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New Southeast University-Allen Institute Collaboration Uses VR to Capture 3D Shapes of Mouse Neurons

By November 8, 2018No Comments

A new international collaboration between the Allen Institute for Brain Science, a division of the Allen Institute, and Southeast University in Nanjing, China, is tackling the difficult problem of capturing the entire 3D shape of mouse neurons, cell by cell, from the entire animal’s brain.

The new effort, called the SEU-Allen Joint Center for Neuron Morphology or the SEU-Allen Center, is using virtual reality headsets that allow researchers to manually trace the cells’ shapes, or morphologies, in 3D as well as computational analyses to help automate the reconstruction of those morphologies.

“Capturing complete neuron morphologies is very complicated. It takes people a long time to reconstruct each cell,” said Hanchuan Peng, Ph.D., Associate Investigator at the Allen Institute for Brain Science and Director of the SEU-Allen Center. “We want to get to a point where our reconstruction is fully automated and then double-checked by a person.”

Picking out one neuron’s complete shape, with all its delicate and microscopically thin axon fibers entangled with thousands of other neurons in the brain, is a laborious and painstaking process. But working with the entire brain is important in understanding the neurons’ true shapes, Peng said, as the cells are so intertangled and their axons so long that any cut in the brain may sever important pieces of the exact neuron a researcher is trying to reconstruct.

This project is an essential part of understanding how all the cells in the brain are different from each other — and ultimately, how they work to carry out all the brain’s different functions — said Hongkui Zeng, Ph.D., Executive Director of Structured Science at the Allen Institute for Brain Science and one of the leaders of the SEU-Allen Center. The collaboration fits in with the Allen Institute’s efforts to create a comprehensive “periodic table” of all the different types of cells in the mouse and human brains, known as the Allen Cell Types Database.