Detailed atlases of the human, monkey, rat and mouse brain

EBRAINS offers detailed atlases for the human, macaque monkey, rat, and mouse brain. These atlases provide comprehensive maps of brain regions defined based on structure, function and neural connections. As spatial reference systems for neuroscience, they are essential for understanding the complexity of the healthy brain, studying brain disorders and seeking to develop new treatments. These services are being further developed in the framework of the EBRAINS 2.0 project.

Launch 3D atlas viewer
Tools and software

Featured Tools

See all tools

Human Brain Atlas

The EBRAINS multilevel human brain atlas provides detailed information on anatomy, connectivity, and function. It links macroanatomical concepts and their intersubject variability with measurements of the microstructural composition and intrinsic variance of brain regions.

Mouse Brain Atlas

The Allen mouse brain atlas is a comprehensive digital resource that provides detailed information on the structure and function of the mouse brain. A wide range of structural and functional experimental data mapped to the Allen mouse brain atlas are shared via the EBRAINS research infrastructure.

Multilevel Macaque Monkey Brain Atlas

The EBRAINS Macaque Monkey Brain Atlas is a comprehensive resource that provides in-depth insights into the anatomy, connectivity, and functions of the macaque monkey brain. It includes detailed information about the organization of the monkey brain at multiple levels, ranging from the microscopic level to the macroscopic level of the entire brain.

Rat Brain Atlas

The Waxholm Space rat brain atlas is a detailed volumetric atlas of the rat brain, to which a wide range of anatomical and functional data have been registered, including detailed data showing cellular distributions, axonal pathways, and gene expression patterns. EBRAINS provides a visualization interface, enabling researchers to explore and compare different aspects of the rat brain in 3D space.

Data integration into a brain atlas

The first step of integrating neuroscience data is to relate them to a common anatomical location. Image data can be spatially aligned with a 3D reference atlas using linear or non-linear deformations. The transformations needed to bring the atlas and images into spatial registration are stored as spatial metadata.

Learn more

Analysis of data in atlas space

By spatially registering images to a 3D atlas, analyses can be performed based on regions of interest specified by the atlas maps.

Learm more
Brain areas of the human brain as displayed in the EBRAINS Human Brain Atlas

Brain Atlas Resources

We offer tutorials, documentation and other digital tools and resources to support researchers using the EBRAINS brain atlases.

See all Brain Atlas Resources

Featured News

See all news
Julich Brain Atlas

New release of the Julich Brain Atlas adds 52 new maps

Release 3.1 of the Julich Brain Atlas has been published and can be freely downloaded through the EBRAINS research infrastructure. The updated brain atlas now gives online access to 52 new probability maps of cortical and subcortical structures in a three-dimensional reference space. Programming interfaces for the computational neurosciences simplify the integration of the data into brain models.

Read more

New Unified Mouse atlas from the KIM lab is now available in the EBRAINS QuickNII image registration tool

New Unified Mouse atlas from the KIM lab is now available in the EBRAINS QuickNII image registration tool

The EBRAINS atlas registration tool QuickNII now incorporates a new mouse brain atlas, providing the community with new opportunities for analysis of their rodent image data in atlas space.

Read more

EBRAINS Brain Atlas enables researchers to gain a deeper understanding of brain organization

EBRAINS Brain Atlas enables researchers to gain a deeper understanding of brain organization

The study demonstrates a method to unravel structure-function relationships by using the multilevel Julich-Brain Atlas on EBRAINS to bridge the different scales of brain organisation. The findings provide insight into the visual, auditory, somatosensory, and motor systems of the brain.

Read more

Complete data package of Julich-Brain Atlas released

Complete data package of Julich-Brain Atlas released

The full dataset of the Julich-Brain probabilistic maps has been published and can be freely downloaded. The data package comprises 148 probability maps in a three-dimensional reference space.

Read more

Featured Resources

See all resources

Create an account

EBRAINS is open and free. Sign up now for complete access to our tools and services.

Register