Brain regions

stratum oriens of CA2CA2orAllen Non-Human Primate Brain Atlas
layer VI of V1V1-6Allen Non-Human Primate Brain Atlas
accessory basal nucleus (basomedial nucleus)ABAllen Non-Human Primate Brain Atlas
amygdalohippocampal area, parvocelluar partAHApcAllen Non-Human Primate Brain Atlas
hippocampal properHipAllen Non-Human Primate Brain Atlas
subpial granular zone of V1V1sgAllen Non-Human Primate Brain Atlas
occipital cortexOcxAllen Non-Human Primate Brain Atlas
presubicular cortex (presubiculum)PrSAllen Non-Human Primate Brain Atlas
layer VI of V2V2-6Allen Non-Human Primate Brain Atlas
layer II of rostral cingulate cortexrCG2Allen Non-Human Primate Brain Atlas
layer II of caudal orbitofrontal cortexcOF2Allen Non-Human Primate Brain Atlas
layer III of V2V2-3Allen Non-Human Primate Brain Atlas
dorsal division of lateral nucleus, lateral partLdlAllen Non-Human Primate Brain Atlas
subpial granular zone of dorsolateral prefrontal cortexdlPFsgAllen Non-Human Primate Brain Atlas
granular layer IV of dorsolateral prefrontal cortexdlPF4Allen Non-Human Primate Brain Atlas
olfactory tubercleTuAllen Non-Human Primate Brain Atlas
central amygdaloid nucleusCEAllen Non-Human Primate Brain Atlas
stratum radiatum of CA2CA2raAllen Non-Human Primate Brain Atlas
ventricular zone (outer)VZoAllen Non-Human Primate Brain Atlas
inner ventricular zone of V1V1vziAllen Non-Human Primate Brain Atlas
layer II/IIIL2/3Allen Non-Human Primate Brain Atlas
outer fiber (plexiform) zone of V1V1ofzAllen Non-Human Primate Brain Atlas
subgranular layer anlage of dentate gyrus (cortex)DGsgaAllen Non-Human Primate Brain Atlas
subplate zone of rostral cingulate cortexrCGspAllen Non-Human Primate Brain Atlas
hippocampal plate of CA1CA1cpAllen Non-Human Primate Brain Atlas
intermediate division of basal nucleusBiAllen Non-Human Primate Brain Atlas
marginal zone of rostral cingulate cortexrCGmzAllen Non-Human Primate Brain Atlas
globus pallidusGPAllen Non-Human Primate Brain Atlas
hippocampal subplate of CA1CA1spAllen Non-Human Primate Brain Atlas
nucleus accumbensNACAllen Non-Human Primate Brain Atlas
layer III of rostral cingulate cortexrCG3Allen Non-Human Primate Brain Atlas
marginal zone of dorsolateral prefrontal cortexdlPFmzAllen Non-Human Primate Brain Atlas
layer II of MECMEC2Allen Non-Human Primate Brain Atlas
layer VI of dorsolateral prefrontal cortexdlPF6Allen Non-Human Primate Brain Atlas
lateral geniculate nucleusLGNAllen Non-Human Primate Brain Atlas
perirhinal cortexPCAllen Non-Human Primate Brain Atlas
inner fiber (plexiform) zone of S1S1ifzAllen Non-Human Primate Brain Atlas
layer III of caudal orbitofrontal cortexcOF3Allen Non-Human Primate Brain Atlas
layer VIL6Allen Non-Human Primate Brain Atlas
core of nucleus accumbensNACcAllen Non-Human Primate Brain Atlas
layer IVA of V1V1-4AAllen Non-Human Primate Brain Atlas
outer subventricular zone of V1V1szoAllen Non-Human Primate Brain Atlas
shell of nucleus accumbens, medial partNACsmAllen Non-Human Primate Brain Atlas
islands of CallejaIsCjAllen Non-Human Primate Brain Atlas
layer IVCb of V1V14CbAllen Non-Human Primate Brain Atlas
stratum oriens of CA1CA1orAllen Non-Human Primate Brain Atlas
subplate zone of V1V1spAllen Non-Human Primate Brain Atlas
hippocampal cortex (hippocampal formation)HFAllen Non-Human Primate Brain Atlas
amygdalopiriform transition areaAPirAllen Non-Human Primate Brain Atlas
amygdaloid intramedullary grayIMGAllen Non-Human Primate Brain Atlas
dorsal (magnocellular) division of basal nucleusBdAllen Non-Human Primate Brain Atlas
layer V of rostral cingulate cortexrCG5Allen Non-Human Primate Brain Atlas
layer IVL4Allen Non-Human Primate Brain Atlas
layer I of V1V1-1Allen Non-Human Primate Brain Atlas
inner ventricular zone of rostral cingulate cortexrCGvziAllen Non-Human Primate Brain Atlas
CA4 regionCA4Allen Non-Human Primate Brain Atlas
outer ventricular zone of rostral cingulate cortexrCGvzoAllen Non-Human Primate Brain Atlas
CA1 regionCA1Allen Non-Human Primate Brain Atlas

1 2 3 258 Brain regions

Help
Brain regions

Brain regions are a type taxonomy defined by brain atlases. In BrainSTEM, brain regions are a shared model across users. New brain atlasses and therefore brain regions are added by the admin team. Please reach to us if you are missing a brain atlas that is publicly available, that you would like to have incorporated.

Brain Atlases

The following brain atlases are available in BrainSTEM:

  • Allen Mouse Brain Atlas: The Allen Mouse Brain Atlas is a genome-wide, three-dimensional map of gene expression throughout the adult mouse brain. The atlas comprises cellular resolution in situ hybridization images with comprehensive anatomic coverage that reveal where each gene is expressed in the mouse brain, as well as an integrated suite of powerful data search, visualization tools, and an annotated reference atlas. The atlas is based on wild type C57BL/6J mice.
  • Allen Developing Mouse Brain Atlas: The Allen Developing Mouse Brain Atlas is a detailed map of gene expression changes during the development of the brain. The atlas provides a framework to explore both when and where genes are activated in the mouse brain from embryo through adulthood. Informatics data processing enables both spatial search and temporal search. Developmental reference atlases provide additional context to interpret the data. Anatomic and temporal search locates enhanced gene expression in primary brain areas, and manual data annotation allows users to view curated summaries of gene expression in small structures.
  • Allen Human Brain Atlas: The Allen Human Brain Atlas is a unique multi-modal atlas that maps gene expression across the healthy human brain. Key features include an “all genes, all structures” RNA microarray survey that is spatially mapped to an MRI reference space, in situ hybridization image data at cellular resolution for selected genes in targeted brain regions, and an annotated human brain atlas guide. Additional data on selected neurological conditions are available in the Aging, Dementia, TBI Study and Ivy Glioblastoma Database.
  • Allen Developing Human Brain Atlas: The BrainSpan Atlas of the Developing Human Brain provides a broad and detailed anatomical analysis of gene expression across multiple stages of early human brain development. It includes in situ hybridization, RNA-sequencing, and microarray data, along with supporting neuroanatomical reference materials.
  • Allen Non-Human Primate Brain Atlas: The NIH Blueprint Non-Human Primate Atlas provides a developmental neuroanatomical framework for exploring the cellular and molecular architecture of the developing postnatal brain of the rhesus macaque.
  • Allen Spinal Column Atlas: The Allen Spinal Cord Atlas is a comprehensive, genome-wide map of gene expression throughout the healthy mouse spinal cord at ages p56 and p4. This resource details gene diversity in the normal spinal cord and provides an essential baseline for understanding how the spinal cord may be altered in disease or injury. The atlas includes image-based in situ hybridization data at cellular resolution for both juvenile (P4) and adult (P56) stages, with anatomic coverage across the full length of the spinal cord, and accompanying histological reference images.
  • Brain Maps 4.0 - Rat brain Atlas: An open access atlas with global nervous system nomenclature ontology and flatmaps. The fourth edition of Brain maps: structure of the rat brain is presented here as an open access internet resource for the neuroscience community. One new feature is a set of 10 hierarchical nomenclature tables that define and describe all parts of the rat nervous system within the framework of a strictly topographic system devised previously for the human nervous system.
  • Paxinos & Franklin 2001 Mouse Brain Atlas (Second edition): Brain Atlas by Paxinos & Franklin based on adult C57BL/J6 Mouse (weight range 26-30 g).
  • Paxinos & Watson 1997 Rat Brain Atlas (Third edition): Paxinos & Watson rat brain atlas based on adult male Wistar rats (weight range 270-310 g).
  • Swanson 2004 Rat Brain Atlas (Third edition): Rat brain atlas based on adult Sprague-Dawley rats.

Fields

  • Name: The name of the brain region (required).
  • Acronym: Acronym used for the brain region (required).
  • Description: A general description of the brain region.
  • Atlas: The brain atlas in which the brain region is defined. Options described above (required).

Permissions

Once a new brain atlas has been implemented it becomes available to everyone.

API Access

The API allows for programmable access, enabling you to read entries through the API. For details about the fields and data structure, refer to the Brain region API endpoint documentation.