The Future of Seeing Life: How Chemigenetic Tools are Transforming Biological Imaging

Illuminating Life at the Molecular Level

For centuries, scientists have relied on light to reveal the hidden structures of the world. The invention of the microscope in the 17^th century was a turning point, allowing humanity to see beyond the limits of the naked eye. Today, light continues to play a critical role in biology—not only as a tool for observation but also as a way to control and manipulate life at the molecular level.

The field of optogenetics—using genetically engineered proteins that respond to light—has revolutionized neuroscience by enabling researchers to turn specific neurons on and off with pulses of blue or red light. Meanwhile, fluorescent biosensors allow scientists to observe the activity of neurons and track the movement of molecules inside living cells with dazzling precision. Yet, despite these advancements, traditional fluorescent biosensors have their limitations. Some are too dim, some are too slow, and others simply cannot be detected deep inside biological tissues.

This is where, an emerging field of research, Chemigenetics comes in—a cutting-edge approach that fuses synthetic chemistry with protein engineering to create next-generation biosensors. Unlike conventional fluorescent proteins that are entirely genetically encoded, chemigenetic biosensors use a hybrid approach, integrating synthetic fluorophores with genetically targeted protein scaffolds. The result is a new class of imaging tools with superior brightness, sensitivity, and the ability to reach deeper into living tissue.

At the forefront of this field is Professor Robert E. Campbell, a biomolecular chemist at the University of Tokyo’s Department of Chemistry. His work is pushing the boundaries of bioimaging by designing chemigenetic indicators for calcium (Ca²⁺) and potassium (K⁺) ions, crucial signals in brain function and metabolism. By engineering sensors that emit red and near-infrared light, Campbell’s lab is making it possible to peer deeper into the brain than ever before, opening up new possibilities for studying neural activity, disease mechanisms, and even further, consciousness itself.

Beyond Traditional Fluorescence: The Birth of Chemigenetics

The history of bioimaging is deeply intertwined with fluorescence. Ever since the isolation of the gene for the green fluorescent protein (GFP) in the early 1990s, 30 years after the discovery of the protein in jellyfish, researchers have used fluorescent proteins to illuminate cellular structures and processes. Fluorescent biosensors—genetically engineered proteins that light up when they interact with specific molecules—have been crucial for tracking biological activities such as calcium signaling, metabolism, and gene expression.

But traditional biosensors have limitations. While GFP and its engineered variants have enabled countless breakthroughs, they come with trade-offs. Many of these proteins emit in the blue-green range of the light spectrum, which is strongly absorbed by tissues, making deep-tissue imaging difficult. Others suffer from low brightness, slow response times, or limited specificity.

A turning point came with the idea of chemigenetics. Instead of relying solely on natural fluorescence, chemigenetic indicators use self-labeling proteins that bind to synthetic fluorophores, unlocking new possibilities for imaging.

According to Professor Robert E. Campbell, this approach allows researchers to “go beyond the limitations of proteins and make systems that are a combination of a protein plus a synthetic part—something that a chemist can design and make in a laboratory.”

The HaloTag System: A Key to Hybrid Fluorescence

One of the most significant advancements in chemigenetics is the HaloTag system, a self-labeling protein engineered to bind synthetic fluorescent dyes. Unlike traditional fluorescent proteins that rely on their own intrinsic fluorescence, HaloTag-based biosensors enable the attachment of a diverse range of fluorophores, making them highly adaptable for different imaging applications.

In the field of potassium imaging, Campbell and his team have designed a chemigenetic K⁺ indicator called HaloKbp1 series that utilizes a potassium-binding protein (Kbp) fused to a self-labeling HaloTag protein, allowing precise control over fluorophore selection. Their work builds on previous approaches that integrate synthetic fluorophores with genetically encoded components, improving specificity and brightness. The ability to track K⁺ flux in real time provides neuroscientists with a powerful tool to study neuronal excitability and ionic homeostasis, both of which are critical for normal brain function.

Potassium ions are fundamental in maintaining neuronal excitability and cellular homeostasis. Disruptions in K⁺ signaling have been linked to various neurological conditions, including epilepsy, stroke, and neurodegenerative diseases. By enabling precise visualization of K⁺ dynamics, Campbell’s work is providing essential tools to understand how neural circuits regulate ionic balance and respond to electrical activity.

“While optogenetics typically refers to the precise control of biological processes using light, much of our research focuses on visualizing and analyzing these processes,” Campbell explained. “The two are inherently interconnected—manipulation through light is only as powerful as our ability to observe its effects. We seek not only to control biological activity but to illuminate its intricate outcomes in real time.”

Calcium and Neuroscience: Visualizing the Brain in Action

If potassium is crucial for cellular stability, then calcium (Ca²⁺) serves as the primary signaling molecule in neurons. Every time a neuron fires, calcium surges through the cell, regulating neurotransmitter release, synaptic activity, and gene expression. These calcium waves are fundamental to memory, cognition, and learning.

“Traditional calcium indicators, such as GCaMP, have been widely used in neuroscience. However, GCaMP and other GFP-based sensors suffer from limitations due to light absorption, limiting their effectiveness for deep-tissue imaging,” Campbell said. Additionally, because many optogenetic tools use blue light for activation, GFP fluorescence can interfere with simultaneous imaging and stimulation experiments.

Recognizing these challenges, Campbell and his team have pioneered the development of red and near-infrared fluorescent Ca²⁺ biosensors. In other pioneering work, Campbell’s team invented a chemigenetic Ca²⁺ biosensors that incorporate synthetic chelators—small molecules that bind Ca²⁺ with high specificity. The result is HaloGFP-Ca, a biosensor that integrates chelators with circularly permuted GFP (cpGFP) to track calcium signaling with exceptional precision.

Tracking Metabolism in the Brain

“Neuroscientists are leaders in technological innovation, driven by the challenge of studying the brain—arguably the most complex structure in the universe.” Campbell’s lab has extended its work beyond calcium imaging, developing fluorescent indicators for lactate and glucose metabolism to study how energy is distributed across neural networks. Lactate is increasingly being considered a key energy shuttle, carrying metabolic energy from support cells to cells that require fuel.

“There’s a hypothesis that lactate is sort of the essential intermediate—almost like the currency, the energy currency of the brain that’s shuttled around to where it’s needed,” Campbell explains. His team’s metabolic indicators are designed to track these transactions in real time, allowing researchers to correlate neural activity with metabolic demand.

By combining calcium indicators with metabolic biosensors, Campbell’s research aims to offer a comprehensive view of how the brain balances electrical activity with energy consumption, addressing one of the most critical challenges in neuroscience: how the brain meets its fluctuating energy demands in real time.

“The calcium biosensors that we have developed are quite important in this context because all cell signaling in biology, such as every time a neuron fires in your brain or a hormone binds to a receptor on a cell surface, the calcium concentration changes inside the cell,” Campbell said. When neurons fire, they require an immediate and precise supply of metabolic fuel. Campbell’s work enables researchers to track not just neuronal activity but also the metabolic pathways that sustain it, offering insights into how glucose and lactate are dynamically utilized in response to neural signaling. “This research will contribute to solving one of the biggest questions of neuroscience these days: how do neurons get the energy that they need where and when they need it,” Campbell explains.

This is particularly crucial in understanding neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and epilepsy, where disruptions in energy metabolism and ionic regulation often precede cognitive and motor dysfunction. By allowing researchers to monitor how neurons interact with supporting glial cells and how metabolic substrates are mobilized within the brain, Campbell’s research could inform new therapeutic strategies aimed at restoring metabolic balance in these disorders.

The Role of Near-Infrared Fluorescence

To optimize imaging resolution and reduce interference with optogenetic tools, Campbell’s team has focused on red and near-infrared (NIR) fluorescence. Traditional biosensors operate in the blue-green spectrum, which is strongly absorbed by tissue and prone to background autofluorescence. By shifting to redder wavelengths, researchers can achieve higher signal clarity and reduced interference from endogenous fluorophores, improving imaging quality and enabling imaging deeper into tissue.

“The general trend is just that redder is better,” Campbell notes. By integrating near-infrared fluorescent proteins (NIR-FPs) into their biosensors, his team has optimized signal-to-noise ratio in fluorescence imaging, enabling more effective real-time monitoring of neuronal and metabolic activity.

This shift is particularly important for optogenetics, where precise light-activated neuronal control is required. Since many optogenetic tools operate in the blue spectrum, the use of red-shifted indicators avoids cross-talk between imaging and stimulation, allowing researchers to simultaneously activate neurons and observe their responses without interference.

Despite its promise, the field of chemigenetics still faces major challenges. The synthetic components—such as fluorophores and chelators—must be delivered efficiently into living tissues while maintaining stability. In neuroscience, this requires overcoming the blood-brain barrier, a highly selective biological shield that prevents most foreign molecules from entering the brain.

Campbell acknowledges this hurdle, likening the process to drug delivery: “The synthetic part has to go inside of an animal, and it has to be administered like a drug… it needs to be injected and ideally go directly to the brain.”

But if and when these hurdles are overcome, Campbell believes that there will still be major limitations to how fluorescence chemigenetic tools are used in mammalian models such as mice. “Even for near-infrared light, tissue is relatively opaque and imaging depths are limited to hundreds of microns or millimeters at best,” he explains. “We need to develop new molecular imaging approaches that don’t rely solely on light and allow deeper imaging.” Towards this goal, researchers are exploring alternative imaging techniques such as photoacoustic sensors, which use light to generate sound waves for deeper imaging, and ultrasound-responsive biosensors, which can be detected through non-invasive methods. MRI-compatible biosensors are also under development, offering a new frontier in tracking brain activity without optical fluorescence.

Curiosity and Persistence: The Core of Scientific Discovery

For students around the world considering a career in science, the path ahead can seem daunting. Research is often unpredictable, experiments fail more often than they succeed, and the answers to fundamental questions remain elusive. Yet, for those who persist, science offers something rare—the chance to push the boundaries of knowledge and contribute to groundbreaking discoveries.

Campbell understands this firsthand. His independent academic journey began in Canada, where he pursued research in bioanalytical chemistry, before moving to Japan to continue his work at the University of Tokyo. Over the years, he has embraced an interdisciplinary approach, integrating synthetic chemistry, spectroscopy, molecular biology, and neuroscience to develop cutting-edge bioimaging tools. “One of the most rewarding parts of being a scientist is that by the time you finish your PhD, you are the world’s expert on a certain topic,” he says. “You know more than anybody else in the whole world.”

For students aspiring to follow in his footsteps, he emphasizes the importance of curiosity, persistence, and adaptability. Scientific inquiry today is no longer confined to traditional boundaries—chemistry, biology, and physics increasingly intersect in ways that drive innovation. “We need people who are comfortable moving between fields,” he explains. “Biology is no longer just biology. It’s chemistry, it’s physics, it’s engineering.”

A Hub for Innovation

Campbell’s work at the University of Tokyo reflects this multidisciplinary approach. His research in chemigenetics and molecular imaging has benefited from collaborations with experts across various scientific domains. For students considering where to study, he sees the University of Tokyo as an ideal environment. “This is a place where people are constantly thinking about new ways to approach problems,” he says. “You’re surrounded by researchers who are at the forefront of their fields.”

He also stresses that research is an international endeavor. Science transcends borders, and collaboration with researchers from different backgrounds and perspectives is essential for progress. Many of his own breakthroughs have come from working with colleagues globally.

For those just beginning their journey, Campbell offers simple but powerful advice: follow your curiosity and don’t be afraid to take risks. “Science is about exploration,” he says. “Start broad, then find your niche.” Research may not always go as planned, but setbacks are part of the process. The key is to stay motivated and keep asking questions.

The next generation of scientists will be the ones to build on today’s discoveries, develop new tools, and solve problems that we can’t yet imagine. Whether in bioimaging, neuroscience, or synthetic biology, the future of science depends on young researchers who are willing to challenge the limits of what is known.

For those ready to take on the challenge of crossing chemistry and biology, the journey begins here and now.

※Year of interview:2025
Interview/Text : Akihiko MORI（translation：Takuya TERAI・Takumi YANAGIMACHI・Shosei IMAI）
Photography: KAIZUKA Junichi

Robert E. Campbell

Professor, Department of Chemistry

Professor Robert E. Campbell specializes in biomolecular chemistry, optogenetics, molecular biology, and chemical biology, focusing on the development of protein-based molecular tools for imaging and manipulating biological systems using light. His research integrates synthetic chemistry and protein engineering to create next-generation biosensors. By developing red and near-infrared indicators, his work enhances deep-tissue imaging and optogenetics, enabling precise visualization of cell signaling and metabolism for applications in neuroscience, diagnostics, and therapeutics. His contributions advance non-invasive bioimaging techniques, shaping the future of multicolor and high-resolution in vivo imaging.