A breakthrough in electron microscopy delivers sharper images of our body’s tiniest proteins - Berkeley News

Mind & body, Research, Science & environment, Technology & engineering

A breakthrough in electron microscopy delivers sharper images of our body’s tiniest proteins

UC Berkeley physicists have introduced phase contrast to the electron microscope, allowing scientists to see much smaller molecules and smaller structures inside cells.

By Robert Sanders

A laser (purple) is powerfully amplified by highly polished mirrors and focused on the electron beam (blue) to shift its phase and increase the cryo-EM microscope’s contrast, allowing biologists to image smaller proteins and the crowded structures inside cells.

SayoStudio

June 11, 2026

Nearly 100 years ago, a seemingly simple discovery revolutionized the microscope. The introduction of phase-contrast, which garnered a Nobel Prize in 1953, brought into clear view structures inside cells that had previously been too faint or washed out for biologists to study.

UC Berkeley physicists have now adapted the phase contrast technique to the electron microscope, which has about 10,000 times the magnification of microscopes using optical light.

The addition of a so-called laser phase plate has the potential to greatly improve cryoelectron microscopy (cryo-EM), a technique for determining the structure of molecules that itself revolutionized the understanding of proteins and accelerated new drug discovery starting a decade ago. Despite its impact, however, cryo-EM still struggles to produce clear images of small molecules — including most human proteins. A laser phase plate promises clear images of most proteins in the cell down to one-third the size of those that are a challenge for today’s machines.

The addition of a laser phase plate seems certain to revolutionize a newer technique referred to as cryoelectron tomography (cryo-ET), which assembles a number of different angular views of a molecule or protein into a 3D image. This makes it possible to analyze proteins in their natural environment — inside cells — instead of in isolation in a solution.

Cryo-EM images of the blood protein hemoglobin, showing the much-improved contrast achieved with a laser phase plate. The images, which show many hemoglobin molecules, are analyzed to assemble a detailed 3D structure of the protein.Holger Müller, Jessie Zhang/UC Berkeley

“Cryo-EM has become the new, fastest-growing method for resolving the structure of biological macromolecules, and cryo-ET is expected to show how these molecules work together in their natural, cellular context,” said Holger Müller, a UC Berkeley professor of physics and faculty scientist at Lawrence Berkeley National Laboratory who led the development effort. “But because of signal-to-noise limitations, the majority of human and animal proteins are too small to be analyzed by these methods. The increase in signal-to-noise ratio provided by this laser phase plate is expected to overcome these important limitations.”

Crucial to the development is the world’s most intense, focused continuous-wave laser, which interacts with the electron beam to change its phase. This phase change boosts contrast for small molecules, such as hemoglobin, and for molecules and structures inside cells, such as the nucleus and mitochondria.

“With cryo-ET, we’re looking at small, very complicated cellular material that’s incredibly crowded inside the cell,” said Bridget Carragher, founding technical director of imaging at Biohub in Redwood City, California “It’s like a forest of trees, and you’re trying to find one leaf on one tree in there. Cryo-ET needs a dramatic step forward in contrast, so we can start to see what’s going on inside the cell. That’s what the laser phase plate promises to give us.”

Biohub provided funding to Müller to purchase a state-of-the-art cryo-EM machine that he then outfitted with a laser phase plate, creating a microscope he calls Theia, named after the ancient Greek Titaness of light and radiance. Carragher is overseeing the development of a similar instrument at Biohub’s imaging lab in Redwood City — this one featuring a dual-laser system, based on theoretical work by Müller and his colleagues. In this system, the two perpendicular laser beams operate at about half power, making the components less likely to burn out and reducing aberrations.

Both groups are collaborating with the firm Thermo Fisher Scientific, the primary manufacturer of cryo-EM machines.

Holger Müller explains how a laser phase plate works and how it improves the contrast of cryoelectron microscope (cryo-EM) images. (Video credit: Biohub)

“Theia is the Formula 1 microscope,” Müller said. “It has extra electron optics that give it better resolution than the standard cryo-EM, even without the laser. With the addition of the laser phase plate, we hope that it really becomes the world’s best instrument overall.”

Müller and his Berkeley team published their...