Scientists at Harvard University have developed a new imaging technique that combines the strengths of electron microscopy and fluorescence microscopy, allowing researchers to visualize cellular structures and specific proteins simultaneously with nanometric resolution and in vivid color. The breakthrough, presented at the 70th Annual Meeting of the Biophysical Society in San Francisco, February 21-25, 2026, addresses a longstanding challenge in biological imaging: the traditional trade-off between observing fine structural details and tracking specific molecules.
The technique, termed multicolor electron microscopy, opens avenues for studying cellular signaling and the organization of molecular groups within cells, whereas precisely observing where these processes occur within the cellular architecture. “I’ve always been fascinated by developing new microscopy techniques that allow us to visualize things we haven’t seen before,” said Debsankar Saha Roy, a postdoctoral researcher in Maxim Prigozhin’s laboratory at Harvard University. “We are building a multicolor electron microscope, a technique that combines the advantages of electron microscopy and fluorescence microscopy.”
Traditional fluorescence microscopy involves attaching luminescent markers to proteins of interest and projecting visible light onto the sample to illuminate them. While effective for locating specific molecules, this method is limited by a resolution of approximately 250 to 300 nanometers, hindering the clear visualization of individual proteins. “The resolution is limited to about 250 to 300 nanometers, so you can’t see individual proteins clearly,” Roy explained. “But the biggest problem is that you don’t see the structure of the cell. You see what is labeled, but not everything around it.”
Electron microscopy, conversely, can reveal cellular structures with exquisite detail, down to a few nanometers. Though, it has traditionally lacked the ability to identify specific molecules in color. Scientists have attempted to combine both approaches by taking separate images with each method and then overlaying them, but accurately aligning the images, particularly in large samples like brain tissue, has proven extremely tough.
The Harvard team’s solution is to use a single electron beam to perform both tasks simultaneously. “We’re not sending light, we’re sending an electron beam,” Roy stated. “We have probes that can attach to a protein that emits visible light when excited by electrons. This process is called cathodoluminescence. So, from the same electron beam, you get two sets of information: the colored signal from the probes and the detailed structural image from the electrons.”
A key advantage of this technique is the ability to utilize existing, widely available, and well-characterized fluorescent dyes. The team had previously developed lanthanide nanoparticles as probes for multicolor electron microscopy and was working to attach them to proteins. More recently, they made a surprising discovery when placing common fluorescent dyes under the electron microscope. “The most surprising thing we observed was that standard dyes used in fluorescence microscopy also emit visible light when excited by electrons,” Roy noted. “This had never been seen before. And these dyes, and their protein labeling methods, are already developed and available; there’s no necessitate to create anything new.”
The team has already demonstrated the technique’s functionality in mammalian cells and biological tissues, including fruit flies infected with fungi.
Looking ahead, the researchers aim to extend the technique to three dimensions. Currently, the method produces two-dimensional, flat images. The next challenge is to adapt it for use with cryo-electron microscopy, a technique that involves rapidly freezing samples, preserving cells in their natural state, and allowing scientists to image them from multiple angles to create 3D reconstructions.
“We want to extend this multicolor electron microscopy approach to 3D,” Roy concluded. “To achieve this, our goal is to implement this technique on ultrafine sections of embedded cell matrices or in cryo-electron microscopy; that’s the next step.”
