Rat Brain Gray Matter Regionalization

The table below provides a searchable list of gray matter regions and their parent divisions for the rat central nervous system (CNS), together with their corresponding atlas levels (rostral to caudal) in a rat brain atlas (Brain Maps 4.0. Swanson, L.W. 2018). Beneath the table are the atlas maps (coronal section), and below those a searchable list of all atlas abbreviations, and a bibliography. For additional information (including for gray matter divisions below the level of gray matter region) see the atlas, and the interactive spreadsheet Brain Maps 4.0 CNS Divisions.

Rat Brain Maps

Maps of rat brain coronal plane sections adapted from Brain Maps 4.0Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps. Swanson, L.W. (2018). The maps, based primarily on cytoarchitecture, are presented on the right side of each figure for one side of the brain. A photomicrograph of the corresponding cytoarchitecture (Nissl-stained section, pseudocolored) is shown on the left side. A schematic of the brain in parasagittal section (top right) indicates (red line) the rostral-caudal location of each level in the atlas (73 levels in total, numbered from rostral to caudal, with the current level indicated below each schematic—also corresponds to the displayed page number). The red grid represents stereotaxic coordinates in millimeters for the x- and y-axes; the z-axis distance from Bregma is shown below the grid (coordinates are based on those used in the atlas of Paxinos & Watson, 1986). See the original publication for complete details, and for complementary information see the interactive spreadsheet Brain Maps 4.0 CNS Divisions.

BM4 Atlas Levels rev1 update1.pdf

The table below lists all structure names and their abbreviations used in Brain Maps 4.0, including for the atlas level maps shown here (above) as well as brain flatmaps and Tables A-J* (see note below the table and refer to Brain Maps 4.0 for further information). To search for a structure abbreviation or name, start typing in the corresponding box.

*The entries in tables A-J (10 tables) are considered standard terms and all other terms can be defined with respect to them because the other terms are either defined subdivisions (children in the hierarchy), synonyms, or partly corresponding terms. The standard terms are primarily in English, following the example of Terminologia anatomica (1998) and Nieuwenhuys et al. (2008). Their formal structure is: term (author, date), that is, the term followed by a reference to the first time the term was used as defined. Thus, the term in not an eponym, but instead assigns priority. If priority has not been rigorously determined, the reference is given as (>1840) (a date corresponding approximately to the begining of the concerted application of cell theory to biology); for further explanation see Swanson (2015). The definition includes a brief but clear description of the relevant part in relation to the nomenclature hierarchy; the species, sex, and age of the animal(s) used in the reference; and the method(s) used to delineate the part. If this information is not found in the annotations for rat terms, they are found in Swanson (2015). Excerpt adapted from the introduction to Brain Maps 4.0, Swanson (2018).


Nieuwenhuys, R., Voogd, J., & Huijzen, Chr. van (2008). The human central nervous system (4nd ed.). Berlin: Springer-Verlag.

Swanson, L. W. (2015). Neuroanatomical terminology: A lexicon of classical origins and historical foundations. New York, NY: Oxford University Press.

Swanson, L. W. (2018). Brain maps 4.0-Structure of the rat brain: An open access atlas with global nervous system nomenclature ontology and flatmaps. J Comp Neurol, 526(6), 935-943. doi:10.1002/cne.24381

The table below is a bibliography for Brain Maps 4.0. To search for a particular reference start typing in the box labeled "References" (results are filtered dynamically as text is entered).

Header Image: Adapted from covers of rat brain atlases: Swanson, 1992; Alvarez-Bolada & Swanson, 1996; Swanson, 1998; Swanson, 2004.