Multicolor electron microscopy reveals proteins and cell architecture at nanoscale resolution

Scientists have developed a new imaging technique that uses a novel contrast mechanism in bioimaging to merge the strengths of two powerful microscopy methods, allowing researchers to see both the intricate architecture of cells and the specific locations of proteins-all in vivid color and at nanometer resolution.

The breakthrough, called multicolor electron microscopy, addresses a longstanding challenge in biological imaging: scientists have traditionally had to choose between seeing fine structural details or tracking specific molecules, but not both at once.

The approach opens doors for studying everything from cell signaling to the organization of molecular clusters within cells, all while seeing exactly where these processes occur within the cell's architecture. The research will be presented at the 70th Biophysical Society Annual Meeting in San Francisco from February 21–25, 2026.

I've always been fascinated by developing new microscopy techniques that can image things we haven't seen before. We're building a multicolor electron microscope-a technique that combines the benefits of electron microscopy and fluorescence microscopy."

Debsankar Saha Roy, a postdoctoral fellow in the laboratory of Maxim Prigozhin at Harvard University

Traditional fluorescence microscopy works by attaching glowing tags to proteins of interest, then shining visible light on the sample to make those tags light up. This approach is excellent for locating specific molecules, but it has significant limitations. "The resolution is limited to about 250 to 300 nanometers, so you can't see individual proteins clearly," Roy explained. "But the bigger issue is that you don't see the structure of the cell. You see whatever is labeled, but you don't see everything else around it."

Electron microscopy, on the other hand, can reveal cellular structures in exquisite detail-down to a few nanometers-but hasn't traditionally been able to identify specific molecules in color. Scientists have tried combining the two approaches by taking separate images with each method and then overlaying them, but aligning the images precisely, especially in large samples like brain tissue, has proven extremely difficult.

The Harvard team's solution is elegant: instead of using two separate imaging sessions, they use a single electron beam to accomplish both tasks simultaneously.

"We're not sending in light-we're sending an electron beam," Roy said. "We have probes that you can attach to a protein that emit 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 also the detailed structural image from the electrons."

A key advantage of the technique is that researchers can use existing fluorescent dyes that are already widely available and well-characterized. The team had previously developed lanthanide nanoparticles as probes for muticolor electron microscopy, and working to attach them to proteins.

More recently, the team made a surprising discovery when they placed some common fluorescent dyes in the electron microscope. "The most surprising thing we observed was that standard dyes used in fluorescence microscopy also emit visible light when you excite them with electrons," Roy said. "That had never been seen before. And these dyes-and their protein labelling methods-are already developed and available; you don't have to create anything new."

The team has already demonstrated the technique works in mammalian cells and biological tissues, including fungus-infected flies.

Looking ahead, the researchers aim to extend the technique into three dimensions. Currently, the method produces flat, two-dimensional images. The next frontier is adapting it for use with cryo-electron microscopy-a technique where samples are flash-frozen, preserving cells in their natural state and allowing scientists to image them from multiple angles to build 3D reconstructions.

"We want to extend this multicolor electron microscopy approach to 3D," Roy said. "To get there, we aim to implement this technique in ultrathin sections of cell embedded matrices and/or in cryo-electron microscopy-that's the next step."