Atlases

Multilevel Human Brain Atlas

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

EBRAINS multilevel human brain atlas captures different facets of brain organisation, going down to the microscopic scale

The EBRAINS human brain atlas integrates different facets of brain organisation, represented by complementary maps of structure, function and connectivity that are defined across multiple reference spaces, going down to the micrometer resolution of the BigBrain model. The atlas can be explored using the 3D Interactive Atlas Viewer, as well as through different programmatic interfaces soon available on EBRAINS.

  • Enter an online framework that lets you explore the human brain in its different dimensions - including cytoarchitecture, fibre architecture, and functional module
  • Zoom in to the micrometer level of the BigBrain - the highest resolution human brain model - in your web-browser
  • Examine interindividual variability of microstructural brain regions using probabilistic cytoarchitectonic maps
  • Get easy access to multimodal data features for different brain regions

Tools

EXPLORE THE ATLAS IN 3D

Explore the different facets of human brain organisation

The multilevel human brain builds on the Julich-Brain cytoarchitectonic maps as a unifying principle of organisation, which are defined at the microscopic scale and well established as a reference for anatomical assignment of neuroimaging signals. The maps reflect intersubject variability in space and localization (“probability maps”). They are complemented with maps that cover complementary aspects of brain organisation, currently represented by fiber bundles from MRI tractography and maps of functional modes (DiFuMo). The atlas supports the MNI Colin27 and ICBM 2009c nonlinear asymmetric spaces to reflect the macroanatomical scale, which are common in functional imaging and whole-brain connectivity studies. It combines those with the microscopic resolution BigBrain model to represent brain organisation at the cellular level. Different brain regions are characterised by multiple levels of brain connectivity and a growing selection of multimodal data features, including transmitter receptor densities, cell distributions, and physiological recordings.

Exploring the human brain atlas in the EBRAINS Interactive Atlas Viewer

Explore the human brain atlas using the Interactive Atlas Viewer

Read about cytoarchitectonic maps in Knowledge Graph

Read about BigBrain in Knowledge Graph

Read about fibre bundle maps in Knowledge Graph

Read about DiFuMo maps in Knowledge Graph

Recorded demo session

Atlas Programming Interface - siibra-python

Connect your workflows to the atlas

As part of the new siibra-toolsuite, we are developing siibra-python, a comprehensive Python client providing access to EBRAINS atlases and offering an easy and well-structured way to include maps, reference templates, region definitions and linked datasets into reproducible programmatic workflows. The software is developed in the public domain under Apache2 licence and maintained on GitHub, with regular releases of development snapshots, and a growing documentation. Since it is under very active development, users are encouraged to be in close interaction with the development team. This can be done by creating pull requests and issues on the siibra-python GitHub or by creating a ticket via support@ebrains.eu. A set of interactive tutorials are also available.

Siibra-python has been designed to allow safe and convenient interaction with brain regions from different parcellations, to provide streamlined access to multimodal data features linked to brain regions, and to perform basic analyses of region-specific data features. The intention is to unify interaction with brain atlas data at different spatial scales, including parcellations and datasets at the millimetre scale in the MNI space, as well as microstructural maps and microscopic data in the BigBrain space.

Siibra hides much of the complexity that would be required to interact with the individual data repositories that host the associated data. By encapsulating many aspects of interacting with different maps and reference templates spaces, it also minimizes common risks like misinterpretation of coordinates from different reference spaces, or utilisation of inconsistent versions of parcellation maps — aiming to provide a safe and reproducible way of using maps defined across multiple spatial scales.

siibra-python github repository

siibra-python documentation

Interactive siibra-python tutorials

Our community

Get connected with the community

Ralf-Uwe Limbach, Forschungszentrum Juelich

Users of the EBRAINS Human Brain Atlas include neuroanatomists, clinicians, computational and experimental neuroscientists, as well as neuroimaging and brain-inspired AI researchers. These communities build mutually beneficial links to better understand the human brain.

There are various ways you can connect with us:

• We organize regular workshops and tutorials, held typically via the Human Brain Project’s Education Programme. To keep up with upcoming events, please check: The HBP Education Programme Website and The HBP Education Programme Twitter

• Join the thriving, regularly interactive BigBrain Community at: bigbrainproject.org/community.html

• If you use the EBRAINS atlases in a programmatic fashion to connect them to your tools and workflows, you can participate in our discussions on GitHub: siibra-python and siibra-API

Access all EBRAINS services