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

Services

Open access 3D anatomical reference atlases for the human, rat, and mouse brain.

    • Atlases

    Mouse Brain Atlas

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

    Rat Brain Atlas

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

    Multilevel Human Brain Atlas

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

Roadmap

The Roadmap describes the upcoming improvements of the services, targeting the needs of the community as identified through continuous monitoring of user feedback through the provided support channels.

A more detailed description of the status of atlases and services developments is provided here.

2022, Q1

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

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

2022, Q2

The LocaliZoom serial section image viewer with atlas overlay and annotation features is available as a web app in the collaboratory

Alpha release of EBRAINS/nilearn interface for connectivity analysis

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

Alpha release of datalad accessibility layer for EBRAINS atlas datasets

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

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

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

Entire QUINT workflow available as a web service

Relevant datasets for QUINT analyses discoverable through links to Knowledge graph dataset cards

Stable release of datalad accessibility layer for EBRAINS datasets

Release of NHP atlas integrated in EBRAINS

Access all EBRAINS services