Hierarchical X-ray microscopy and mesoscopic diffusion MRI in the same brain reveal the human connectome across scales

Preprint

We present a multimodal pipeline for 3D imaging of cerebral white-matter archi-tecture across scales, from whole-brain axonal projections down to individual myelinated axons. After diffusion MRI, an adult ex vivo human hemisphere undergoes label-free imaging with Hierarchical Phase-Contrast Tomography (HiP-CT) from 20 µm/voxel in the whole hemisphere to 2 µm/voxel in areas of interest, with intrinsic cross-scale alignment. A 4 cm tissue block extracted from the hemisphere is reimaged with HiP-CT at 0.857 µm/voxel, enabling direct visualisation of single myelinated axons. After osmium staining, micro-CT at 0.364 µm/voxel and electron microscopy at 4 nm/voxel are acquired in biop-sies from the tissue block to validate the presence of myelinated axons in the label-free HiP-CT contrast. Spanning three orders of magnitude in resolution, these co-registered multimodal datasets bridge microscopic wiring and macro-scopic brain organisation, providing a foundation for anatomically grounded whole-brain connectomics.

Authors: Chourrout, M; Gong, T; Schalek, R; Keenlyside, A; Balbastre, Y

• Publication status: Published
• Peer review status: Not peer reviewed
• Preprint server: bioRxiv
• Publication date: 2026-04-06
• DOI: 10.64898/2026.04.02.716198
• EISSN: 2692-8205
• Language: English
• Keywords: ex vivo; multimodal; HiP-CT