Scientists create first complete brain-wide activity map during decision-making
Researchers from the International Brain Laboratory have unveiled the first brain-wide activity map showing how decision-making unfolds across the entire brain in mice at single-cell resolution. The comprehensive study recorded from over 621,000 neurons across 279 brain areas, revealing that decision-making is distributed across many regions in a highly coordinated way.
Brain-wide map showing 75,000 analysed neurons, each dot is linearly scaled according to the raw average firing rate of that neuron up to a maximum size. © Dan Birman, International Brain Laboratory
An international consortium of neuroscientists has achieved a milestone in brain research by creating the first comprehensive activity map showing how decision-making unfolds across the entire brain. The International Brain Laboratory (IBL) researchers published their findings in two papers in Nature on 3 September 2025, revealing insights into how decision-making occurs at the resolution of single cells across 279 brain areas, representing 95% of the mouse brain volume.
Unprecedented scale challenges traditional views
The research team recorded from over 621,000 neurons across mice in 12 laboratories, using state-of-the-art Neuropixels probes to measure brain activity whilst mice performed a sophisticated decision-making task. The scale represents a quantum leap from previous neuroscience studies, which typically examined brain regions in isolation.
“This is the first time anyone has produced a full, brain-wide map of the activity of single neurons during decision-making. The scale is unprecedented as we recorded from over half a million neurons across mice in 12 labs, covering 279 brain areas, which together represent 95% of the mouse brain volume. The decision-making activity, and particularly reward, lit up the brain like a Christmas tree,” explained Professor Alexandre Pouget, Co-Founder of IBL and Group Leader at the University of Geneva.
The findings challenge the traditional hierarchical view of brain information processing. Neural correlates of some variables, such as reward and action, were found in many neurons across essentially the whole brain. By contrast, correlates of other variables, such as the input stimulus, could be decoded from a narrower range of regions and significantly influenced the activity of fewer individual neurons.
Complex task reveals distributed processing
The research employed an elegant behavioural paradigm where mice learned to respond to visual stimuli appearing on either side of a screen by turning a wheel. The task required sensory, motor and cognitive components, with stimulus probability changing in blocks between 20:80% and 80:20% ratios, forcing mice to integrate prior expectations with sensory information.
Representations of visual stimuli transiently appeared in classical visual areas after stimulus onset and then spread to ramp-like activity in a collection of midbrain and hindbrain regions that also encoded choices. Neural responses correlated with impending motor action almost everywhere in the brain. Responses to reward delivery and consumption were also widespread.
International collaboration drives breakthrough
The achievement was made possible by an unprecedented level of international coordination. Officially launched in 2017, IBL introduced a new model of collaboration in neuroscience that uses a standardised set of tools and data processing pipelines shared across multiple labs, ensuring data reproducibility.
“We’d seen how successful large-scale collaborations in physics had been at tackling questions no single lab could answer, and we wanted to try that same approach in neuroscience. The brain is the most complex structure we know of in the universe and understanding how it drives behaviour requires international collaboration on a scale that matches that complexity,” commented Professor Tom Mrsic-Flogel, Director of the Sainsbury Wellcome Centre at UCL and one of the core members of IBL.
Prior expectations reshape brain activity
The second Nature paper revealed equally striking findings about how the brain encodes prior expectations. The researchers found that mice estimate this prior probability and thereby improve their decision accuracy. Furthermore, they report that this subjective prior activity is encoded in at least 20% to 30% of brain regions that, notably, span all levels of processing, from early sensory areas (the lateral geniculate nucleus and primary visual cortex) to motor regions (secondary and primary motor cortex and gigantocellular reticular nucleus) and high-level cortical regions (the dorsal anterior cingulate area and ventrolateral orbitofrontal cortex).
The second paper showed that prior expectations, our beliefs about what is likely to happen based on our recent experience, are encoded throughout the brain. Surprisingly, these expectations are not only found in cognitive areas, but also brain areas that process sensory information and control actions. For example, expectations are even encoded in early sensory areas such as the thalamus, the brain’s first relay for visual input from the eye.
Methodological rigour ensures reproducibility
The collaboration’s commitment to rigorous methodology distinguished this work from previous studies. “The efforts of our collaboration generated fundamental insights about the brain-wide circuits that support complex cognition; this is really exciting and a major step forward relative to the ‘piecemeal’ approach (1-2 brain areas at a time) that was previously the accepted method in the field. Moreover, our team took rigor and reproducibility very seriously. We developed an entire task force that leveraged our unique, multi-lab approach to determine the extent to which our efforts at standardisation enhanced reproducibility,” commented Dr Anne Churchland, Professor of Neurobiology at UCLA and core IBL member.
After recordings, probe tracks were reconstructed using serial-section two-photon microscopy, and each recording site and neuron was assigned a region in the Allen Common Coordinate Framework. This meticulous approach ensured precise anatomical localisation of neural activity patterns.
Clinical implications for neurological conditions
The research holds particular promise for understanding neurological and psychiatric conditions. These findings could have implications for understanding conditions such as schizophrenia and autism, which are thought to be caused by differences in the way expectations are updated in the brain.
This widespread representation of the prior activity is consistent with a neural model of Bayesian inference involving loops between areas, as opposed to a model in which the prior activity is incorporated only in decision-making areas. This understanding could inform therapeutic approaches for conditions where prediction and expectation processing are disrupted.
Data availability accelerates discovery
True to their commitment to open science, the researchers have made their entire dataset publicly available. “It’s immensely gratifying to see the IBL deliver the first brain-wide map of neural activity with such high spatial and temporal resolution. The map describes the activity of over 650,000 individual neurons with single-spike resolution. This activity underlies the brain’s sensory and motor activity that constitutes a decision. The map is a fantastic resource that is already being mined by myriad scientists, and yielding unexpected discoveries,” commented Dr Matteo Carandini, Professor of Visual Neuroscience at UCL and core IBL member.
All data from these studies, along with detailed specifications of the tools and protocols used for data collection, are openly accessible to the neuroscience community for further analysis and research. This open availability of data promises to accelerate discoveries across multiple research groups worldwide.
Future directions and expanding scope
The team envisions broader applications of their collaborative model. “The brain-wide map is undoubtedly an impressive achievement, but it marks a beginning, not the grand finale. The IBL has shown how a global team of scientists can unite, pushing each other beyond comfort zones into uncharted territories no single lab could reach alone,” commented Tatiana Engel, Associate Professor at Princeton University and core IBL member.
Looking ahead, the team at IBL plan to expand beyond their initial focus on decision-making to explore a broader range of neuroscience questions. With renewed funding in hand, IBL aims to expand its research scope and continue to support large-scale, standardised experiments.
The research represents a paradigm shift towards understanding the brain as an integrated system rather than a collection of specialised modules. By revealing the distributed nature of cognitive processes, these findings lay the groundwork for developing more sophisticated models of brain function and dysfunction, potentially leading to more effective treatments for neurological and psychiatric disorders.
The research was supported by grants from Wellcome, the Simons Foundation, The National Institutes of Health, the National Science Foundation, the Gatsby Charitable Foundation, and the Max Planck Society and Humboldt Foundation.
References
- International Brain Laboratory. (2025). A brain-wide map of neural activity during complex behaviour. Nature. https://doi.org/10.1038/s41586-025-09235-0
- Findling, C., Hubert, F., International Brain Laboratory, et al. (2025). Brain-wide representations of prior information in mouse decision-making. Nature. https://doi.org/10.1038/s41586-025-09226-1
