Siibra: A software tool suite for realizing a Multilevel Human Brain Atlas from complex data resources

Dickscheid, Timo; Bludau, Sebastian; Leprince, Yann; Mangin, Jean-Francois; Schiffer, Christian; Simsek, Ahmet Nihat; Bjaalie, Jan G.; Jirsa, Viktor; Gui, Xiaoyun; Amunts, Katrin; Leergaard, Trygve B.

doi:10.1101/2025.05.20.655042

Preprint

FZJ-2025-02658

Siibra: A software tool suite for realizing a Multilevel Human Brain Atlas from complex data resources

Dickscheid, T. (Corresponding author)FZJ* ; Gui, X.FZJ* ; Simsek, A. N.FZJ* ; Schiffer, C.FZJ* ; Mangin, J.-F. ; Leprince, Y. ; Jirsa, V. ; Bjaalie, J. G. ; Leergaard, T. B. ; Bludau, S.FZJ* ; Amunts, K.FZJ*

2025

biorxiv (2025) [10.1101/2025.05.20.655042]

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Please use a persistent id in citations: doi:10.1101/2025.05.20.655042 doi:10.34734/FZJ-2025-02658

Abstract: Computational technology opens new possibilities towards understanding the complexity of the human brain, but it requires integrating measurements from different modalities and scales in anatomical context and exposing them in interoperable, actionable form. Especially with growing big data resources, accessing information from different scales and modalities coherently for visual exploration, reproducible analysis and application development remains challenging. We present siibra, a tool suite that connects diverse data from cloud resources to reference atlases and coordinate spaces. It supports different use cases by making contents accessible through a web viewer, Python library and HTTP API. Using siibra we implemented a Multilevel Human Brain Atlas linking macro-anatomical concepts and their inter-subject variability with measurements of the microstructural composition and intrinsic variance of brain regions, building on cytoarchitecture as a reference and supporting MRI-based and microscopic templates. The atlas is integrated with the EBRAINS research infrastructure. All software and content are openly accessible.

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