Analysing the brain with atlases

The Human Brain Project uses a new generation of three-dimensional (3-D) reference atlases as tools for analysing and integrating research data.

The human atlases and one of the rodent atlases (WHS rat brain atlas) are developed and maintained by HBP. The mouse atlas is provided by the Allen Institute.

All atlases are embedded in HBP workflows for data registration, visualisation, and analysis.

The Big Brain   JuBrain   WHS rat brain atlas   Allen Mouse CCF


The Big Brain

A high-resolution whole brain model of the human brain


The BigBrain is a microscopic resolution 3D model of a complete human brain, based on a 3D reconstruction from 7404 digitized histological brain sections (Amunts, Evans et al., Science 2013). It provides a highly detailed anatomical reference space at 20 micrometer (isotropic) spatial resolution. We provide maps of different structures, including neo- and allocortical cytoarchitectonic areas and subcortical nuclei (Amunts et al.) as well as maps of  cortical layers and brain surfaces (Wagstyl et al.).

 Explore the BigBrain online

Explore the BigBrain high resolution human brain model online in the open source Neuroglancer viewer.

 Dataset information for BigBrain maps

Dataset information for BigBrain maps

 Download BigBrain

Download the BigBrain dataset from Loris, hosted by the Montreal Neurological Institute.


Human Cytoarchitectonic Atlas


The JuBrain probabilistic cytoarchitectonic atlas consists of cytoarchitectonic probabilistic maps for human brain structures, defined by histological analysis in a sample of ten post-mortem brains (Amunts and Zilles, 2015). The spatial resolution is 1mm isotropic. Capturing human intersubject variability, they describe how likely a particular structure is found at each voxel position of the reference space. Another way to present these maps are maximum probability maps, which provide a parcellation by assigning each voxel in the brain the most likely histological area according to the probabilistic maps (Eickhoff et al., 2005, 2006).

 Explore the Jubrain cytoarchitectonic atlas online

Explore JuBrain online with the specialised Neuroglancer viewer or using Jülich’s cytoarchitectonic atlas viewer.

 Detailed information

Detailed information


Rodent Atlas - Waxholm Space Rat Brain Atlas


The Waxholm Space (WHS) rat brain atlas is an open access volumetric atlas offering comprehensive anatomical delineations of the rat brain based on structural contrast in isotropic magnetic resonance (39 μm) and diffusion tensor (78 μm) images acquired ex vivo from an 80 day old male Sprague Dawley rat at the Duke Center for In Vivo Microscopy. Spatial reference is provided by the Waxholm Space coordinate system.

 Explore the WHS rat brain atlas online

Explore the WHS Rat Brain Atlas online with the open source Neuroglancer viewer (beta).

 Download the WHS rat brain atlas

Download the WHS Rat Brain Atlas dataset from NITRC.

 Detailed information

Detailed information

Rodent Atlas - Allen Mouse Common Coordinate Framework


The Allen Mouse Common Coordinate Framework (CCF) has been adopted as the standard HBP mouse brain atlas to view and integrate data from the mouse brain.

The Allen Mouse CCF includes a full-colour, high-resolution anatomical reference atlas accompanied by a systematic, hierarchically organised taxonomy of mouse brain structures. Anatomical annotations in classical histological atlas plates were extracted to create a comprehensive volumetric reference atlas of the mouse brain.

Allen Mouse Brain Connectivity Atlas [Internet]. Seattle (WA): Allen Institute for Brain Science. ©2011.

Oh, S.W. et al. (2014) A mesoscale connectome of the mouse brain, Nature 508: 207-214

 Explore the Allen Mouse CCF online

Explore the Allen Mouse CCF online with the open source Neuroglancer viewer (beta).

 Allen Institute Informatics Archive

Allen Institute Informatics Archive