News Release

See a 3D mouse brain with single-cell resolution

Peer-Reviewed Publication

Cell Press

The Allen Mouse Brain Common Coordinate Framework

video: The Allen Mouse Brain Common Coordinate Framework, (CCFv3), a 3D reference atlas, is based on an average of the inherent fluorescence in the brains of mice imaged using serial two-photon tomography. view more 

Credit: Allen Institute for Brain Science

A manually constructed 3D atlas offers a cellular-level view of the entire mouse brain. Presented May 7 in the journal Cell, this reference brain, called the Allen Mouse Brain Common Coordinate Framework (CCFv3,, is derived from serial two-photon tomography images of 1,675 mice.

"We hope the wider neuroscience community will use it as a new standard reference atlas," says co-senior author Lydia Ng (@2queues) of the Allen Institute for Brain Science. "By making our atlas and related tools open access, new data and data types generated across our community can be more easily integrated and compared in the same spatial context, and the atlas in turn can be modified as our knowledge about brain structure evolves."

"Reference atlases are truly multi-purpose tools that are used for teaching neuroanatomy, providing common nomenclature to identify brain regions, supporting analyses to describe where data was collected, and representing our collective current knowledge on the organization of brain structure," says co-senior study author Julie Harris of the Allen Institute for Brain Science.

Historically, the development and refinement of brain atlases have co-evolved with advances in the field of neuroanatomy. Knowledge of mouse brain neuroanatomy has advanced dramatically over the past decade, with the advent of whole-brain mapping projects adding new data types and revealing cellular architecture in rich new detail.

"Modern digital reference atlases must evolve to stay current," Harris says. "Yet classic standard atlases do not meet the demands of these cellular-resolution datasets in 3D. So, we produced a truly 3D atlas to serve as a standard anatomical framework for the whole-brain datasets being produced."

Aligning different types of datasets into CCFv3 allowed the researchers to label more than 800 brain structures. By doing so, the researchers identified several brain structures not previously described in standard mouse brain atlases, and several new nerve fiber tracts not described in other atlases.

"Given that each dataset reveals a unique labeling pattern for certain mouse brain regions, combining all these data types should complement or confirm each other, demonstrating a tremendous methodological advantage for accurately defining brain structures," Ng says.

The authors say that CCFv3 has higher spatial resolution than any currently existing 3D mouse brain reference space based on magnetic resonance imaging. Because CCFv3 is an average from a large population of mice, it can be used to study inter-individual variability in the volumes of 3D brain structures in the context of different disease states. In addition, many anatomical details were apparent in the average brain that were not readily discernable in any single mouse brain.

"We are now using this atlas as the common anatomical reference space for many large-scale projects, including whole-brain circuit mapping, single-cell reconstructions, and the generation of a comprehensive brain cell-type census," Harris says. "All these data, and what we learn about brain architecture in turn, will at some point necessitate an updated, next-generation 3D atlas, although it is likely to be constructed with different, more automated, data-driven methods."


This work was funded by the Allen Institute for Brain Science and in part by National Institutes of Health.

Cell, Wang, Ding, and Li et al.: "The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas"

Cell (@CellCellPress), the flagship journal of Cell Press, is a bimonthly journal that publishes findings of unusual significance in any area of experimental biology, including but not limited to cell biology, molecular biology, neuroscience, immunology, virology and microbiology, cancer, human genetics, systems biology, signaling, and disease mechanisms and therapeutics. Visit: To receive Cell Press media alerts, contact

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.