Brain regions

ambiguus nucleus, semicompact partAmbSCAllen Developing Human Brain Atlas
rostral subdivision of area 40/39A40/39rAllen Developing Human Brain Atlas
layer V of area M1ulM1ul5Allen Developing Human Brain Atlas
SP in perirhinal cortexSPpcAllen Developing Human Brain Atlas
periventricular area of thalamusPeVAAllen Developing Human Brain Atlas
inner VZ in posteror frontal cortex (motor cortex)fVZm1iAllen Developing Human Brain Atlas
marginal layer of posterior cortical nucleusCoP-mAllen Developing Human Brain Atlas
lateral fissure, middle (ascending) ramuslas-mAllen Developing Human Brain Atlas
medial vestibular nucleusMVeAllen Developing Human Brain Atlas
layer IV of area 36cA36c4Allen Developing Human Brain Atlas
pyramidal cells of rostral CA4CA4RpyAllen Developing Human Brain Atlas
SP in caudal presubicular cortex (postsubiculum)SPprscAllen Developing Human Brain Atlas
SZ in posterosuperior (dorsal) parietal cortexpSZpdAllen Developing Human Brain Atlas
caudal subdivision of area 21A21cAllen Developing Human Brain Atlas
layer II of area 45opA45op2Allen Developing Human Brain Atlas
corticorubral fiberscruAllen Developing Human Brain Atlas
stratum moleculare of rostral CA3CA3RsmoAllen Developing Human Brain Atlas
Purkinje cell layer of PVAPVApAllen Developing Human Brain Atlas
lamina dissecans of caudal presubiculumPrScldAllen Developing Human Brain Atlas
extreme capsuleextrCAllen Developing Human Brain Atlas
layer IV of area TFOTFO4Allen Developing Human Brain Atlas
pyramidal layer of uncal subiculumSUpyAllen Developing Human Brain Atlas
caudal subdivision of BNSTmBSTmcAllen Developing Human Brain Atlas
root of accessory nerver11Allen Developing Human Brain Atlas
polymorphic layer of rostral subiculumSRpfAllen Developing Human Brain Atlas
SP in entorhinal cortexSPecAllen Developing Human Brain Atlas
medial olfactory striamostAllen Developing Human Brain Atlas
layer III of area 14cA14c3Allen Developing Human Brain Atlas
lower limb region of S1S1lmAllen Developing Human Brain Atlas
inner SZ in dorsomedial extrastriate cortexoSZdmiAllen Developing Human Brain Atlas
parasolitary nucleusPSolAllen Developing Human Brain Atlas
SP in retrosplenial cortexSPrsAllen Developing Human Brain Atlas
root of glossopharyngeal nerver9Allen Developing Human Brain Atlas
rhombomere DRhDAllen Developing Human Brain Atlas
motor nucleus of trigeminal nerveMo5Allen Developing Human Brain Atlas
SP in medial (posterior) entorhinal cortexSPmecAllen Developing Human Brain Atlas
deep (subplate) layer of TTTTdAllen Developing Human Brain Atlas
supraoculomotor nucleusSu3Allen Developing Human Brain Atlas
MZ in posterior parahippocampal cortextMZphAllen Developing Human Brain Atlas
layer I of area 11lA11l1Allen Developing Human Brain Atlas
rhombic lipRhLAllen Developing Human Brain Atlas
retrolenticular portionrelpAllen Developing Human Brain Atlas
layer V of area 17V1-5Allen Developing Human Brain Atlas
layer V of area 22prA22pr5Allen Developing Human Brain Atlas
ventral hippocampal commissurevhicAllen Developing Human Brain Atlas
layer V of area 32mcA32mc-5Allen Developing Human Brain Atlas
layer II of area 31A31-2Allen Developing Human Brain Atlas
spino-olivary tractspolAllen Developing Human Brain Atlas
rhabdoid nucleusRbdAllen Developing Human Brain Atlas
dorsolateral temporal neocortexDLTCAllen Developing Human Brain Atlas
SP in dorsolateral temporal cortextSPdlAllen Developing Human Brain Atlas
caudal (posterior) transverse temporal gyrusTTGcAllen Developing Human Brain Atlas
external sagittal stratumssteAllen Developing Human Brain Atlas
dorsal motor nucleus of the vagus (vagal nucleus)10NAllen Developing Human Brain Atlas
substantia nigraSNAllen Developing Human Brain Atlas
layer I of area 14cA14c1Allen Developing Human Brain Atlas
general somatic afferent cell column of hindbrainGSAAllen Developing Human Brain Atlas
dorsal division of MCC (area 32mc)A32mcAllen Developing Human Brain Atlas
external segment of globus pallidusGPeAllen Developing Human Brain Atlas
lateral column of BNSTscBSTsclAllen Developing Human Brain Atlas
epicoeruleus nucleusEpCAllen Developing Human Brain Atlas
parainterfascicular nucleusPIFAllen Developing Human Brain Atlas
layer V of area 22pcA22pc5Allen Developing Human Brain Atlas
layer IV of area 45opA45op4Allen Developing Human Brain Atlas
magnocellular nucleus of lateral hypothalamic areaLHmcAllen Developing Human Brain Atlas
layer I of area 21rA21r1Allen Developing Human Brain Atlas
tuberoinfundibular pathtuinAllen Developing Human Brain Atlas
layer I of lateral intermediate entorhinal cortexELI1Allen Developing Human Brain Atlas
layer I of area 42A42-1Allen Developing Human Brain Atlas
layer II of area 22rA22r2Allen Developing Human Brain Atlas
layer I of area LOLO1Allen Developing Human Brain Atlas
caudal subdivision of medial nucleusMeCAllen Developing Human Brain Atlas
paramedian nucleusPNparAllen Developing Human Brain Atlas
paracentral lobule, caudal partPCLcAllen Developing Human Brain Atlas
nucleus UUAllen Developing Human Brain Atlas
inferior occipital gyrusIOGAllen Developing Human Brain Atlas
layer III of area M1lmM1lm3Allen Developing Human Brain Atlas
group of noradrenergic neurons in ponsPnNAAllen Developing Human Brain Atlas
lambdoid septal zoneLdAllen Developing Human Brain Atlas
layer IV of area 22iA22i4Allen Developing Human Brain Atlas
basolateral nucleus (basal nucleus)BLAllen Developing Human Brain Atlas
VZ in subcallosal regionscVZAllen Developing Human Brain Atlas
layer IVCa of area 17V1-4CaAllen Developing Human Brain Atlas
interpeduncular nucleus, rostral subnucleusIPrAllen Developing Human Brain Atlas
SP in dysgranular insular cortexiSPdgAllen Developing Human Brain Atlas
SP in midinferior temporal cortextSPmiAllen Developing Human Brain Atlas
ambiguus nucleus, loose partAmbLAllen Developing Human Brain Atlas
layer IV of caudal dysgranular insular cortexCIdg4Allen Developing Human Brain Atlas
layer VI of area 5mA5m6Allen Developing Human Brain Atlas
layer I of area 29A29-1Allen Developing Human Brain Atlas
layer VI of area 7rA7r6Allen Developing Human Brain Atlas
spinal lemniscus, midbrain portionsl-mAllen Developing Human Brain Atlas
MZ in medial (posterior) entorhinal cortexMZmecAllen Developing Human Brain Atlas
spinovestibular tractspveAllen Developing Human Brain Atlas
periaqueductal gray substance, dorsolateral portionPAGDAllen Developing Human Brain Atlas
SG in dorsolateral temporal cortextSGdlAllen Developing Human Brain Atlas
layer V of area 7ipcA7ipc5Allen Developing Human Brain Atlas
rhinal sulcusrsAllen Developing Human Brain Atlas
oculomotor sulcusocsAllen Developing Human Brain Atlas
layer II of area 41A41-2Allen Developing Human 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.