ALLEN Mouse Brain Atlas
Introduction
As the Allen Institute’s inaugural project, the ALLEN Mouse Brain Atlas pioneered large-scale integration of genomic and anatomic data, resulting in a comprehensive genome-wide, three-dimensional map of gene activity throughout the adult mouse brain. Completed in 2006, the Allen Mouse Brain Atlas is now a staple neuroscience resource that is used regularly by thousands of researchers worldwide and has contributed to studies in addiction, obesity, Alzheimer’s disease, multiple sclerosis and more.
About the Atlas
Similar in scale to the Human Genome Project, the Allen Mouse Brain Atlas—the original ALLEN BRAIN ATLAS resource—is a comprehensive genome-wide map of the adult mouse brain revealing where each gene is expressed, or “turned on. This groundbreaking resource has become a fundamental tool for neuroscience research programs worldwide. More than 10,000 unique users from university, government, and pharmaceutical company labs among others access it each month, and it has been cited by hundreds of publications in the peer-reviewed scientific literature.
The Allen Mouse Brain Atlas comprises a vast collection of image-based gene expression data, an integrated anatomic reference atlas of the adult mouse brain custom-drawn by Hong-Wei Dong, M.D., Ph.D., and a suite of sophisticated data search and viewing tools that includes the Allen Institute’s Brain Explorer® 3D viewer. The gene expression data was produced using an industrialized version of a process called in situ hybridization, which pinpoints and marks where a gene is expressed in thin tissue sections, offering microscopic detail down to the cellular level.
The Allen Institute’s high-throughput model and infrastructure for collecting data using an assembly-line approach was initially engineered for the Allen Mouse Brain Atlas project and is now leveraged for our other initiatives. The combination of laboratory robots, automated imaging devices and high-powered computational systems enables the generation of data on an unprecedented scale. Whereas it could take several months to map the expression of a single gene throughout the brain in a traditional research laboratory, approximately 20,000 genes were mapped in three years to create the Allen Mouse Brain Atlas.
Key Features
- Open, public online access
- Image-based data comprising genome-wide coverage
- Comprehensive anatomic coverage of the adult mouse brain
- Microscopic resolution down to the cellular level
- Sophisticated data search and viewing tools
- Interactive Brain Explorer 3D viewer
- Detailed anatomic reference atlas of the adult mouse brain that can be viewed with the data
“ By taking advantage of the data, we can really start identifying the specific circuitry that went astray in a specific disease condition. Neuroscience has been around many decades. But combining the classical approaches of brain research with this new genetic approach is a breakthrough in neuroscience. It’s a new, extremely powerful approach to try to understand the brain. I would say it’s revolutionary. ”