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Allen Institute kicks brain wave recording into overdrive with Neuropixels probe

Alan Boyle
Severine Durand and Tamina Ramirez, researchers at the Allen Institute for Brain Science, review data collected from mice using the Neuropixels brain-probing system. (Allen Institute Photo)

Seattle’s Allen Institute for Brain Science is sharing 70 trillion bytes’ worth of data documenting electrical activity in mouse brains, collected by a new type of silicon probe that can monitor hundreds of neurons simultaneously.

The Neuropixels system, developed by an international collaboration that includes the Allen Institute, could be adapted to record brain activity in human patients as well, said Josh Siegle, a senior scientist at the institute who works with the probes.

“The application I’m most interested in is decoding the communication patterns of the brain, and really understanding how information is transmitted between regions,” Siegle told GeekWire. “What are the transmission protocols?”

Neuropixels has already produced insights into the brain’s inner workings, Siegle said. This week, the institute is due to publish findings on the BioRxiv preprint server that confirm hierarchical patterns of connectivity in the brain.

The key advance has to do with the hundreds of electrodes that are built into the brain-reading system’s needle-like probes.

Each of the six probes on the institute’s system is about as thin as a human hair (70 microns) and measures less than a half-inch (10 millimeters) in length. But each probe contains 960 electrodes that can pick up electrical activity from networks of brain cells with sub-millisecond precision once they’re implanted. Siegle said more than 370 readings can be recorded by each probe at any given time.

A single Neuropixels probe consists of a needle-like shank (barely visible at lower right) that’s connected to the system’s electronics. The technology was developed at IMEC, an international nanoelectronics research center in Belgium, with the help of a team including the Howard Hughes Medical Institute, the Allen Institute for Brain Science, University College London, the Gatsby Charitable Foundation and Wellcome. (IMEC Photo)

“Previously, because the tools were limited, we were only recording from one area of the brain at a time,” he said in a news release. “But it’s really the interactions between many areas that generate perceptions and decisions and all the other complex actions our brains allow us to do.”

Siegle said the Allen Institute’s first Neuropixels study is based on more than 50 experiments conducted on mice. The experiments focused on interconnections involving six regions of the visual cortex plus two other areas of the brain, the hippocampus and the thalamus.

Thanks to Neuropixels, researchers were able to monitor the symphony of electrical impulses that spread across the brain as the lab mice processed a variety of images and videos — including the opening scene of Orson Welles’ 1958 classic film, “Touch of Evil.”

The same visuals were used in earlier experiments to study visual processing. “We wanted to keep the stimuli as similar as possible to what was used in our imaging experiments, so we could try to make as direct as possible a comparison between the Neuropixel recordings and the imaging data,” Siegle explained.

Each experiment monitored the activity of thousands of neurons, adding up to a data set that documents how 100,000 brain cells behave. That’s still just a small fraction of the 75 million neurons in the mouse brain, but it’s a huge step forward from the neuron-by-neuron monitoring methods that have been used in the past.

“There are a vast number of neurons in this data set whose activity has never been seen by a human eye,” said Christof Koch, chief scientist and president of the Allen Institute for Brain Science. “These data are unprecedented — and we’re releasing them publicly and in a standardized format to that anybody on the planet can use them for their own discovery.”

The Neuropixels system uses multiple probes to monitor the electrical activity of well more than 1,000 neurons simultaneously. (Allen Institute Photo)

Outwardly, the Neuropixels device looks similar to another brain-monitoring system that’s been developed by Neuralink, a venture backed by billionaire Elon Musk. But Siegle said Neuropixels is designed for a completely different purpose.

“Neuralink optimized their technology for implanting in human surgical patients — people who have quadriplegia and can’t move their limbs, and they need a direct interface to their brain in order to be able to move a robot arm and regain control over their limbs, potentially,” he said. “The Neuropixels probes were optimized specifically as a device for scientific research.”

Today’s data release also adds transcriptional data from about 75,000 mouse brain cells and 50,000 human brain cells to the Allen Cell Types Database. The database for mouse cell types now completely covers the brain’s cortex and hippocampus, sampling 25 different regions in all.

“These data cover areas of the brain that, in humans, play roles in conditions ranging from Alzheimer’s disease to psychiatric disorders,” said Hongkui Zeng, executive director for structured science at the Allen Institute for Brain Science. “Defining the cell types in these regions is an important first step to better understanding the origins of brain disease.”

But wait … there’s more: The data release includes the first readings from customized “octopatch” rigs of electrodes that let researchers monitor electrical patterns from up to eight neurons at a time.  The method provides another avenue for studying the connections between neighboring neurons.

“These experiments allow us to go beyond understanding the individual cell types to understanding the signals that are passed between these cells, which will in turn help us better define the cell types themselves,” said Gabe Murphy, associate director of electrophysiology at the Allen Institute for Brain Science.

The Allen Institute was launched in 2003 with a $100 million commitment of support from Microsoft co-founder Paul Allen. Since then, it has expanded its open-science operations, thanks to additional contributions from Allen as well as support from other private donors, foundations and government agencies. Allen passed away one year ago this week, at the age of 65.

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