Chemoarchitectural studies of the rat hypothalamus and zona incerta. - A downloadable interactive spatial database of five co-visualizable neurochemical systems, with novel feature- and grid-based mapping tools.

The hypothalamus and zona incerta of the brown rat (), a model organism important for translational neuroscience research, contain diverse neuronal populations essential for survival, but how these populations are structurally organized as systems remains elusive. With the advent of novel gene-editing technologies, there has been a growing need for high-spatial-resolution maps of rat hypothalamic neurochemical cell types to aid in their functional interrogation by virus-directed cell type-specific gene manipulation or to validate their expression in transgenic lines. Here, we present a draft report describing , a chemoarchitecture database for the rat hypothalamus (HY) and zona incerta (ZI), which will eventually feature downloadable interactive maps featuring the census distributions of five immunoreactive neurochemical systems: (1) vasopressin (as detected using its gene co-product, copeptin); (2) neuronal nitric oxide synthase (EC 1.14.13.39); (3) hypocretin 1/orexin A; (4) melanin-concentrating hormone; and (5) alpha-melanocyte-stimulating hormone. These maps are formatted for the widely used (BM4.0) open-access rat brain atlas. Importantly, this dataset retains atlas stereotaxic coordinates that facilitate the precise targeting of the cell bodies and/or axonal fibers of these neurochemical systems, thereby potentially serving to streamline delivery of viral vectors for gene-directed manipulations. The maps will be presented together with novel open-access tools to visualize the data, including a new Python programming language-based workflow to quantify cell positions and fiber densities for BM4.0. The workflow produces "heat maps" of neurochemical distributions from multiple subjects: 1) that represent consensus distributions independent of underlying atlas boundary conditions, and 2) that provide distribution differences based on cytoarchitectonic boundaries. These multi-subject cartographic representations are produced in Python from exported atlas maps first generated in the Adobe Illustrator vector graphics environment, which are then reimported and placed directly into the atlas. The soon-to-be-released files can also be opened using the free vector graphics editor, Inkscape. We also introduce a refined grid-based coordinate system for this dataset, register it with previously published spatial data for the HY and ZI, and introduce (Frequencies Mapped with Reference to Stereotaxy), as a new adaptation of long-used ephemeris systems for grid-based annotation of experimental observations. This database, which includes all data described in greater detail in Navarro (2020) and Peru (2020), provides critical spatial targeting information for these neurochemical systems unavailable from mRNA-based maps and allows readers to place their own datasets in register with them. It also provides a space for the continued buildout of a community-driven atlas-based spatial model of rat hypothalamic chemoarchitecture, allowing experimental observations from multiple laboratories to be registered to a common spatial framework.