Scientists have developed a new imaging technique that uses a new contrast mechanism in bioimaging to merge the strengths of two powerful microscopy methods, allowing researchers to see both the complex architecture of cells and the specific locations of proteins, all in vivid color and at nanometer resolution.
This advance, called multicolor electron microscopy, addresses a long-standing challenge in biological imaging: Scientists have traditionally had to choose between observing fine structural details or tracking specific molecules, but not both.
The approach opens the door to studying everything from cell signaling to the organization of molecular groups within cells, while seeing exactly where these processes occur in cellular architecture. The research will be presented at the 70th Annual Meeting of the Biophysical Society in San Francisco February 21-25, 2026.
I have always been fascinated by the development of new microscopy techniques that can image things we have never seen before. We are building a multicolor electron microscope, a technique that combines the advantages of electron microscopy and fluorescence microscopy. »
Debsankar Saha Roy, postdoctoral researcher in the laboratory of Maxim Prigozhin at Harvard University
Traditional fluorescence microscopy works by attaching light tags to proteins of interest, then shining visible light onto the sample to illuminate those tags. This approach is excellent for localizing 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 biggest problem is that you don’t see the structure of the cell. You see everything that’s 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 is traditionally unable to identify specific molecules in color. Scientists have tried to combine the two approaches by taking separate images with each method and then superimposing 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 light, we’re sending a beam of electrons,” 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 of the electrons. »
One of the main advantages of this 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 multicolor electron microscopy and worked to attach them to proteins.
More recently, the team made a surprising discovery when putting common fluorescent dyes under an electron microscope. “The most surprising thing we observed is that standard dyes used in fluorescence microscopy also emit visible light when excited by electrons,” Roy said. “This has never been seen before. And these dyes – and their protein labeling methods – are already developed and available; you don’t have to create anything new. »
The team has already demonstrated that the technique works on mammalian cells and biological tissues, including fungus-infected flies.
For the future, the researchers aim to extend the technique into three dimensions. Currently, the method produces flat two-dimensional images. The next frontier is adapting it to cryo-electron microscopy, a technique in which samples are flash frozen, thereby 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 said. “To achieve this, we aim to implement this technique in ultrathin sections of embedded cell matrices and/or in cryoelectron microscopy – this is the next step. »
