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Now in stunning, whole-brain resolution: neurons

A new study traced the 3D shape of more than 1700 complete mouse neurons across the entire brain

October 12, 2021

Anna Marie Yanny / Allen Institute

NoneComplete, brain-wide reconstructions of several different types of mouse neurons in 3D. A new study led by researchers at the Allen Institute in collaboration with Wenzhou Medical University and Southeast University in China, captured the detailed complete 3D shapes of more than 1,700 individual neurons in the mouse brain, the largest dataset of its kind to date. Shown here, neurons in the structure known as the claustrum send long processes called axons in a crown-like fashion around the entire circumference of the neocortex. Each color represents a different individual neuron.


If asked to picture a neuron, most of us probably think of a star-shaped cell with an arm that’s only slightly longer than its body — like the standard textbook drawing. We think of it sitting in the brain and using this little arm along with the points of its star-shaped tendrils, technically known as an axon and dendrites, to talk to nearby cells. 

But in reality, a neuron’s axon can be hundreds of times longer than its body, sometimes reaching across the entire brain or all the way down the length of our spinal cord to connect with other cells. If that surprises you, you wouldn’t be the first.  

You can think of an axon like a long, delicate telephone wire running across city blocks and branching into different neighborhoods. We know that axons connect different brain regions so they can communicate, but we don’t know what each individual cell’s role is in that communication, said Staci Sorensen, Ph.D., Associate Director of Neuroanatomy at the Allen Institute for Brain Science, a division of the Allen Institute. Sorensen is one of a team of authors on a recent paper published on Oct. 6th in the journal Nature that describes a new neuron-tracing technique which helped researchers reconstruct the detailed 3D shape of more than 1,700 individual neurons in the mouse brain, the largest dataset of its kind to date. 


“In some regions, a neuron will just touch in and send one branch while in another region, the same neuron will need to send 50,000 branches. I’m curious - Why?” — Staci Sorensen, Ph.D.


This kind of whole-neuron tracing gives us more information than other forms of reconstructing neurons from thin brain slices, which capture important information about the cells' shapes but don’t trace their entire axons. By illuminating an individual neuron’s unique axon connections and branching patterns throughout the brain, scientists can distinguish it from other types of neurons. 

NoneFour full reconstructions of neurons from different regions in the mouse brain. Their arms extend to and communicate with a variety of different areas in the cortex, the brain's outer shell. These neurons are thought to be involved with sensory perception, motion, and learning and memory. 

The paper debuted along with a package of other studies, through a large research collaboration brought together by the National Institutes of Health’s BRAIN Initiative. The goal of the effort was to create a detailed atlas of brain cell types in individual regions of the mammalian brain, and in doing so, Allen Institute teams and collaborators outlined methods and techniques to help scientists map the entire brain one day. The novel form of neuron-tracing highlighted in this article laid the groundwork for many future discoveries. For example, neurons from this mouse study can be linked to molecularly similar neurons in the human brain, allowing researchers to predict what long-range connections our own neurons might be making.

Tracing the entire length of a neuron is trickier than you might think because their axons are so thin, along with being far-reaching and branched in most excitatory neuron types (the kinds of neurons that activate other neurons). It’s the equivalent of tracing a sewing thread the length of a football field (if the football field was full of hundreds of millions of other sewing threads). Traditionally, axons have been studied in groups (think: ‘neural pathways’) or they are cut short by classical brain slicing methods. Even neuroscientists may study a specific neuron type without understanding what it looks like in its entirety, explained Yun Wang, Ph.D., Senior Scientist at the Allen Institute for Brain Science and co-author on the paper. 

“A scientist may have studied a specific region their whole life by just using brain slices,” Wang said. “But they might be curious to know how the whole neuron, the complete neuron looks.”

NoneSeveral different types of neurons shown in position against a rendering of the mouse brain. Reconstructions of multiple cells in a circuit will help neuroscientists better piece together complete neural circuits. These neurons sit in the neocortex, the outermost shell of the mammalian brain. 


Wang, along with Hongkui Zeng, Ph.D., Executive Vice President and Director of the Allen Institute for Brain Science, led a team of researchers and collaborators from the Allen Institute, Wenzhou Medical University and Southeast University in China to map these complete neurons by using a whole brain imaging technique called fMOST. This technology allowed researchers to image entire mouse brains, region by region, and capture dendrites and axons of neurons which had been sparsely labeled with fluorescence (using mice genetically engineered to express fluorescent labels in the brain). The captured images were then traced by researchers using specially designed software tools, yielding different types of the most complete reconstructions of neurons in the mammalian brain. 

Researchers also collected data on the genes expressed in each reconstructed neuron, which may offer clues to each cell’s type and function.   For example, using reconstruction and gene expression data, researchers found that a single neuron, located in a tiny region known as the claustrum, extended its axon around the entire outer shell of the brain in a crown-like fashion to facilitate communication between the brain’s sensory, motor and executive function regions.

NoneA single excitatory neuron colored in red, reaching to communicate with other areas of the brain

Of course, more data, like the detailed shape of individual neurons, only leads to more questions. Researchers find that different types of neurons can have vastly different axon branching patterns and reach different parts of the brain; even those with common molecular features (such as gene expression) can choose very different target regions. 

“In some regions, a neuron will just touch in and send one branch while in another region, the same neuron will need to send 50,000 branches. I’m curious - Why?” Sorensen remarked.

It's a question that hints at where researchers are headed next: Figuring out what the neurons are doing with these long-range connections. Armed with the entire shape of a neuron and its molecular markers, scientists can design experiments to determine why certain cell types are talking to others, and what happens when that communication is ruptured. By preventing individual neurons from communicating normally, scientists can model diseases and bring us closer to understanding how certain neurons and their connections might be involved in disease progression. Full neuron reconstructions from the mouse brain can also give us clues to how similar neurons in the human brain may deliver information.

“It’s a vast treasure trove that brings up a million different questions; the hardest question is figuring out which one to follow up on,” said Sorensen.

The research described in this article was partially funded by awards from institutes under the National Institutes of Health, including award number R01EY023173 from The National Eye Institute, U01MH105982 from the National Institute of Mental Health and Eunice Kennedy Shriver National Institute of Child Health & Human Development, and U19MH114830 from the National Institute Of Mental Health. The content is solely the responsibility of the authors and does not necessarily represent the official views of NIH and its subsidiary institutes.


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