siibra-explorer is an frontend module wrapping around nehuba for visualizing volumetric brain volumes at possible high resolutions, and connecting to siibra-api for offering access to brain atlases of different species, including to navigate their brain region hierarchies, maps in different coordinate spaces, and linked regional data features. It provides metadata integration with the EBRAINS knowledge graph, different forms of data visualisation, and a structured plugin system for implementing custom extensions.
A detailed atlas of the human brain that integrates information on brain structure, function, and connectivity across multiple modalities and spatial scales.
- Probabilistic 3D maps of cytoarchitecture, fiber bundles and functional modules, capturing cross-subject variability.
- Integration of the microscopic 3D model “BigBrain” with the MNI and freesurfer reference spaces, linking macroanatomy with cellular detail.
- Measures of molecular, cellular and fiber architecture, characterizing the composition and intrinsic variance of brain regions.
- Structural and functional connectivity from different neuroimaging cohorts.
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.
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 covering complementary aspects of brain organisation, represented by fiber bundles from MRI tractography and maps of functional modes. The atlas supports multiple reference spaces, including the MNI Colin27, ICBM 152 2009c and average spaces which are common in functional imaging and whole-brain connectivity studies. It integrates these with the microscopic resolution BigBrain model as a link from the macroscopic to the cellular scale. Brain regions are characterised by multiple levels of brain connectivity and multimodal regional measurements including neurotransmitter receptor densities, cell densities, fiber orientations, genomics and physiological data.
Most relevant resources
- Julich-Brain in atlas viewer: https://atlases.ebrains.eu/viewer/go/julichbrain
- BigBrain in atlas viewer: https://atlases.ebrains.eu/viewer/go/bigbrain
- Video tutorial for the atlas viewer: https://www.youtube.com/watch?v=xAU70QLLUO4
- More information about the Julich-Brain cytoarchitectonic maps: https://julich-brain-atlas.de/
- Amunts K, Mohlberg H, Bludau S, Zilles K. Julich-Brain: A 3D probabilistic atlas of the human brain’s cytoarchitecture. Science. 2020;369(6506):988-992. doi:10.1126/science.abb4588
- Guevara M, Román C, Houenou J, Duclap D, Poupon C, Mangin JF, Guevara P. Reproducibility of superficial white matter tracts using diffusion-weighted imaging tractography. NeuroImage. 2017;147:703-725. doi:10.1016/j.neuroimage.2016.11.066
- Dadi K, Varoquaux G, Machlouzarides-Shalit A, Gorgolewski KJ, Wassermann D, Thirion B, Mensch A. Fine-grain atlases of functional modes for fMRI analysis. NeuroImage. 2020;221:117126. doi:10.1016/j.neuroimage.2020.1171261.
- Amunts K, Lepage C, Borgeat L, Mohlberg H, Dickscheid T, Rousseau ME, Bludau S, Bazin PL, Lewis LB, Oros-Peusquens AM, Shah NJ, Lippert T, Zilles K, Evans AC. BigBrain: An Ultrahigh-Resolution 3D Human Brain Model. Science. 2013;340(6139):1472-1475. doi:10.1126/science.1235381
- Schiffer C, Spitzer H, Kiwitz K, Unger N, Wagstyl K, Evans AC, Harmeling S, Amunts K, Dickscheid T. Convolutional neural networks for cytoarchitectonic brain mapping at large scale. NeuroImage. 2021;240:118327. doi:10.1016/j.neuroimage.2021.118327
- Wagstyl K, Larocque S, Cucurull G, Lepage C, Cohen JP, Bludau S, Palomero-Gallagher N, Lewis LB, Funck T, Spitzer H, Dickscheid T, Fletcher PC, Romero A, Zilles K, Amunts K, Bengio Y, Evans AC. BigBrain 3D atlas of cortical layers: Cortical and laminar thickness gradients diverge in sensory and motor cortices. PLoS biology. 2020;18(4):e3000678. doi:10.1371/journal.pbio.3000678
Other softwareAll software
siibra-api is an HTTP API for querying and retrieving contents of EBRAINS atlases. Originally built as a backend service for the interactive atlas viewer siibra-explorer, the API has been documented for connecting the brain atlases to other applications and web services.