Brain regions

ventral (parvocellular) division of basal nucleusBvAllen Non-Human Primate Brain Atlas
medial nucleusMeAllen Non-Human Primate Brain Atlas
dorsal thalamusDThAllen Non-Human Primate Brain Atlas
cortical plate (outer)CPoAllen Non-Human Primate Brain Atlas
ventricular portion of RMSRMSvzAllen Non-Human Primate Brain Atlas
transitory migratory zoneTMZAllen Non-Human Primate Brain Atlas
putamenPuAllen Non-Human Primate Brain Atlas
polyform layer anlage of dentate gyrus (cortex)DGpfaAllen Non-Human Primate Brain Atlas
amygdalohippocampal areaAHAAllen Non-Human Primate Brain Atlas
dorsolateral prefrontal cortex (areas 9 and 46)dlPFAllen Non-Human Primate Brain Atlas
cerebral nucleiCxNAllen Non-Human Primate Brain Atlas
claustrumClaAllen Non-Human Primate Brain Atlas
intermediate cell dense zone of V1V1icdAllen Non-Human Primate Brain Atlas
stratum radiatum of CA1CA1raAllen Non-Human Primate Brain Atlas
caudal periamygdaloid cortex (cPAC)cPACAllen Non-Human Primate Brain Atlas
layer II of medial orbitofrontal cortexmOF2Allen Non-Human Primate Brain Atlas
polyform layer of dentate gyrus (cortex)DGpfAllen Non-Human Primate Brain Atlas
cortical plate of V1V1cpAllen Non-Human Primate Brain Atlas
ventricular zone of S1S1vzAllen Non-Human Primate Brain Atlas
layer V of V1V1-5Allen Non-Human Primate Brain Atlas
striatumSTRAllen Non-Human Primate Brain Atlas
lateral division of central nucleusCElAllen Non-Human Primate Brain Atlas
medial (posterior) entorhinal cortex (MEC)MECAllen Non-Human Primate Brain Atlas
entorhinal cortexECxAllen Non-Human Primate Brain Atlas
hippocampal subplate of CA3CA3spAllen Non-Human Primate Brain Atlas
outer cortical plate of rostral cingulate cortexrCGcpoAllen Non-Human Primate Brain Atlas
rostral migratory stream (RMS)RMSAllen Non-Human Primate Brain Atlas
cortical plate (inner)CPiAllen Non-Human Primate Brain Atlas
dorsal lateral geniculate nucleusDLGAllen Non-Human Primate Brain Atlas
basolateral nuclear complexBLNAllen Non-Human Primate Brain Atlas
primary visual cortex (V1, striate cortex, area 17)V1Allen Non-Human Primate Brain Atlas
layer I of medial orbitofrontal cortexmOF1Allen Non-Human Primate Brain Atlas
CA2 regionCA2Allen Non-Human Primate Brain Atlas
outer cortical plate of S1S1cpoAllen Non-Human Primate Brain Atlas
layer V of S1S1-5Allen Non-Human Primate Brain Atlas
intermediate zone of S1S1izAllen Non-Human Primate Brain Atlas
layer IVB of V1V1-4BAllen Non-Human Primate Brain Atlas
basal nucleus (basolateral nucleus)BAllen Non-Human Primate Brain Atlas
subventricular zoneSZAllen Non-Human Primate Brain Atlas
amygdalohippocampal area, magnocellualr partAHAmcAllen Non-Human Primate Brain Atlas
subventricular zone of S1S1szAllen Non-Human Primate Brain Atlas
ventral striatumvSTRAllen Non-Human Primate Brain Atlas
medial orbital frontal cortex (area 14)mOFAllen Non-Human Primate Brain Atlas
layer III of V1V1-3Allen Non-Human Primate Brain Atlas
rostral (anterior) presubiculumPrSrAllen Non-Human Primate Brain Atlas
layer III of S1S1-3Allen Non-Human Primate Brain Atlas
subventricular zone (outer)SZoAllen Non-Human Primate Brain Atlas
medial ganglionic eminenceMGEAllen Non-Human Primate Brain Atlas
marginal zone of S1S1mzAllen Non-Human Primate Brain Atlas
layer VI of caudal orbitofrontal cortexcOF6Allen Non-Human Primate Brain Atlas
subventricular zone of V1V1szAllen Non-Human Primate Brain Atlas
layer VI of medial orbitofrontal cortexmOF6Allen Non-Human Primate Brain Atlas
granular layer IV of S1S1-4Allen Non-Human Primate Brain Atlas
layer I of rostral cingulate cortexrCG1Allen Non-Human Primate Brain Atlas
inner cortical plate (infragranular layer) of S1S1-cpiAllen Non-Human Primate Brain Atlas
ventricular zone of rostral cingulate cortexrCGvzAllen Non-Human Primate Brain Atlas
intercalated nucleus of amygdalaINAAllen Non-Human Primate Brain Atlas
ventricular zoneVZAllen Non-Human Primate Brain Atlas
layer I of V2V2-1Allen Non-Human Primate Brain Atlas
layer V of medial orbitofrontal cortexmOF5Allen Non-Human Primate Brain Atlas
hippocampal stratum lucidum of CA3CA3slAllen Non-Human Primate Brain Atlas
caudal periamygdaloid cortex, dorsal partcPACdAllen Non-Human Primate Brain Atlas
stratum lacunosum-moleculare of CA3CA3lmAllen Non-Human Primate Brain Atlas
external segment of globus pallidusGPeAllen Non-Human Primate Brain Atlas
granular layer IV of caudal orbitofrontal cortexcOF4Allen Non-Human Primate Brain Atlas
periamygdaloid cortex (cortical amygdaloid nucleus)PACAllen Non-Human Primate Brain Atlas
caudal ganglionic eminenceCGEAllen Non-Human Primate Brain Atlas
white matter of V2V2wmAllen Non-Human Primate Brain Atlas
subventricular zone of rostral cingulate cortexrCGszAllen Non-Human Primate Brain Atlas
white matter of caudal orbitofrontal cortexcOFwmAllen Non-Human Primate Brain Atlas
transitory migratory zone of V1V1tmzAllen Non-Human Primate Brain Atlas
hippocampal plate of subiculumScpAllen Non-Human Primate Brain Atlas
marginal zone of CA2CA2mzAllen Non-Human Primate Brain Atlas
lateral (anterior) entorhinal cortex (LEC)LECAllen Non-Human Primate Brain Atlas
marginal zone of dentate gyrus (cortex)DGmzAllen Non-Human Primate Brain Atlas
hippocampal plate of CA2CA2cpAllen Non-Human Primate Brain Atlas
subplate zone of S1S1spAllen Non-Human Primate Brain Atlas
lateral perirhinal cortex (area 36)LPCAllen Non-Human Primate Brain Atlas
hippocampal plate of CA3CA3cpAllen Non-Human Primate Brain Atlas
CA3 regionCA3Allen Non-Human Primate Brain Atlas
marginal zone of CA1CA1mzAllen Non-Human Primate Brain Atlas
layer II of LECLEC2Allen Non-Human Primate Brain Atlas
subventricular zone (inner)SZiAllen Non-Human Primate Brain Atlas
inner subventricular zone of S1S1sziAllen Non-Human Primate Brain Atlas
caudate nucleusCaAllen Non-Human Primate Brain Atlas
hippocampal intermediate zone of CA1CA1izAllen Non-Human Primate Brain Atlas
shell of nucleus accumbensNACsAllen Non-Human Primate Brain Atlas
outer fiber (plexiform) zone of S1S1ofzAllen Non-Human Primate Brain Atlas
lateral nucleusLAllen Non-Human Primate Brain Atlas
ventral division of lateral nucleus, lateral partLvlAllen Non-Human Primate Brain Atlas
caudal orbital frontal cortex (area 13)cOFAllen Non-Human Primate Brain Atlas
basal nuclei (basal ganglia)BNAllen Non-Human Primate Brain Atlas
basal forebrainBFAllen Non-Human Primate Brain Atlas
amygdaloid complexAmyAllen Non-Human Primate Brain Atlas
internal segment of globus pallidusGPiAllen Non-Human Primate Brain Atlas
subiculumSAllen Non-Human Primate Brain Atlas
cerebral cortexCxAllen Non-Human Primate Brain Atlas
layer V of perirhinal cortex (area 35)MPC5Allen Non-Human Primate Brain Atlas
pyramidal layer of subiculumSpyAllen Non-Human Primate Brain Atlas
outer subventricular zone of S1S1szoAllen Non-Human Primate Brain Atlas

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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.