Biotech Connector explores the high-resolution world of electron microscopy

The spring Biotech Connector, a quarterly networking and speaker series, on May 23 gave an overview of the electron microscope and its uses—from the first electron microscopy (EM) image of an intact cell published in 1944 to an array of modern techniques that are changing our understanding of cell biology. The event featured two speakers from the Frederick National Laboratory for Cancer Research (FNL) and one from ZEISS Microscopy. 

History of electron microscopy  

Ru-ching Hsia, Ph.D., head of the FNL’s Electron Microscopy Laboratory, leverages high-resolution EM to study cell biology, or as she joked, to “look for tiny things in a big instrument.” 

She provided an overview of the history of EM, explaining that since its development in the 1930s, EM has greatly advanced our understanding of cell biology and enabled the discovery of organelles, such as the mitochondria. 

She presented the two broad types of EM: the transmission EM and scanning EM. Transmission EM shines an electron beam through a very thin slice of a sample, imaging the interior of the cell. With scanning EM, the electrons scatter off the surface of the sample, and as the beam moves, it creates a 3D-like image of the sample’s surface.  

She noted four key areas where EM plays a critical role: 

• Nanotechnology and nanomedicine 

• Ultra-structure characterization, or viewing the cell at a higher magnification 

• Characterization of the temporal-spatial expression, or the activity of genes in a specific cell or group of cells of potential new therapy or vaccine targets over a period of time 

• Higher-order 3D structural analysis to study tissue regeneration, biofilms, tissue engineering, and stem cell research 

“This structure characterization started in 1940s, and we still keep going,” Hsia explained. “There are still new structures and new functions that we are identifying by using EM.” 

However, she noted that the EM field also faces several challenges, including expensive instruments, a laborious sample preparation process that makes it difficult to conduct high-throughput automatic testing of large numbers of chemical and/or biological compounds for a specific biological target, and a lack of training opportunities. Modern advances, such as robotic automations, are helping researchers overcome some of these challenges. 

Volume electron microscopy and artificial intelligence 

Kedar Narayan, Ph.D., group leader at FNL’s Center for Molecular Microscopy, presented on volume EM , which was named one of Nature’s “seven technologies to watch” in 2023, because of its ability to capture 3D cell structures at nanoscale. 

To do this, volume EM takes iterative slices of a cell and images each one, creating a stack of images that, once put together, creates a full 3D model that captures both the interior and exterior of the cell. 

“For complex biological structures like mitochondria, they only look like kidney beans in textbooks. In real life, they can look dramatically complex,” Narayan said as he showed a long and twisted mitochondrion captured by volume EM. “To truly understand what these organelles are, you need to image them at high resolution in their entirety, and in 3D.”  

Narayan is also leveraging artificial intelligence (AI) with volume EM to enable visualization and analysis of cellular organelles, such as mitochondria. To this end, his group developed empanada, an open-source software plugin that allows users to deploy state-of-the-art AI models to segment features from EM images, and MitoNet, which is an AI model specifically for mitochondria. Using these tools, he showed how researchers can identify all the mitochondria within a volume EM image in mere seconds and then quantify the volume or other features of the organelles to allow for statistical comparisons.  

“Volume EM and AI can now rediscover cell biology in ways that were previously inaccessible,” he said.  

A vast menu of modern techniques  

Joseph Mowery, product and application specialist at ZEISS Microscopy, rounded out the session with an overview of some of the cutting-edge techniques used today. He noted advantages and challenges of each, and he discussed the importance of sample preparation techniques.  

“You can’t just put biological tissue inside a vacuum chamber, right?” Mowery said. “All the water and moisture will get pulled out, and the tissue will shrink. You have to fix things, dehydrate them, and even coat them in metal.”  

He showed how the preparation methods (e.g., a chemical fixative and heavy-metal staining vs. rapid cryogenic freezing) can alter the sample structure and the resulting image. Variable-pressure imaging techniques—which keep the chamber at a higher pressure—can reduce the need for some sample preparation work. 

He showed two volume EM techniques: the serial block-face scanning EM and focused ion beam scanning EM. Both techniques sequentially remove small layers of a specimen and scan the remaining sample. The serial-block face technique cuts the samples with a diamond knife, creating slices in the 25–10 nm range, whereas the FIB- scanning EM’s laser can cut 5–3 nm slices, which creates an isotropic resolution—meaning it’s uniform in all directions.  

To finish, Mowery showed the multi-beam scanning EM, which uses 91 beams and enables high-throughput imaging.  

Join us in August 

This quarterly networking and speaker series, co-hosted with the Frederick County Chamber of Commerce, brings together local biotech professionals for networking and an inside look into local scientific advances. The next Biotech Connector event will be August 22 at 8:00 AM ET.