The findings—and how they were made—could be used to help assess fatigue, develop therapeutics and address mental health issues

An international research team has revealed how brain activity shifts throughout the day by developing a method that can image which neurons and networks are active in mouse brains at different times. Image courtesy: Konstantinos Kompotis

An international team led by the University of Michigan has introduced new methods that reveal which regions of the brain were active throughout the day with single-cell resolution.

Using mouse models, the researchers developed an experimental protocol and a computational analysis to follow which neurons and networks within the brain were active at different times. Published in the journal PLOS Biology, the study provides new insights into brain signaling during sleep and wakefulness, which hints at the bigger questions and goals that motivated the work.

Daniel Forger

“We undertook this difficult study to understand fatigue,” said senior author Daniel Forger, U-M professor of mathematics. “We’re seeing profound changes in the brain over the course of the day as we stay awake and they seem to be corrected as we go to sleep.”

What the team found and how they found it could help lead to new ways to objectively assess fatigue in humans. These could in turn be used to help ensure people with high-stakes responsibilities, such as pilots and surgeons, are adequately rested before starting a flight or an operation.

“We’re actually terrible judges of our own fatigue. It’s based on our subjective tiredness,” Forger said. “Our hope is that we can develop ‘signatures’ that will tell us if people are particularly fatigued, and whether they can do their jobs safely.”

The study was supported by federal funding from the U.S. National Science Foundation and the U.S. Army Research Office. It also received funding from the Human Frontier Science Program, or HFSP, that enables pioneering work in the life sciences through international collaboration, which was key to this study.

A more global view

While researchers at U-M created the mathematical and computational workflows to analyze and interpret data, collaborators in Japan and Switzerland were developing a powerful new experimental approach.

They leveraged a cutting-edge form of imaging called light sheet microscopy that enabled them to generate 3D images of mouse brains. They also introduced a genetic tagging method that resulted in active neurons glowing under the microscope, allowing the researchers to see which cells were active across the brain and when.

“We know from studies over the last 20 or 30 years, how to decipher how one aspect—a gene or a type of neuron, for instance—can contribute to behavior,” said Konstantinos Kompotis, a study co-author and senior scientist at the Human Sleep Psychopharmacology Laboratory at the University of Zurich. “But we also know that whatever governs our behavior, it’s not just one gene or one neuron or one structure within the brain. It’s everything and how it connects and interacts at a given time.”

An international research team has mapped how brain activity changes over time using mouse models. Two brains are shown for four different time windows, hours of wakefulness increasing from top left to bottom right. Image credit: G. Sun et al. PLOS Biol. 2025. DOI: 10.1371/journal.pbio.3003472 (Used under a CC-BY license)

The HSFP brought together teams across three countries to investigate those connections and interactions more deeply. That included the U-M team, the Zurich team and a Japanese team, led by Hiroki Ueda of the Laboratory for Synthetic Biology at the RIKEN Center for Biosystems and Dynamics Research.

Working together, the team saw that, generally speaking, as mice wake up, activity starts in inner, or subcortical, layers of the brain. As the mice progressed throughout their day—or night, rather (they are nocturnal)—hubs of activity moved to the cortex at the brain’s surface.

“The brain doesn’t just change how active it is throughout the day or during a specific behavior,” Kompostis said. “It actually reorganizes which networks or communicating regions are in charge, much like a city’s roads serve different traffic networks at different times.”

This finding, and how it was made, provide foundational steps toward identifying signatures of fatigue and more, Forger said. For example, he also suspects that exploring this general pattern further could yield ties to mental health.

“This study doesn’t touch on that,” Forger said. “But I do think the activity we saw in different regions is going to be important for understanding certain psychiatric disorders.”

Furthermore, Kompotis has already started working with industrial partners to use the team’s experimental techniques to probe how different therapeutics and drug candidates affect brain activity.

Although the new experimental techniques are not applicable to humans, researchers can translate certain findings from mouse models to human physiology, Forger said. And the computational approaches developed for this study are generalizable, said co-author Guanhua Sun. Sun worked on this project as a doctoral student at U-M and is now a Courant Lecturer at New York University.

“The mathematics behind this problem are actually quite simple,” Sun said.

That simple math enabled the team to combine their new data with existing data sets on mouse brains. The challenge, Sun said, was making sure that how they combined that data was done in a manner that was consistent with biology and neurology. So long as that standard is upheld, the team’s computational approach could be applied to human data gleaned from EEG, PET and MRI scans, he said.

“The way we detect human brain activity is more coarse-grained than what we see in our study,” Sun said. “But the method we introduced in this paper can be modified in a way that applies to that human data. You could also adapt it for other animal models, for example, that are being used to study Alzheimer’s and Parkinson’s. I would say it’s quite transferable.”

On a more personal note, the team dedicated this study to Steven Brown, a colleague who died in a plane crash during the project.

“Steve was a perfect collaborator,” Forger said.

Brown is a senior co-author on the new study and was a professor and section leader for chronobiology and sleep research at the University of Zurich.

“We learned how important one person can be in scientific research, be it in brainstorming or in bridging ideas and concepts. Steve was a core element of this collaboration,” Kompotis said. “It is yet another reason for us to be very proud of this story.”