Brain regions

dentate nucleus, magnocellular partDNmSwanson 2004 Rat Brain Atlas
ambiguus nucleus, semicompact partAmbSCAllen Developing Human Brain Atlas
rostral subdivision of area 40/39A40/39rAllen Developing Human Brain Atlas
Temporal association areas, layer 4TEa4Allen Mouse Brain Atlas
paracochlear glial substancePCGSPaxinos & Watson 1997 Rat Brain Atlas
basolateral amygdalar nucleus anterior part (>1840)BLAaBrain Maps 4.0 - Rat brain Atlas
striatal part of olfactory tuberculumTuStrAllen Developing Mouse Brain Atlas
intermediate stratum of isADLisADLiAllen Developing Mouse Brain Atlas
field CA2 of hippocampusCA2Paxinos & Franklin 2001 Mouse Brain Atlas
mantle zone of r5BIr5BImAllen Developing Mouse Brain Atlas
cuneocerebellar tract (>1840)cctBrain Maps 4.0 - Rat brain Atlas
lateral posterior thalamic nucleus, mediocaudal partLPMCPaxinos & Watson 1997 Rat Brain Atlas
mantle zone of m1ALm1ALmAllen Developing Mouse Brain Atlas
pontine reticular nucleus, caudal partPRNcSwanson 2004 Rat Brain Atlas
sacral splanchnic nerves (>1840)saspBrain Maps 4.0 - Rat brain Atlas
I-IIVe-I-IIAllen Human Brain Atlas
paraventricular nucleus of the hypothalamus, right, descending division, dorsal parvicellular partPVHdpAllen Human Brain Atlas
layer 4 of PRh-EctPRh-Ect-4Allen Developing Mouse Brain Atlas
striatumStrAllen Human Brain Atlas
Edinger-Westphal nucleus, leftEWAllen Human Brain Atlas
posterolateral fissure (Larsell, 1937)plfBrain Maps 4.0 - Rat brain Atlas
layer V of area M1ulM1ul5Allen Developing Human Brain Atlas
r1 part of lateral pontine nucleir1LPnAllen Developing Mouse Brain Atlas
r10 part of dorsal parvicellular reticular formationr10DPCRtAllen Developing Mouse Brain Atlas
field CA2, pyramidal layerCA2spSwanson 2004 Rat Brain Atlas
suprachiasmatic nucleus, ventrolateral partSChVLPaxinos & Franklin 2001 Mouse Brain Atlas
left coronary plexus (Scarpa, 1794)copllBrain Maps 4.0 - Rat brain Atlas
optic chiasm (Galen, c173)ochBrain Maps 4.0 - Rat brain Atlas
lateral amygdalar nucleusLASwanson 2004 Rat Brain Atlas
SP in perirhinal cortexSPpcAllen Developing Human Brain Atlas
ventral (parvocellular) division of basal nucleusBvAllen Non-Human Primate Brain Atlas
posteromedial visual area layers 1-6 (>1840)VISpm1-6Brain Maps 4.0 - Rat brain Atlas
medial nucleusMeAllen Non-Human Primate Brain Atlas
oculomotor nerve root (>1840)IIIrBrain Maps 4.0 - Rat brain Atlas
cuneate tubercle (>1840)cutBrain Maps 4.0 - Rat brain Atlas
periventricular area of thalamusPeVAAllen Developing Human Brain Atlas
mantle zone of DgDgmAllen Developing Mouse Brain Atlas
PostsubiculumPOSTAllen Mouse Brain Atlas
internal cortical nucleus of inferior colliculusICICAllen Developing Mouse Brain Atlas
ventricular zone of JcPVJcPVvAllen Developing Mouse Brain Atlas
supraoptic commissuresocAllen Developing Mouse Brain Atlas
anterior lobe cerebellumAntPaxinos & Franklin 2001 Mouse Brain Atlas
basal nucleus of meynert, rightnbMAllen Human Brain Atlas
sacral spinal ganglia (>1840)GSNsa1-4Brain Maps 4.0 - Rat brain Atlas
ventral nucleus of the lateral lemniscusVLLPaxinos & Watson 1997 Rat Brain Atlas
Field CA2, pyramidal layerCA2spAllen Mouse Brain Atlas
Lateral group of the dorsal thalamusLATAllen Mouse Brain Atlas
inner VZ in posteror frontal cortex (motor cortex)fVZm1iAllen Developing Human Brain Atlas
dorsal thalamusDThAllen Non-Human Primate Brain Atlas
lateral hypothalamic area, juxtadorsomedial regionLHAjdSwanson 2004 Rat Brain Atlas
central amygdalar nucleus lateral part (Swanson, 1992)CEAlBrain Maps 4.0 - Rat brain Atlas
inferior olive, subnucleus A of medial nucleusIOAPaxinos & Watson 1997 Rat Brain Atlas
bed nuclei of terminal stria interfascicular nucleus (Ju & Swanson, 1989)BSTifBrain Maps 4.0 - Rat brain Atlas
nucleus of the solitary tract, dorsomedial partSolDMPaxinos & Watson 1997 Rat Brain Atlas
precommissural pretectal domainPcPAllen Developing Mouse Brain Atlas
ventricles, r6 basal platev_r6BAllen Developing Mouse Brain Atlas
posterolateral fissureplfPaxinos & Franklin 2001 Mouse Brain Atlas
granule cell layer of the accessory olfactory bulbGrAPaxinos & Watson 1997 Rat Brain Atlas
brachial plexus (Camper, 1760)bpBrain Maps 4.0 - Rat brain Atlas
agranular insular cortex, ventral partAIVPaxinos & Franklin 2001 Mouse Brain Atlas
paramedian sulcus pmsPaxinos & Watson 1997 Rat Brain Atlas
AOB, mitral cell layerAMtrAllen Developing Mouse Brain Atlas
frontal operculum, leftfroAllen Human Brain Atlas
ventral anterior nucleus of the thalamus, leftVAAllen Human Brain Atlas
olfactory bulb (Weitbrecht, 1751)OBBrain Maps 4.0 - Rat brain Atlas
marginal layer of posterior cortical nucleusCoP-mAllen Developing Human Brain Atlas
lateral fissure, middle (ascending) ramuslas-mAllen Developing Human Brain Atlas
epifascicular nucleusEFPaxinos & Franklin 2001 Mouse Brain Atlas
nucleus of the solitary tractSolPaxinos & Franklin 2001 Mouse Brain Atlas
medial vestibular nucleusMVeAllen Developing Human Brain Atlas
layer IV of area 36cA36c4Allen Developing Human Brain Atlas
Mediomedial anterior visual area, layer 2/3VISmma2/3Allen Mouse Brain Atlas
subiculum, ventral part, molecular layerSUBv-mSwanson 2004 Rat 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
median preoptic nucleusMEPOSwanson 2004 Rat Brain Atlas
Orbital area, lateral part, layer 5ORBl5Allen Mouse Brain Atlas
intermediate stratum of LAPLAPiAllen Developing Mouse Brain Atlas
periventricular stratum of PO1PO1pAllen Developing Mouse Brain Atlas
upper basal lateral hypothalamic areaUBLHAllen Developing Mouse Brain Atlas
nigrothalamic tract (>1840)nttBrain Maps 4.0 - Rat brain Atlas
agranular insular area, ventral partAIvSwanson 2004 Rat Brain Atlas
olivocerebellar tract (>1840)octBrain Maps 4.0 - Rat brain Atlas
caudal subdivision of area 21A21cAllen Developing Human Brain Atlas
layer II of area 45opA45op2Allen Developing Human Brain Atlas
r4 part of basointermediate reticular formationr4BIRtAllen Developing Mouse Brain Atlas
Lateral tegmental nucleusLTNAllen Mouse Brain Atlas
prepontine hindbrainPPHAllen Developing Mouse 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
cortical plate (outer)CPoAllen Non-Human Primate Brain Atlas
nucleus circularisNCSwanson 2004 Rat Brain Atlas
Magnocellular reticular nucleusMARNAllen Mouse Brain Atlas
ventricular zone of the SpALSpALvAllen Developing Mouse Brain Atlas
lateropallial amygdalopiriform areaLAPAllen Developing Mouse Brain Atlas
intercollicular nucleus, leftICNAllen Human Brain Atlas
nucleus of the brachium inferior colliculusNBSwanson 2004 Rat Brain Atlas
ventricles, m2 alar platev_m2AAllen Developing Mouse 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.