The formation of a brain is one of nature’s most staggeringly complex accomplishments. The intricate intermingling of neurons and labyrinth of connections also make it a particularly difficult feat for scientists to study.

Now, Yale researchers and collaborators have devised a strategy that allows them to see this previously impenetrable process unfold in a living animal — the worm Caenorhabditis elegans, they report Feb. 24 in the journal Nature.

“Before, we were able to study single cells, or small groups of cells, in the context of the living C. elegans, and for relatively short periods of time,” said Mark Moyle, an associate research scientist in neuroscience at Yale School of Medicine and first author of the study. “It has been a breathtaking experience to now be able to watch development unfold for hours, across the entire brain of the organism, and visualize this highly orchestrated dance.”

Moyle works in the lab headed by corresponding author Daniel Colón-Ramos, the Dorys McConnell Duberg Professor of Neuroscience and Cell Biology and senior author of the study.

In collaboration with computational and microscopy scientists, the lab developed novel network algorithms and imaging technologies that allowed them to study complex webs of interconnected neurons in living C. elegans, a common type of roundworm often used in research. Despite its simplicity, it shares key molecular and genetic characteristics with human biology.

The researchers found that interconnected neurons, densely packed into units called neuropils, are organized to sort signals which dictate many functions and behaviors in the organisms. The study details architectural principles in the neuropil structure that determines how functional brain circuits are developed and assembled.

The authors found that neuronal processes and connections in the worm’s brain are organized into layers, each containing modular components of functional circuits that are linked to distinct behaviors.

Then, using high-resolution light sheet microscopy, the researchers were able to track single cells over the course of the organism’s development, providing insights into how these cells help choreograph the assembly of the brain.

“When you see the architecture, you realize that all this knowledge that was out there about the animal’s behaviors has a home in the structure of the brain,” Colón-Ramos said.

For instance, researchers can trace reflex behavior in animals to circuits leading to muscles and how these same circuits integrate with still others to regulate the animal’s movement.

He said the brain is organized like a city such as New York, with areas like Wall Street or Broadway organized to carry out the specific functions of finance and entertainment, respectively.

“Suddenly you see how the city fits together and you understand the relationships between the neighborhoods,” Colon-Ramos said.

The work is the result of a decade long collaboration between the labs of Colón-Ramos and Smita Krishnaswamy of Yale; Hari Shroff of the National Institutes of Health; Zhirong Bao of the Sloan Kettering Institute; and William A. Mohler of the University of Connecticut Health Center. The Colón-Ramos, Shroff, Bao, and Mohler labs are part of the consortium WormGUIDES.