Allen Cell Types Database

The Allen Institute for Brain Science is taking the first major scientific step to create a searchable standards database for the brain with the launch of the Allen Cell Types Database.

The first release includes information on just 240 neurons out of hundreds of thousands in the mouse visual cortex, with a focus on the electrophysiology of those individual cells: the electrical pulses that tell a neuron to fire, initiating a pattern of neural activation that results in perception and action.

Link to Allen Cell Types Database Hub


This year Hanchuan Peng (Allen Institute for Brain Science) began the next phase of the effort called BigNeuron. However, rather than a competition, this time the project would be a collaboration.

The key idea is to create a single platform on which all algorithms can be run, compared, and their results combined to form reconstructions better than any one could achieve alone.

Link to BigNeuron Hub

See also Allen Cell Type Data Bases post.

Allen Institute

Allen Institute's mission is to accelerate the understanding of how the human brain works in health and disease. Allen has been a major catalyst and facilitator of The BRAIN Initiative.

Launched in 2003 with a seed contribution from founder and philanthropist Paul G. Allen, the Allen Institute takes on large-scale initiatives designed to push brain research forward, enabling the global scientific community to more efficiently make discoveries that bring real-world utility.

A map of the brain

"How can we begin to understand the way the brain works? The same way we begin to understand a city: by making a map. In this visually stunning talk, Allan Jones shows how his team is mapping which genes are turned on in each tiny region, and how it all connects up."

Filmed July 2011 at TED Global 2011
Uploaded to YouTube on November 10, 2011 by TED

Single Cell Molecular Profiling

A virtual journey through the Allen Institute for Brain Science's single cell molecular profiling program.

Published on September 22, 2014 by Allen Institute for Brain Science

Allen Mouse Brain Connectivity Atlas

A virtual journey through the Allen Mouse Brain Connectivity Atlas.

Published September 19, 2014 by Allen Institute for Brain Science

Allen Institute for Brain Science: Fueling Discovery

Founded by philanthropist Paul G. Allen and Jody Allen, the Allen Institute for Brain Science was established to accelerate the understanding of the human brain, compelled by the need to improve the treatment of brain-related disorders and inspired by our quest to uncover the essence of what makes us human.

Published on October 3, 2013 by Allen Institute for Brain Science

Tutorials: Allen Institute Technical Tours

The twelve videos in this post are tutorials on the various Allen Brain Atlases published between 2011 and 2015.

Hongkui Zeng, PhD – Allen Institute

Senior Director, Research Science
Allen Institute Research and Development

Zeng explores novel technologies and develop high-throughput paradigms for generating large-scale, public datasets and tools to fuel neuroscience discovery. Zeng has broad scientific experience and a keen interest in using a combined molecular, genetic and physiological approach to unravel mechanisms of brain circuitry and potential approaches for treating brain diseases.

Cell Type Characterization Platform

PI: Hongkui Zeng, Allen Brain Atlases
Allen Institute for Brain Science
Title: "Establishing a Comprehensive and Standardized Cell Type Characterization Platform"
BRAIN Category: Census of Cell Types (RFA MH-14-215)

Dr. Zeng's group will characterize cell types in brain circuits controlling sensations, such as vision and emotions, as a first step to better understand information processing across circuits. The data generated will be posted as a public online resource for the scientific community.

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