An open access mouse brain flatmap and upgraded rat and human brain flatmaps based on current reference atlases

Abstract

Here we present a flatmap of the mouse central nervous system (CNS) (brain) and substantially enhanced flatmaps of the rat and human brain. Also included are enhanced representations of nervous system white matter tracts, ganglia, and nerves, and an enhanced series of 10 flatmaps showing different stages of rat brain development. The adult mouse and rat brain flatmaps provide layered diagrammatic representation of CNS divisions, according to their arrangement in corresponding reference atlases: Brain Maps 4.0 (BM4, rat) (Swanson, The Journal of Comparative Neurology, 2018, 526, 935-943), and the first version of the Allen Reference Atlas (mouse) (Dong, The Allen reference atlas, (book + CD-ROM): A digital color brain atlas of the C57BL/6J male mouse, 2007). To facilitate comparative analysis, both flatmaps are scaled equally, and the divisional hierarchy of gray matter follows a topographic arrangement used in BM4. Also included with the mouse and rat brain flatmaps are cerebral cortex atlas level contours based on the reference atlases, and direct graphical and tabular comparison of regional parcellation. To encourage use of the brain flatmaps, they were designed and organized, with supporting reference tables, for ease-of-use and to be amenable to computational applications. We demonstrate how they can be adapted to represent novel parcellations resulting from experimental data, and we provide a proof-of-concept for how they could form the basis of a web-based graphical data viewer and analysis platform. The mouse, rat, and human brain flatmap vector graphics files (Adobe Reader/Acrobat viewable and Adobe Illustrator editable) and supporting tables are provided open access; they constitute a broadly applicable neuroscience toolbox resource for researchers seeking to map and perform comparative analysis of brain data.

Connectivity characterization of the mouse basolateral amygdalar complex

“…An AAV-RFP injection in VMH validates the VMH→LA connection showing strong label in LA, but also in BMAp (VMH→BMAp). The outputs of BLA.am ( e ), BLA.al ( f ), and BLA.ac ( g ) domains are represented at the macroscale level (gray matter region resolution) on a partial mouse brain flatmap 75 . The strength values of detected connections were binned into tertiles, and these are represented qualitatively as strong (maroon), moderate (red), weak (pink), and none (gray).…”

Structure–function subsystem models of female and male forebrain networks integrating cognition, affect, behavior, and bodily functions

“…What are the regional members of these subsystems, and how are they distributed spatially within the FB? Instead of distributing spatially in a checkerboard pattern, the region sets forming the first-through third-level subsystems tend to aggregate spatially in CTX, CNU, TH, and HY, as viewed schematically on a flat map (28) and an atlas (9) of transverse section maps (Figs. 3C and 4).…”

The physiological control of eating: signals, neurons, and networks

“…Its foundation is a hierarchically organized set of brain and spinal cord parts (collectively the cerebrospinal trunk) whose parcellation derives from historical convention, and embryological and developmental principles (59,(63)(64)(65). It also favors English rather than Latin or Greek names, e.g., 'endbrain' rather than the Greek synonym 'telencephalon'.…”

“…Body Figure 1 The hierarchy for the standardized nomenclature of brain parts used in this review is from previously published schemes for the rat and mouse brains. For more detailed descriptions and derivations see (59,(63)(64)(65)649).…”