High-throughput light-sheet 3D microscopy of whole rodent brain microstructure for integration with MRI
- 1Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham
Abstract
Whole-brain cellular mapping is essential for understanding how differences in cellular architecture shape brain organisation and function. Magnetic Resonance Imaging (MRI) provides whole-brain coverage in humans and animal models but is only indirectly sensitive to cellular features. Integrating MRI with whole-brain microscopy is therefore critical for interpreting existing microstructural MRI metrics and developing new, more specific ones. Here, we present a scalable cross-resolution framework that integrates 3D light-sheet microscopy (LSM) of intact rodent brains with diffusion MRI (dMRI) to bridge cellular and macroscopic brain imaging. By combining active electrotransport-based tissue clearing and immunolabelling with accelerated LSM acquisitions, we achieve whole-brain multiplexed mapping of neuronal and glial populations in intact rodent brains on timescales comparable to conventional histology and 2D microscopy. This throughput enables LSM and MRI integration at scale, linking macroscopic MRI contrasts to microscopic cellular features within the same tissue. We apply this framework across eight genetically diverse mouse strains to develop predictive models of 3D microscopy-derived cellular features from multi-shell dMRI-derived contrasts. We demonstrate that data-driven combinations of state-of-the-art dMRI contrasts predict neuronal and astrocytic features better than individual contrasts, across all animals. Our novel approach enables 3D microscopy to guide the development and interpretation of microstructural MRI measures that are ultimately translatable to the living human brain.
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BibTeX
@misc{hanmer2026highthroughput,
title = {{High-throughput light-sheet 3D microscopy of whole rodent brain microstructure for integration with MRI}},
author = {J. M. Hanmer and F. D'Antonio and J.-P. Manzano-Patron and S. Assimopoulos and S. C. Wood and M. Tachrount and Q. Shen and M. Craig and C. Lai and G. J. Hickman and E. Radfar and K. I. Chisholm and T. D. Farr and A. Jasanoff and A. Hoerder-Suabedissen and Z. Molnar and C. Ligneul and C. Tisca and S. Jbabdi and A. F. D. Howard and K. L. Miller and E. de Guzman and J. P. Lerch and S. N. Sotiropoulos},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.12.758500},
url = {https://www.biorxiv.org/content/10.64898/2026.10.12.758500v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - High-throughput light-sheet 3D microscopy of whole rodent brain microstructure for integration with MRI
AU - J. M. Hanmer
AU - F. D'Antonio
AU - J.-P. Manzano-Patron
AU - S. Assimopoulos
AU - S. C. Wood
AU - M. Tachrount
AU - Q. Shen
AU - M. Craig
AU - C. Lai
AU - G. J. Hickman
AU - E. Radfar
AU - K. I. Chisholm
AU - T. D. Farr
AU - A. Jasanoff
AU - A. Hoerder-Suabedissen
AU - Z. Molnar
AU - C. Ligneul
AU - C. Tisca
AU - S. Jbabdi
AU - A. F. D. Howard
AU - K. L. Miller
AU - E. de Guzman
AU - J. P. Lerch
AU - S. N. Sotiropoulos
PY - 2026
DA - 2026/10/12
PB - bioRxiv
DO - 10.64898/2026.10.12.758500
UR - https://www.biorxiv.org/content/10.64898/2026.10.12.758500v1
AB - Whole-brain cellular mapping is essential for understanding how differences in cellular architecture shape brain organisation and function. Magnetic Resonance Imaging (MRI) provides whole-brain coverage in humans and animal models but is only indirectly sensitive to cellular features. Integrating MRI with whole-brain microscopy is therefore critical for interpreting existing microstructural MRI metrics and developing new, more specific ones. Here, we present a scalable cross-resolution framework that integrates 3D light-sheet microscopy (LSM) of intact rodent brains with diffusion MRI (dMRI) to bridge cellular and macroscopic brain imaging. By combining active electrotransport-based tissue clearing and immunolabelling with accelerated LSM acquisitions, we achieve whole-brain multiplexed mapping of neuronal and glial populations in intact rodent brains on timescales comparable to conventional histology and 2D microscopy. This throughput enables LSM and MRI integration at scale, linking macroscopic MRI contrasts to microscopic cellular features within the same tissue. We apply this framework across eight genetically diverse mouse strains to develop predictive models of 3D microscopy-derived cellular features from multi-shell dMRI-derived contrasts. We demonstrate that data-driven combinations of state-of-the-art dMRI contrasts predict neuronal and astrocytic features better than individual contrasts, across all animals. Our novel approach enables 3D microscopy to guide the development and interpretation of microstructural MRI measures that are ultimately translatable to the living human brain.
ER -