The Allen Institute for Brain Science announced Wednesday that Microsoft co-founder Paul Allen had donated $300 million to launch an effort to map the brain’s basic circuitry of perception. The Seattle-based nonprofit institute plans to build over the coming decade a series of “brain observatories,” computational tools designed to map all aspects of neural behavior. The aim is to systematically explore the roots of vision and decision-making by analyzing the billions of cells and synapses in the brain’s cerebral cortex, which plays a critical role in vision, memory, language and awareness.

“They want to really characterize the parts list of the brain and map all its circuits to see how they connect and communicate,” said neurobiologist Ed Boyden at the Massachusetts Institute of Technology. “It is impossible for an ordinary lab group to bring all these pieces together.”

The Allen Institute has made a name for itself by developing new technology for basic brain research, then making it freely available to scientists around the world. “They are trying to bring something new and a little different to the understanding of how the brain works,” said neuroscientist Stephen Smith at Stanford University Medical School. Last April, for example, the institute released a $55 million computerized atlas that combines many different imaging techniques to document human brain structure, biochemistry and genetics, along with new computational tools to analyze the data. So far, it has been adopted by 4,000 scientists to probe the brain’s biology.

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By laying bare the basic mechanisms of thought, the institute’s work could eventually yield clues to conditions such as Alzheimer’s disease and autism and mental disorders like depression. “Our dream is to uncover the essence of what makes us human,” Mr. Allen said. “There is really no greater challenge with a potentially more huge impact than understanding how brains work.” He added: “I have been touched by the impact of neurodegenerative disease. My mother has Alzheimer’s.”

The brain is the ultimate computer, with so many cells and synapses and such intricate circuitry that it defies conventional analytical tools. Neuroscience offers a way to use new computer technology and advanced software—Mr. Allen’s area of expertise—to drive basic biomedical advances.

Mr. Allen has given $500 million to the institute, including Wednesday’s donation. His new grant will fund the first four years of the 10-year research project; then the institute will have to find new funding. Generally, the institute has raised about 20% of its annual funding from other sources.