An Ultra-High-Resolution 17.2 T MRI Atlas (HypoAtlas) and Multimodal Pipeline to Study the Mouse Hypothalamus: Sexual Dimorphism and Lateralization Insights

Abstract Structural and functional insights into the mouse hypothalamus are hampered by its small size and deep location. Here, we leverage ultra-high-field magnetic resonance imaging (UHF-MRI) at 17.2 Tesla to achieve unprecedented spatial resolution in structural, functional and neurochemical imaging of the mouse hypothalamus, including sexual dimorphism in certain nuclei. High-resolution ex vivo anatomical MRI enabled precise hypothalamic parcellation, improving on existing atlases and revealing nuclei previously unresolved by MRI. Diffusion MRI and tractography mapped intra- and extra-hypothalamic pathways, facilitating circuit-level exploration without a priori assumptions. Resting-state fMRI combined with independent component analysis identified novel hypothalamic networks, demonstrating the enhanced capacity of UHF MRI to detect deep-brain activity. ¹H-magnetic resonance spectroscopy quantified neurochemical profiles, revealing sexually dimorphic heterogeneity within the hypothalamus. Our comprehensive multimodal approach uncovers sex differences in hypothalamic anatomy, microstructure, and neurochemistry, emphasizing the importance of sex as a biological variable. This integrated pipeline offers a valuable resource for dissecting hypothalamic circuits and functions, advancing our understanding of neuroendocrine regulation, behavior, and disease mechanisms, with direct translational relevance. Competing Interest Statement The authors have declared no competing interest.