BrainScope: Visualizing the human brain

January 31, 2017

A new open-source tool called BrainScope harnesses powerful data from the Allen Institute for Brain Science on both the adult and developing human brains as the basis for an interactive visualization tool. The tool is profiled in a publication this week in the journal Nucleic Acids Research.

Created by scientists at the Delft University of Technology and the Leiden University Medical Center in the Netherlands, BrainScope links data on genes with anatomical data from different samples across developmental time periods to create a powerful way of visualizing data on the human brain.

“We are thrilled that researchers are taking our open data and finding ways to move forward with it, creating even more open-source applications that allow users to get as much as possible out of the data,” says Michael Hawrylycz, Ph.D., Investigator at the Allen Institute for Brain Science.

The Allen Institute has collected and shared robust human gene expression data in the Allen Human Brain Atlas and the BrainSpan Atlas of the Developing Human Brain, both available through the portal. 

Many current analysis tools, including the AGEA tool from the Allen Institute, focus on gene similarities and differences within given regions of the brain. Understanding how gene expression varies across regions is also a crucial part of the picture.

BrainScope uses a clustering technique called t-SNE to create maps that show the relationships between genes across the entire brain, and at different developmental time points. The tool is highly interactive and allows users to explore the data in many different ways.

By presenting the data in this highly visual way, scientists hope to build on the resources from the Allen Institute to open new avenues to hypothesis- and data-driven research on the human brain.

For more information, visit the BrainScope website and watch their tutorial videos on YouTube. The Allen Institute’s publicly available resources can be found at