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

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

2025-05-25 bioinformatics
10.1101/2025.05.20.655042 bioRxiv
Show 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.

Published in Nature Methods (predicted rank #1) · training set

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