Brain atlases provide spatial reference systems for neuroscience, giving the ability to navigate, characterise and analyse information on the basis of anatomical location. Atlases define shape, location and variability of brain regions in common coordinate spaces, and allow interpretation, integration, and comparison of observations and measurements collected from different sources and different brains.

EBRAINS develops open access 3D atlases for the human, rat, and mouse brain

EBRAINS develops open access 3D atlases for the human, rat, and mouse brain. Explore brain regions in an interactive 3D viewer at microscopic detail and discover related multimodal data features from the EBRAINS Knowledge Graph. Programmatic access via a Python client, HTTP API, and command line interface is in development, coming soon to EBRAINS. Integrate your own data of different scale and type to EBRAINS atlases to make them available in a common spatial framework for reuse and quantitative analysis. Use EBRAINS atlas analysis tools to extract, quantify, and compare data in specific brain regions



    • Atlases

    Multilevel Human Brain Atlas

    A three-dimensional atlas that integrates the different facets of human brain organisation at the millimeter and micrometer level
    • Atlases

    Rat Brain Atlas

    Explore open access 3D anatomical atlas for the rat brain
    • Atlases

    Mouse Brain Atlas

    Explore open access 3D anatomical atlas for the mouse brain
    • Atlases


    Extract, quantify and analyse labelled features from rodent histological images
    • Atlases

    QuickNII and VisuAlign

    Spatially register mouse and rat serial 2D brain images to 3D reference atlases
    • Atlases


    Spatially register high-resolution volumes of interest to 3D reference atlases
    • Atlases


    Gene expression analysis in human brain atlas regions


For more details on current developments click here.

2021, Q2

Launch of an integrated toolsuite which brings together the 3D interactive atlas viewer and the new Python client and HTTP API

Viewing of 2D image series with brain atlas overlays available through the EBRAINS Knowledge Graph

2021, Q3

Atlas viewer supports overlaying local Nifti files with atlases and "virtual dissections" in BigBrain

Initial release of non-human primate (NHP) atlas. Parcellation maps and functional data will be linked in the future

Waxholm space rat atlas update with 45 new delineations in cerebral cortex, basal ganglia, thalamus

2021, Q4

Human brain atlas supports freesurfer space and spatial relationships between complementary parcellation maps

2022, Q1

First release of an atlasing toolbox for neuroimaging, allowing probabilistic assignment of whole-brain signals to anatomical regions

Alpha release of EBRAINS/nilearn interface for connectivity analysis

ilastik accessible as an EBRAINS web service, allowing to perform interactive image segmentation on EBRAINS image data

Release of WebAlign, combining QuickNII and VisuAlign in a web-accessible tool

2022, Q2

New workflow allowing to project individual MRI scans to the human brain atlas for analysis

Alpha release of datalad accessibility layer for EBRAINS atlas datasets

2022, Q3

Beta release of EBRAINS/nipy software interface for connectivity analysis

Beta release of Neuron Morphology registration pipeline integrated to EBRAINS

QUINT workflow available as web-based workflow

VoluBA updated with basic nonlinear registration capabilities

2022, Q4

Interactive segmentation of user supplied files in web-ilastik, with the possibility to submit results to EBRAINS curation services

Major release of updated human and rodent atlases with online documentation and tutorials

WebAlign and VoluBA allow submission of registration results to EBRAINS curation

2023, Q1

Stable and fully documented release of EBRAINS/nilearn interface for connectivity analysis

neurogenpy library integrated with EBRAINS which allows analysis of gene expression data and learning of gene regulatory networks

Stable release of Neuron Morphology registration pipeline, allowing submission of outputs to EBRAINS data curation

QUINT workflow provides Nutil as a web service and direct links to Knowledge graph dataset cards

Stable release of datalad accessibility layer for EBRAINS datasets

Release of non-human primate (NHP) atlas integrated in EBRAINS

Access all EBRAINS services