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

Abstract

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.

Background field removal using a region adaptive kernel for quantitative susceptibility mapping of human brain

“…Using this assumption, B loc can be obtained by solving the partial differential equation Δ B Δ = Δ B loc with appropri ate boundary conditions [20]. In addition, using the harmonic mean value theorem from the SHARP method [7], we can introduce an interim variable B inter as $$B_{\mathit{inter}}=B^{\mathrm{\Delta }}-\rho false\otimes B^{\mathrm{\Delta }}=B_{\mathit{loc}}-\rho false\otimes B_{\mathit{loc}}$$where ρ is a nonnegative, radially symmetric, normalized convolution kernel and the symbol ⊗ denotes the 3D convolution operator. Rewriting Eq.…”

“…If tissue susceptibility changes, such as those induced by local brain iron deposition or myelin loss [6], can be estimated accurately, they may serve as a potential biomarker for clinical diagnosis of these diseases. Recent developments in quantitative susceptibility mapping (QSM) have made it possible to obtain high-resolution susceptibility maps [7] by solving the field to source inverse problem using MR phase commonly acquired using a gradient echo (GRE) sequence, which is a sensitive measure of magnetic susceptibility induced field perturbation [8–13]. However, the field perturbation inside certain volume of interest (VOI), e.g.…”

Foundations of layer-specific fMRI and investigations of neurophysiological activity in the laminarized neocortex and olfactory bulb of animal models

“…4A) that can be easily identified with endogenous anatomical MRI contrast (Poplawsky et al, 2015; Wei et al, 2016) or MEMRI (Pautler et al, 1998). During odor stimulation, odorant molecules bind to receptors on olfactory receptor neurons (ORNs), located in the olfactory epithelium anterior to the bulb, and evoke action potentials that propagate through unmyelinated axons into the outermost bulb layer, the olfactory nerve layer (ONL).…”

Measurement of multispectral scattering properties in mouse brain tissue

“…However, the resolution is limited to approximately 1 mm and the contrast without labels is not always optimal. Although the resolution limit spans to a few tens of microns in microCT and MRI for ex vivo brain imaging, the technologies are time-consuming, and the resolution and contrast are not sufficient to visualize cellular structure [4,5]. Optical imaging, on the other hand, can extract information with submicron resolution.…”