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Brain atlas gets printed … all 350 pages’ worth

Image: Human brain atlas
These are just a few of the brain images that appear in a newly published atlas of the human brain. (Credit: Allen Institute for Brain Science)

As neuroscience marches on, researchers are creating more and more brain mapsand atlases – but the Allen Human Brain Reference Atlas is a rarity. This week it’s actually being published as a 350-page atlas you can hold in your hands.

Like most brain references, the detailed map of a single human brain is available online. The Allen Institute for Brain Science’s reference atlas shows brain structure down to the cellular level, at a resolution of 1 micron per pixel. The anatomical map, based on trillions of bytes of imaging data, is supplemented by readings from two different types of brain scans.

This sort of atlas usually stays online. In contrast, the illustration-heavy Comprehensive Cellular-Resolution Atlas of the Adult Human Brain takes up pretty much all of the latest issue of the Journal of Comparative Neurology.

“It’s actually a highly unusual publication. … We’re pretty much lacking in structural maps of the human brain,” Allen Institute neuroscientist Ed Lein, the study’s senior author, told GeekWire. By some accounts, it could be the first such anatomical map of the full human brain to make its print debut in more than a century.

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Monkey genes shed light on brain mysteries

Image: Monkey brain
A cross-section of the neocortex and cerebellum from an adult rhesus monkey brain has been labeled with a stain that highlights brain cells. (Credit: Allen Institute)

A project led by Seattle’s Allen Institute for Brain Science has mapped out how genes get fired up in key areas of a rhesus monkey’s brain as it develops – and the results could help researchers unlock the mysteries surrounding autism, microcephaly, schizophrenia and other neurological conditions.

The gene expression map, laid out today in research published by the journal Nature, shows that rhesus macaque monkeys are much better models than the usual mice for humans when it comes to brain development. It also confirms the view that different neurological disorders follow dramatically different genetic pathways.

“The sets of genes that turn on early, and the sets of genes that turn on in the adult, shift dramatically,” Allen Institute neuroscientist Ed Lein, the study’s senior author, told GeekWire.

The gene map follows up on earlier work that Lein and his colleagues have done with mice, to track how the brain develops from its fetal stage to adulthood. The Allen Institute has done similar work with adult human brains and fetal brains as well.

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Brain Observatory peers into the minds of mice

Brain Observatory research
Senior scientist Jerome Lecoq and research associate Kate Roll inspect a microscope platform from the Allen Brain Observatory that was used to record real-time cellular activity in the visual cortex of mice as they were shown pictures and movies. (Credit: Allen Institute)

The Allen Brain Observatory is open for business, revealing what’s running through the mind of a mouse as it sees patterns of light and dark, pictures of butterflies and tigers – or even the opening scene of Orson Welles’ 1958 classic film, “Touch of Evil.”

The online repository of 30 trillion bytes’ worth of brain-cell readings represents the latest scientific offering from the Allen Institute for Brain Science, funded by Microsoft co-founder Paul Allen. It follows through on a $300 million pledge that Allen made more than four years ago.

The Allen Institute’s president and chief scientific officer, Christof Koch, has compared the project to a Hubble Space Telescope for the brain.

“No one has ever taken this kind of industrial approach to surveying the active brain at cellular resolution in order to measure how the brain processes information in real time,” Koch said today in the institute’s announcement of the data release. “This is a milestone in our quest to decode how the brain’s computations give rise to perception, behavior and consciousness.”

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Scientists join forces to study aging brains

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This brain tissue has undergone antibody labeling for the Aging, Dementia and TBI Study. Dark brown spots are amyloid plaques, implicated in Alzheimer’s Disease. (Credit: Allen Institute)

Scientists from Seattle’s Allen Institute for Brain Science, the University of Washington and Group Health Research Institute have put together a first-of-its-kind database of brain imagery and medical data, to help unravel the potential links between brain injuries, aging and dementia.

The database for the Aging, Dementia and Traumatic Brain Injury Study is hosted at the Allen Institute’s Brain-Map.org website. For years, the institute has been mapping the connections between brain function and gene expression, but this database goes way beyond genetics.

The study’s brain samples come from a bigger study called Adult Changes in Thought. That longitudinal research effort, led by Eric Larson and Paul Crane of the Group Health Research Institute and UW, looks at health records and cognitive assessments from thousands of aging adults.

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Semantic Scholar dives into scientific search

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Oren Etzioni, CEO of the Allen Institute for Artificial Intelligence, scribbles on a whiteboard to illustrate who’s connected to whom in research. (Geekwire photo by Alan Boyle)

Baseball players are judged by their batting averages, RBIs, ERAs and other statistics voluminous enough to fill a scorecard. But how do you rate researchers?

The classic measure is citations: that is, who’s quoting whom in their research papers. But just as in baseball, the statistics are becoming more nuanced. NowSemantic Scholar, a scientific search engine developed at Seattle’s Allen Institute for Artificial Intelligence, is introducing a whole new set of stats.

If you’re in the “publish-or-perish” game, get ready to find out how you score in acceleration and velocity. Get ready to find out who influences your work, and whom you influence, all with the click of a mouse.

“We give you the tools to slice and dice to figure out what you want,” said Oren Etzioni, CEO of the Allen Institute for AI, a.k.a. AI2.

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Scientists straighten out a tangle of brain cells

Image: Brain neurons
This graphic traces a network of cortical neurons from a trillions of bytes’ worth of 3-D data. Some of the neurons are color-coded according to their activity patterns in the living brain. (Credit: Clay Reid, Allen Institute; Wei-Chung Lee, Harvard Medical School; Sam Ingersoll, graphic artist)

Scientists say they’ve analyzed trillions of bytes’ worth of mapping data from the brain of a mouse to trace the connections within a tangle of neurons that’s smaller than a pinhead.

The results, published today in the journal Nature, mark a preliminary step toward an even more ambitious neuron-mapping project called MICrONS.

“This is the culmination of a research program that began almost 10 years ago,” study co-author R. Clay Reid, senior investigator at the Allen Institute for Brain Science, said in a news release. “Brain networks are too large and complex to understand piecemeal, so we used high-throughput techniques to collect huge data sets of brain activity and brain wiring.”

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Big project aims to build a bit of a virtual brain

Image: Neuron network
This image shows a network of neurons reconstructed with large-scale electron microscopy. (Credit: Clay Reid, Allen Institute / Wei-Chung Lee, Harvard Medical School / Sam Ingersoll)

Seattle’s Allen Institute for Brain Science is in on a multimillion-dollar campaign to trace the connections between the neurons in a mouse’s brain and figure out what they do, well enough to create a 3-D wiring diagram.

The five-year project – backed by the federal government’s Intelligence Advanced Research Projects Activity, or IARPA – is aimed at reverse-engineering the way the brain processes information. The project is called Machine Intelligence From Cortical Networks, or MICRONS.

“The reason IARPA is funding this is not merely to get a better understanding of the brain, but to get inspiration from biology to do the next iteration of machine learning,” R. Clay Reid, the Allen Institute’s principal investigator for the project, told GeekWire.

IARPA is the U.S. intelligence community’s equivalent of the Pentagon’s DARPA think tank, and you can assume that the new types of artificial intelligence programs inspired by MICrONS could help give the United States an edge when it comes to analyzing data for national security purposes.

At the same time, neuroscientists will benefit from seeing how neurons work together in unprecedented detail. “It’s absolutely a win-win situation,” Reid said.

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Scientists list brain’s common gene patterns

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An image from the Allen Brain Explorer shows gene expression across the human brain. (Credit: Allen Institute for Brain Science)

Researchers say they’ve traced 32 of the most common genetic patterns at work in the human brain, as part of a mapping project that could lead to new insights about Alzheimer’s and other diseases.

“We’re really trying to understand the genetic basis for the architecture of the human brain,” said Ed Lein, a researcher at the Allen Institute for Brain Science and one of the authors of a study published online on Monday by Nature Neuroscience.

Lein told GeekWire that the study, based on data from the Allen Human Brain Atlas, demonstrates “we’re really much more similar than we are dissimilar” when it comes to the genetic code for our brain’s wiring. The genes that are most consistently associated with specific regions of the brain include some associated with Alzheimer’s, Parkinson’s and Huntington’s disease, as well as epilepsy and disorders associated with cocaine and nicotine use.

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