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Introducing the Allen Brain Observatory

July 13, 2016

Understanding the brain requires more than a census of its genes or a catalog of its parts--we need to watch it in action as it performs the tasks that give rise to activity, perception, cognition and ultimately consciousness.

As part of the suite of tools publicly available on brain-map.org, the Allen Institute for Brain Science has launched the Allen Brain Observatory: the first tool of its kind to provide a highly standardized survey of cellular-level activity in the mouse visual system. With the data and tools in this resource, researchers around the world are empowered to investigate how circuits in the mouse brain coordinate while the mouse performs visual tasks, taking in and processing a wide range of visual stimuli.

“The Allen Institute is known for our atlases—deep, high quality data sets revealing where genes are expressed and how cells and connections are arranged in the mouse and human brain,” says Allan Jones, Ph.D., CEO of the Allen Institute. “With the Allen Brain Observatory, we’ve taken an important leap into measuring natural brain activity as it is actually happening.”

“The Allen Brain Observatory is a stunning window into the visual brain of the mouse,” says Christof Koch, Ph.D., President and Chief Scientific Officer of the Allen Institute for Brain Science. “No one has ever taken this kind of standardized approach to surveying the active brain at cellular resolution in order to measure how the brain processes information in real time. This is a milestone in our quest to decode how the brain’s computations give rise to perception, behavior, and consciousness. Just like in astronomy, modelers and theoreticians worldwide can now study this wealth of data using their own analysis tools.”

The first data in the Allen Brain Observatory survey four areas in the mouse visual cortex at multiple depths, sampling more than 18,000 neurons in total. The mice were presented with a large variety of visual stimuli to determine the “tuning,” or preference, of each individual cell to visual features like motion and shape orientation, as well as complex images like natural scenes and movies that reveal integrative dynamics of visual processing.

The data from thousands of individual cells and populations of cells are presented in a novel visualization format through the Allen Brain Atlas data portal, and are accompanied by analysis tools and access to all raw data, which allows scientists to deeply explore the rules that govern how networks of cells in the visual cortex communicate. 

More than 100 people at the Allen Institute were involved in the creation of the Allen Brain Observatory, from animal care technicians to neuroscientists, engineers, microscopy experts, optical physiologists, physicists, mathematicians and computer scientists.

Learn more about the Allen Brain Observatory in our press release, or visit the Allen Brain Observatory at brain-map.org.

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