Brain maps 4.0—Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps

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The new generation of genetically‐based tools for dissecting and manipulating neural circuits (Luo, Callaway, & Svoboda, 2008), combined with the recent application of formal network analysis methods to connectomics projects (Sporns, 2011), has revived interest in systematic accounts of nervous system structural organization. Precise scientific communication relies on the use of a clearly defined, internally consistent, and complete nomenclature for a given domain, and for the brain and nervous system this nomenclature includes a comprehensive parts list with textual and spatial definitions, and an explicitly defined schema of relationships between the parts. Conceptually, a neural circuit, network, or system may be viewed as a set of nodes or “parts”—including gray matter regions, neuron types, individual neurons, and synapses, considered at descending, nested levels of granularity—with a set of connections between nodes. Data about these nodes and connections are obtained experimentally from specific spatial locations and animals, with specific experimental and analysis methodologies.
Traditionally, systematic and internally consistent brain part spatial definitions have been provided by atlases of maps based on interpretations of sections through the organ in one or more standard planes. It is common knowledge that the many brain atlases within and between species vary widely in terminology and parcellation, and that no widely accepted “standard” nomenclature has emerged, unlike the case for most parts of human gross anatomy except the central nervous system (Bota, Dong, & Swanson, 2003; Swanson, 2015a). This situation is particularly unfortunate for comparisons between rodent and human brains. Most research on the human brain is currently done with structure‐function imaging techniques having less than naked eye resolution (routinely about 1 mm), whereas in contrast, research on animal brains is carried out with cellular and subcellular resolution (from microns to nanometers) (see Swanson & Lichtman, 2016).
Ideally, the results of human brain imaging studies should inform and stimulate research on underlying biological mechanisms in animals, and conversely, animal research on biological mechanisms should inform the interpretation of human imaging studies. There is room for great improvement in such interactions, and one fundamental requirement is a common structural framework and nomenclature for comparing brain parts among mammals as a class, based on the taxonomic principal of a common body plan shared by mammals.
The first edition of Brain maps: structure of the rat brain was published in 1992 and had four unique features: it was the first computer graphics, digital brain atlas (designed in Adobe Illustrator; see Swanson, 1992); the 73 Atlas Level maps were spatially aligned to facilitate 3‐D reconstructions; it contained the first systematic set of four hierarchically ordered brain atlas nomenclature tables, which later became the foundation for a brain architecture knowledge management system (Bota et al., 2003; Dashti, Ghandeharizadeh, Stone, Swanson, & Thompson, 1997); and it had a rat flatmap of the central nervous system based on a fate map model of the vertebrate embryonic neural plate.
Since publication of the third edition in 2004 (Swanson, 2004), the need for a panmammalian neuroanatomical nomenclature has become more obvious because of the animal‐human research interactions mentioned above, and because the application of network analysis methods to connection matrices for connectomics research requires the use of internally consistent lists of nodes. To address this need we have published a Foundational Model of Structural Connectivity that provides a controlled vocabulary and set of general principles for describing the nervous system of all animals at all levels of granularity (Swanson & Bota, 2010), and have published a scholarly analysis of human (and mammalian generally) neuroanatomical terminology for all parts of the central nervous system and peripheral nervous system (Swanson, 2015a).
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