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An unprecedented brain map reveals how thousands of neurons in a mouse connect while processing images, in a reconstruction that combines technology, artificial intelligence, and a rare volume of data about the visual cortex.
A fragment of a mouse’s brain allowed scientists to produce what researchers describe as the largest functional map of an animal brain made so far.
The work reconstructed, in three dimensions, part of the communication network between about 84 thousand neurons and approximately 524 million synapses, the junctions through which nerve cells transmit signals.
The research is part of the MICrONS project, an acronym for Machine Intelligence from Cortical Networks, and was published in the Nature journal on April 9, 2025.
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The analyzed sample was about one cubic millimeter of brain tissue, a volume often compared by researchers to the size of a small seed.
Even restricted to a fraction of the animal’s visual cortex, the map revealed a structure with dense branches, overlapping connections, and colorful circuits in different layers.
The visualization led scientists involved in the project to compare the result to images of galaxies, due to the number of connections gathered in a microscopic space.
The aim of the study was not just to reconstruct a detailed image of the brain tissue.
The team sought to relate the physical structure of the connections with the activity of the neurons during image processing.
In other words, the researchers tried to observe not only how the cells were connected but also how they responded to visual stimuli.
Mouse watched videos during brain experiment
One of the most well-known stages of the study involved a mouse awake in front of videos.
The animal watched short scenes from movies, sports, animations, and nature, including clips from “The Matrix,” while scientists recorded the activity of neurons in the visual cortex.
To monitor this brain response, the researchers used a genetically modified mouse so that certain neurons would glow when active.
With the aid of microscopy, the team observed which cells reacted to the stimuli displayed on the screen and how different neuronal groups participated in processing the images.
This phase was conducted by scientists from Baylor College of Medicine in the United States.
After recording the brain activity, the analyzed tissue was sent to the Allen Institute in Seattle, where it underwent a preparation process for microscopic reconstruction.
The material was cut into tens of thousands of extremely thin slices, each much thinner than a human hair.
This step allowed researchers to observe, in sequence, the layers of brain tissue and reconstruct the path of cells and their connections.
3D Brain Map Shows Connections Between Neurons
With electron microscopes, the team produced high-resolution images of the slices.
The volume of data generated was used to identify axons, dendrites, and synapses, essential structures for communication between neurons.
Axons carry signals to other cells, while dendrites receive some of this information.
Synapses function as contact points between neurons, allowing signals to pass through chemical and electrical processes.
The next stage involved scientists from Princeton University.
They used artificial intelligence and machine learning techniques to trace the path of cells through the image layers and reconstruct the network in three dimensions.
According to Forrest Collman, a researcher at the Allen Institute and one of the project leaders, the map can evoke the same sensation as observing astronomical images.
“It definitely inspires a sense of wonder, just like looking at images of galaxies,” he said, commenting on the complexity found in such a small area of the brain.
The reconstruction includes more than 200,000 cells, including the mapped neurons, and about half a billion synaptic connections.
According to the researchers, if the identified microscopic wiring were stretched in a straight line, it would reach about 5.4 kilometers.
Connectomics helps investigate brain circuits
The brain relies on the constant exchange of signals between nerve cells.
This process is linked to functions such as seeing, recognizing movements, interpreting the environment, and responding to external stimuli.
However, knowing the existence of these connections is not enough to understand how entire circuits produce behaviors or perceptions.
Clay Reid, a scientist at the Allen Institute, stated that hypotheses about the functioning of brain cells depend on a basic piece of information: how they are connected.
According to him, understanding this wiring is an important condition for testing explanations about the role of different neurons.
The area that studies this type of mapping is known as connectomics.
Its goal is to describe, with increasing resolution, how cells of the nervous system organize into circuits.
In the case of MICrONS, the differential was combining anatomical reconstruction with functional activity observed while the animal viewed images.
This combination allows researchers to analyze relationships between the form of the connections and the response of the neurons.
Instead of observing only the structure of the tissue or only the activity of the cells, the study brought the two pieces of information closer in the same data set.
Data reveal patterns in the mouse’s visual cortex
Among the points highlighted by the team is the behavior of inhibitory neurons, cells responsible for reducing the activity of other cells.
According to the study’s authors, these neurons did not seem to connect randomly.
The data indicate specific patterns of connection with other cell groups.
This type of observation can help formulate new questions about the organization of brain circuits.
Even so, the researchers do not present the map as a complete explanation of brain functioning.
The study is limited to a specific area of the visual cortex of a single mouse.
The sample, therefore, does not represent the entire brain of the animal nor does it allow direct conclusions about functions such as memory, emotion, consciousness, or language.
The result shows, with a high level of detail, a part of the network involved in visual processing.
Another relevant aspect is that the dataset was made available to the scientific community.
With this, other groups can consult the reconstruction, test new questions, and develop digital models related to the functioning of the visual cortex.
Map can support studies on neurological diseases
The scientists involved in the project treat the map as a basis for future studies, not as an immediate tool for diagnosis or treatment.
The expectation is that such maps will help compare circuits considered healthy with changes observed in neurological diseases and developmental disorders.
The Allen Institute states that understanding connectivity rules can contribute to investigations into conditions such as Alzheimer’s, autism, and addiction.
The relationship between these diseases and specific patterns of brain connection, however, still depends on new research.
Sebastian Seung, a neuroscientist and computer scientist at Princeton, said that the technologies developed by the project can give scientists new ways to identify abnormal connectivity patterns associated with disorders.
The statement refers to the potential of the technique, not to a clinically available application.
The comparison with the Human Genome Project appears in researchers’ statements because both efforts seek to create reference maps.
In the case of the genome, reading the genes paved the way for new lines of research and therapies over the years.
In the brain, the challenge involves three-dimensional structures, cellular activity, and very high data volumes.
Brain sample shows limits and scope of research
The study does not map the entire brain of a mouse.
The research focuses on a specific visual region and a limited sample.
This delimitation is important to avoid interpretations beyond what the data can assert.
Even so, the project offers a way to observe the relationship between brain activity and the physical structure of connections.
The mouse saw images, the neurons responded, the researchers recorded this activity, and then reconstructed the connections between the cells involved in this process.
More than 150 scientists participated in the MICrONS consortium.
The project received funding from the BRAIN Initiative, the United States National Institutes of Health, and IARPA, a U.S. agency dedicated to advanced intelligence research.
For the public, the image of the brain map draws attention due to its visual resemblance to astronomical structures.
For researchers, each colored line represents a connection that can help investigate how the brain transforms visual stimuli into processed information.
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