Imaging whole-brain cytoarchitecture of mouse with MRI-based quantitative susceptibility mapping

- We present a new MRI method for imaging whole brain cytoarchitecture at 10-μm isotropic resolution non-destructively in 3D.
- Cell layers are visualized in the olfactory bulb, eye ball, barrel cortex, hippocampus and cerebellum.
- Axonal fiber trajectories are identified in both white matter and gray matter.
- A network of medium spiny neurons are demonstrated in striatum.

The proper microstructural arrangement of complex neural structures is essential for establishing the functional circuitry of the brain. We present an MRI method to resolve tissue microstructure and infer brain cytoarchitecture by mapping the magnetic susceptibility in the brain at high resolution. This is possible because of the heterogeneous magnetic susceptibility created by varying concentrations of lipids, proteins and irons from the cell membrane to cytoplasm. We demonstrate magnetic susceptibility maps at a nominal resolution of 10-μm isotropic, approaching the average cell size of a mouse brain. The maps reveal many detailed structures including the retina cell layers, olfactory sensory neurons, barrel cortex, cortical layers, axonal fibers in white and gray matter. Olfactory glomerulus density is calculated and structural connectivity is traced in the optic nerve, striatal neurons, and brainstem nerves. The method is robust and can be readily applied on MRI scanners at or above 7 T.