The Allen Institute for Brain Science, founded more than a decade ago and backed by $500 million from co-founder Paul Allen, said today it has launched a new database that marks a major step towards creating a comprehensive map of the human brain. It’s called the Allen Cell Types Database, and it’s the first initiative in the philanthropist’s 10-year plan to untangle the intricacies of human thoughts and actions—and in so doing, to unlock the mysteries behind some of the brain’s most debilitating diseases.

The Allen Cell Types Database contains information about 240 neurons found in the brains of mice—cells that are similar to those in the human brain. That data includes information about the neurons’ electrical activity and “morphology,” or shape, as well as their location. The idea is for scientists to use the data to understand how normal brains work, which in turn might help them to solve diseases such as Alzheimer’s and Parkinson’s. And it’s not just diseases of cognition that the Allen Institute wants to help cure: The foundation simultaneously released an update to its Ivy Glioblastoma Atlas Project, a tool that provides detailed genetic information about one of the brain’s deadliest cancers.

“This is part of a substantial plan in the global scheme of [brain research],” says Allan Jones, CEO of the Allen Institute, which is based in Seattle. “We want to map the entire brain in terms of cell types.”

The Allen Institute was founded in 2003 with the mission of providing scientific data, free to the public, designed to speed up the understanding of both the healthy and diseased brain. The foundation created several brain atlases, searchable online data warehouses of the spinal cord, the developing human and mouse brains, and more. In 2011, Paul Allen challenged the institute’s scientific leadership to go beyond those atlases and create one massive map showing how individual cell types in the brain create perception—almost like the periodic table in chemistry, but one that gets to the very essence of what makes us human, Jones says.

“We’re trying to really get at how information processing occurs in the brain—the real fundamentals that we don’t understand about how the brain works,” Jones says.

Researchers at the Allen Institute gather recordings from single neurons. (Credit: Photo courtesy of the Allen Institute)


The 240 neurons in the Allen Cell Types Database reflect a tiny fraction of the 86 billion neurons in the human brain, but it’s a good start, Jones contends. The cells come from the mouse visual cortex, which is the part of the brain that creates sight. Scientists will be able to use the data to look at such properties as gene expression, or the proteins produced by individual genes, and electrical signaling between each type of neuron. That could yield important new insights into how the visual cortex processes information.

The foundation plans to add to the database over time, expanding the cell types that are included, and ultimately including human brain cells, as well. (For more on the Allen Cell Types Database, check out the video at the end of this post.)

If the past is any indication, this latest iteration of the open-source brain will likely generate a lot of interest from the scientific community. The Allen Institute’s online atlases attract about 50,000 unique users per month, including scientists from every major pharmaceutical company and academic institution worldwide, Jones reports. At least 5% of users stay an hour or longer mining the data. There is so much demand for Allen’s resources that the institute employs a scientist full-time to do on-site training sessions at academic labs and pharma R&D facilities.

But it’s not just the mysteries of perception—and what can cause it to go awry—that Allen wants to unlock. In 2010, his institute created the glioblastoma atlas, a resource for oncology researchers working in the field of brain cancer. Glioblastoma is one of the most aggressive forms of cancer: Most patients don’t live much longer than a year beyond their diagnosis, and the disease takes about 12,000 lives per year in the U.S. alone. The atlas was designed to provide data about genes found in various areas of glioblastoma tumors, as well as the presumed stem cells that may cause the tumors to form in the first place.

Today’s update expands the glioblastoma atlas from eight tumor samples to 42, each of which is intricately sliced into annotated images that scientists can use to study how the cancer grows and invades healthy brain tissue. The database also includes 270 “transcriptomes,” which are measurements of gene expression within the glioblastoma tumors. “It’s a much richer and more complex database now,” says Ralph Puchalski, a scientific program manager at the Allen Institute.

Stained an annotated cells in the Allen Institute glioblastoma atlas. (Credit: Photo courtesy of the Allen Institute)

Stained and annotated cells in the Allen Institute glioblastoma atlas. (Credit: Photo courtesy of the Allen Institute)

The Swedish Neuroscience Institute in Seattle, which collaborated with the Allen group on the glioblastoma project, has big plans for the newly expanded atlas. A research team there is now drawing up a proposal to deploy the data towards figuring out why some patients in glioblastoma trials respond well to experimental therapies, while others do not respond at all.

There have been many recent advances in glioblastoma treatment, ranging from immunotherapy drugs to highly personalized therapeutic regimens that target genetic mutations. But virtually all of the medicines that are currently used or that are being tested to treat the disease produce wide variations in response, says Nameeta Shah, a research scientist at the Swedish Neuroscience Institute’s Ben and Catherine Ivy Center for Advanced Brain Tumor Treatment. “All of these therapies show some promise, but all of them work only for a subset of patients,” Shah says. “What we’re hoping is to identify those patients—to create a gene signature of them that we could apply retrospectively to patients. The way the atlas helps with this is to show how that signature is influenced by [gene] location.”

The Allen Institute’s Jones says he hopes users of the glioblastoma database and the other atlases will ultimately be able to build on their research by incorporating data from the newly introduced Cell Types Database. “This is the next step,” he says. “What we hope is that knowing as much as we can about individual cell types and how they behave in a normal circuit will allow us to start to understand them in a disease state. The techniques to do this are developing very rapidly.”