ∫ I(x,y,z) dx dy dz ;
A = ∫ ∫ sqrt [ ( ∂I/∂x )2 + ( ∂I/∂y )2 + ( ∂I/∂z )2 ] dx dy ; d = sqrt [ (x2 − x1)2 + (y2−y1)2 + (z2−z1)2 ] ;

5. Computational Challenges:

    • Parallel Computing: Parallelized algorithms may be implemented to optimize processing time.
    • Image Compression: Compression algorithms, such as JPEG or PNG, may be used to manage large datasets.

It’s important to note that these equations are simplified representations, and the actual mathematics involved in ASEM can be much more complex, depending on the specific techniques and algorithms employed by researchers in their implementations.

VI. Challenges and Future Prospects

While ASEM holds great promise, it is not without its challenges. Overcoming these challenges will be crucial for the widespread adoption and further development of this revolutionary technique.

  1. Computational Challenges

The immense amount of data generated by ASEM requires sophisticated computational tools for image processing, analysis, and reconstruction. Developing efficient algorithms and software capable of handling large datasets is a critical area of ongoing research.

  1. Sample Preparation

Achieving consistent and high-quality sample preparation for ASEM remains a challenge, especially for biological specimens. Innovations in sample preparation techniques, such as cryofixation and improved staining methods, are essential for preserving the native state of samples.

  1. Integration with other Techniques

Integrating ASEM with other imaging modalities, such as fluorescence microscopy, can provide a more comprehensive understanding of biological processes. Developing seamless integration protocols and multi-modal imaging approaches will enhance the versatility and applicability of ASEM in diverse research areas.

  1. Instrument Accessibility

The widespread adoption of ASEM depends on the accessibility of the technology to researchers across different institutions and disciplines. Efforts to develop cost-effective and user-friendly ASEM systems will play a crucial role in democratizing access to this transformative technology.

Final Words

In this article by Academic Block we have seen that, Automated Serial Electron Microscopy represents a paradigm shift in the field of microscopy, offering unprecedented capabilities for high-throughput, three-dimensional imaging. As researchers continue to refine the technology and address its challenges, ASEM is poised to become an indispensable tool in various scientific disciplines, unlocking new insights into the complex and dynamic world at the nanoscale. The fusion of automation, advanced imaging techniques, and computational tools positions ASEM at the forefront of microscopy, paving the way for groundbreaking discoveries in the years to come. Please provide your comments below, it will help us in improving this article. Thanks for reading!

Automated Serial Electron Microscopy

Hardware and software required for Automated Serial Electron Microscopy


  1. Electron Microscope:

    • High-resolution transmission electron microscope (TEM) or scanning electron microscope (SEM) equipped for serial sectioning.

  2. Automated Stage and Sample Handling System:

    • Precision motorized stage for moving and positioning samples.
    • Robotic manipulator or sample loader for automated sample handling.
  3. Cameras and Detectors:

    • High-speed cameras for capturing images rapidly.
    • Detectors optimized for electron microscopy, such as scintillation or direct electron detectors.
  4. Computing Hardware:

    • High-performance computing (HPC) cluster or GPU-accelerated computing for processing large datasets.
    • Multi-core processors for parallel processing.
  5. Robotics:

    • If applicable, robotic arms or systems for automating tasks such as sample loading, sectioning, or handling.

  6. Vacuum System:

    • Electron microscopes operate in a vacuum; therefore, a vacuum system is essential for maintaining optimal conditions.


  1. Image Acquisition and Control Software:

    • Software for controlling the electron microscope, adjusting parameters, and automating the imaging process.

  2. Automation and Control Software:

    • Algorithms and software for automating sample handling, stage movement, and robotic manipulation.

  3. Image Processing and Analysis Software:

    • Software for image registration, alignment, and stitching of serial sections.
    • Tomographic reconstruction software for generating three-dimensional models.
    • Image processing tools for feature detection and segmentation.
  4. Data Management and Storage Software:

    • Database systems for efficiently storing and managing large datasets.
    • File systems optimized for handling microscopy data.
  5. Computational Software:

    • Computational tools for parallel processing and distributed computing, if applicable.

  6. Visualization Software:

    • 3D visualization software for exploring reconstructed models.
    • Software for rendering and visualizing large-scale datasets.
  7. Data Analysis and Statistics Software:

    • Statistical analysis tools and software for quantitative analysis.
    • Machine learning frameworks if automated analysis or classification is employed.
  8. Integration Software:

    • Software for integrating ASEM with other imaging modalities, if applicable.
    • Middleware for coordinating communication between different components.

Facts on Automated Serial Electron Microscopy

  1. Automation Advancements: ASEM integrates advanced robotic systems and automated sample handling, reducing the need for manual intervention and enabling high-throughput imaging.

  2. Serial Sectioning: ASEM involves sequentially slicing a specimen into ultra-thin sections, imaging each section, and reconstructing a three-dimensional representation of the original sample. This allows for detailed examinations of internal structures.

  3. Applications Across Disciplines: ASEM has diverse applications in neuroscience, cell biology, materials science, paleontology, cancer research, and more. Its versatility makes it a valuable tool for researchers in various scientific fields.

  4. High-Resolution Imaging: ASEM leverages the capabilities of transmission electron microscopes (TEM) or scanning electron microscopes (SEM), providing high-resolution imaging at the nanoscale.

  5. Neuroscience Insights: In neuroscience, ASEM has been used to map synaptic connections and study neural circuitry in three dimensions. This technology contributes to a deeper understanding of brain structure and function.

  6. Cellular Dynamics: ASEM allows researchers to study the dynamic processes within cells, including organelle movements and interactions. This provides insights into cellular functions and behaviors.

  7. Materials Characterization: In materials science, ASEM facilitates the study of nanomaterials in three dimensions, aiding in the characterization of their structure and properties. This has implications for the development of advanced materials.

  8. Paleontological Applications: ASEM is applied in paleontology to analyze fossilized specimens in three dimensions, contributing to our understanding of ancient life forms and evolutionary processes.

  9. Challenges in Sample Preparation: Achieving optimal sample preparation for ASEM, especially in biological specimens, remains a challenge. Innovations in sample preparation techniques, such as cryofixation, are ongoing to preserve the native state of samples.

  10. Computational Demands: ASEM generates large datasets, requiring sophisticated computational tools for image processing, analysis, and reconstruction. Parallel computing is often employed to handle the computational demands.

  11. Integration with Other Techniques: ASEM can be integrated with other imaging modalities, such as fluorescence microscopy, to provide a more comprehensive understanding of biological structures and processes.

  12. Potential for Drug Discovery: The high-throughput capabilities of ASEM make it a promising tool for drug discovery and development, allowing researchers to study the effects of drugs on cellular structures in detail.

Academic References on Automated Serial Electron Microscopy

  1. Kreshuk, A., Koethe, U., Pax, E., Bock, D. D., & Hamprecht, F. A. (2014). Automated detection of synapses in serial section transmission electron microscopy image stacks. PloS one, 9(2), e87351.

  2. Mishchenko, Y. (2009). Automation of 3D reconstruction of neural tissue from large volume of conventional serial section transmission electron micrographs. Journal of neuroscience methods, 176(2), 276-289.

  3. Baena, V., Schalek, R. L., Lichtman, J. W., & Terasaki, M. (2019). Serial-section electron microscopy using automated tape-collecting ultramicrotome (ATUM). In Methods in cell biology (Vol. 152, pp. 41-67). Academic Press.

  4. Graham, B. J., Hildebrand, D. G. C., Kuan, A. T., Maniates-Selvin, J. T., Thomas, L. A., Shanny, B. L., & Lee, W. C. A. (2019). High-throughput transmission electron microscopy with automated serial sectioning. Biorxiv, 657346.

  5. Lee, K., Turner, N., Macrina, T., Wu, J., Lu, R., & Seung, H. S. (2019). Convolutional nets for reconstructing neural circuits from brain images acquired by serial section electron microscopy. Current opinion in neurobiology, 55, 188-198.

  6. Kubota, Y., Sohn, J., Hatada, S., Schurr, M., Straehle, J., Gour, A., … & Kawaguchi, Y. (2018). A carbon nanotube tape for serial-section electron microscopy of brain ultrastructure. Nature Communications, 9(1), 437.

  7. Smith, D., & Starborg, T. (2019). Serial block face scanning electron microscopy in cell biology: Applications and technology. Tissue and Cell, 57, 111-122.

  8. Deerinck, T. J., Bushong, E. A., Lev-Ram, V., Shu, X., Tsien, R. Y., & Ellisman, M. H. (2010). Enhancing serial block-face scanning electron microscopy to enable high resolution 3-D nanohistology of cells and tissues. Microscopy and microanalysis, 16(S2), 1138-1139.

  9. Knott, G., Marchman, H., Wall, D., & Lich, B. (2008). Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling. Journal of Neuroscience, 28(12), 2959-2964.

  10. Hildebrand, D. G. C., Cicconet, M., Torres, R. M., Choi, W., Quan, T. M., Moon, J., … & Engert, F. (2017). Whole-brain serial-section electron microscopy in larval zebrafish. Nature, 545(7654), 345-349.

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