Fig. 1.

Overview of MRH contrast (SI Appendix, Table S1, specimen 200302-1:1) at a plane equivalent to level 74 of the ABA coronal series (https://tinyurl.com/CCFv3-Level74). (A) Reference image from the ABA of an inverted contrast Nissl-stained section. Several regions and tracts are labeled: cortex (CTX), corpus callosum (cc), primary somatosensory area (SSp), hippocampus (HPF), fimbria (fi), thalamus (TH), hypothalamus (HY), basolateral amygdala (BLA), and lateral ventricle (VL, in blue). (B) Average MGRE with dark blood vessels (arrow – perforating artery) and darker heavily myelinated tracts (e.g., cc, cpd, and fi in A and B). (C) Mean diffusivity (MD) with light regions defining both cell-dense regions such as the granule cell layer (D, sg) dentate gyrus, and blood vessels (arrow) and ventricle. (D) Axial diffusivity (AD) is similar to C, but differentiates additional hippocampal layers. (E) Fractional anisotropy (FA) defines finer details of neurite orientation—white in the heavily myelinated corpus callosum and corticofugal projections and the margins of barrels in the somatosensory cortex (arrow). The barrel field cortex is revealed in an enface tangential plane in SI Appendix, Fig. S2. (F) Color FA provides additional differentiation of fiber tracts based on their orientation (Top Right Inset). The yellow asterisk marks a complex of intersecting tracts around the internal capsule (SI Appendix, Fig. S1). The corpus callosum (red) is distinct from both the cingulum (green above) and the dorsal hippocampal commissure (green below). Lower rows (a–f) are corresponding 2× magnifications of the hippocampus that illustrate MRH resolution of layers. Abbreviations—so: stratum oriens; sp: pyramidal cell layer; sr: stratum radiatum; slm: stratum lacunosum-moleculare; mo molecular layer of the dentate gyrus; sg: granule cell layer of the dentate gyrus; po: polymorphic layer of the dentate gyrus. Video available @ https://bit.ly/MouseBrain15micron