Brain regions

communicating branch (Winslow, 1733)cbrBrain Maps 4.0 - Rat brain Atlas
Ammon’s horn field CA1 ventral part stratum lacunosum-moleculare (>1840)CA1v-slmBrain Maps 4.0 - Rat brain Atlas
distal glossopharyngeal ganglion (>1840)GDIXBrain Maps 4.0 - Rat brain Atlas
presubiculum (Swanson & Cowan, 1977)PREBrain Maps 4.0 - Rat brain Atlas
area 25 (Brodmann, 1909)25Brain Maps 4.0 - Rat brain Atlas
tegmental striatotegmental fascicle (Swanson, 2018)stgtBrain Maps 4.0 - Rat brain Atlas
optic tract (Vicq d’Azyr, 1784)optBrain Maps 4.0 - Rat brain Atlas
cerebellar fissures (>1840)cbfBrain Maps 4.0 - Rat brain Atlas
pontine medial reticulospinal tract (Swanson, 2015)mrstpBrain Maps 4.0 - Rat brain Atlas
medial lemniscus (>1840)mlBrain Maps 4.0 - Rat brain Atlas
thyrohyoid branch of hypoglossal nerve (Meckel, 1817)tXIIBrain Maps 4.0 - Rat brain Atlas
central cervical nucleus (>1840)CECBrain Maps 4.0 - Rat brain Atlas
medial hypothalamic zone (Nauta & Haymaker, 1969)HYmBrain Maps 4.0 - Rat brain Atlas
olfactory tubercle polymorph layer (>1840)OT3Brain Maps 4.0 - Rat brain Atlas
fimbria (Honegger, 1890)fimBrain Maps 4.0 - Rat brain Atlas
striatal ridge (>1840)SRIBrain Maps 4.0 - Rat brain Atlas
lateral intersegmental tract (>1840)itlBrain Maps 4.0 - Rat brain Atlas
cutaneous branch of dorsal branch of ulnar nerve (>1840)undcBrain Maps 4.0 - Rat brain Atlas
anterior esophageal plexus (Haller, 1762)espaBrain Maps 4.0 - Rat brain Atlas
spinal tract of trigeminal nerve (>1840)sptVBrain Maps 4.0 - Rat brain Atlas
anteroventral thalamic nucleus (>1840)AVBrain Maps 4.0 - Rat brain Atlas
hypothalamic striatotegmental fascicle (Swanson, 2018)stghBrain Maps 4.0 - Rat brain Atlas
paratenial nucleus (>1840)PTBrain Maps 4.0 - Rat brain Atlas
fourth ventricle general (Galen, c192)V4gBrain Maps 4.0 - Rat brain Atlas
medullary ventrolateral fascicle (Swanson, 2015)vlfmBrain Maps 4.0 - Rat brain Atlas
glossopharyngeal nerve (Huber, 1744)IXnBrain Maps 4.0 - Rat brain Atlas
mesomere 1 and 2 (>1840)mem1,2Brain Maps 4.0 - Rat brain Atlas
olfactory limb of anterior commissure (>1840)acoBrain Maps 4.0 - Rat brain Atlas
ansoparamedian fissure (>1840)apfBrain Maps 4.0 - Rat brain Atlas
anterior cutaneous branch of intercostal nerves (>1840)icnaBrain Maps 4.0 - Rat brain Atlas
trigeminal nerve central motor root (>1840)moVcBrain Maps 4.0 - Rat brain Atlas
cerebellar vermis central lobule sublobule a of lobule II (>1840)CENT2aBrain Maps 4.0 - Rat brain Atlas
bed nuclei of terminal stria posterior division (Ju & Swanson, 1989)BSTpBrain Maps 4.0 - Rat brain Atlas
paraventricular hypothalamic nucleus magnocellular division posterior magnocellular part (>1840)PVHpmBrain Maps 4.0 - Rat brain Atlas
lateral hypothalamic area middle group medial tier juxtaventromedial region ventral zone (Swanson, 2004)LHAjvvBrain Maps 4.0 - Rat brain Atlas
area 41 (Brodmann, 1909)41Brain Maps 4.0 - Rat brain Atlas
external nasal branches of infraorbital nerve (>1840)ioneBrain Maps 4.0 - Rat brain Atlas
Ammon’s horn field CA1 dorsal part deep pyramidal layer (>1840)CA1d-spdBrain Maps 4.0 - Rat brain Atlas
bed nuclei of terminal stria interfascicular nucleus premedullary nucleus (Ju & Swanson, 1989)BSTpmBrain Maps 4.0 - Rat brain Atlas
ansa cervicalis (>1840)ancBrain Maps 4.0 - Rat brain Atlas
inferior rectal nerves (>1840)irnBrain Maps 4.0 - Rat brain Atlas
hypothalamus anterior level (>1840)ANTBrain Maps 4.0 - Rat brain Atlas
nucleus of lateral lemniscus dorsal part (>1840)NLLdBrain Maps 4.0 - Rat brain Atlas
perireuniens nucleus (Brittain, 1988)PRBrain Maps 4.0 - Rat brain Atlas
cerebral nuclei (Swanson, 2000a)CNUBrain Maps 4.0 - Rat brain Atlas
tenia tecta (Swanson, 1992)TTBrain Maps 4.0 - Rat brain Atlas
area 26 (Brodmann, 1909)26Brain Maps 4.0 - Rat brain Atlas
third ventricle (Galen, c173)V3Brain Maps 4.0 - Rat brain Atlas
pretectal brachium of superior colliculus (Swanson, 2015)bscpBrain Maps 4.0 - Rat brain Atlas
area 22 (Brodmann, 1909)22Brain Maps 4.0 - Rat brain Atlas
anteroventral periventricular nucleus (Simerly et al., 1984)AVPVBrain Maps 4.0 - Rat brain Atlas
hypothalamic medullary stria (Swanson, 2018)smhBrain Maps 4.0 - Rat brain Atlas
lacrimal nerve (Meckel 1748; Bonhomme, 1748)lanBrain Maps 4.0 - Rat brain Atlas
submedial thalamic nucleus (>1840)SMTBrain Maps 4.0 - Rat brain Atlas
glossopharyngeal nerve root (>1840)IXrBrain Maps 4.0 - Rat brain Atlas
bed nuclei of terminal stria fusiform nucleus (Ju & Swanson, 1989)BSTfuBrain Maps 4.0 - Rat brain Atlas
radiation of corpus callosum occipital forceps (>1840)ocfBrain Maps 4.0 - Rat brain Atlas
spinal nucleus of trigeminal nerve oral part rostral dorsomedial part (>1840)SPVOrdmBrain Maps 4.0 - Rat brain Atlas
spinal lateral reticulospinal tract (Swanson, 2015)lrstsBrain Maps 4.0 - Rat brain Atlas
left gastric plexus (>1840)lgpBrain Maps 4.0 - Rat brain Atlas
retrohippocampal region (Swanson et al., 1987)RHPBrain Maps 4.0 - Rat brain Atlas
interpeduncular nucleus lateral subnucleus ventral part (>1840)IPNlvBrain Maps 4.0 - Rat brain Atlas
glossopharyngeal nerve central root (>1840)IXcBrain Maps 4.0 - Rat brain Atlas
stapedial nerve (>1840)stapBrain Maps 4.0 - Rat brain Atlas
rhinal sulcus (>1840)rhsBrain Maps 4.0 - Rat brain Atlas
tectal nigrotectal tract (Swanson, 2018)ntetBrain Maps 4.0 - Rat brain Atlas
Ammon’s horn field CA1 ventral part superficial pyramidal layer (>1840)CA1v-spsBrain Maps 4.0 - Rat brain Atlas
lateral hypothalamic area middle group perifornical tier subfornical region posterior zone premammillary subzone (Swanson, 2004)LHAsfpmBrain Maps 4.0 - Rat brain Atlas
lateral pectoral nerve (>1840)lpenBrain Maps 4.0 - Rat brain Atlas
denticulate ligament (Monro, 1783)delBrain Maps 4.0 - Rat brain Atlas
pontine nuclei (Jacobsohn, 1909)PONBrain Maps 4.0 - Rat brain Atlas
hepatic branches of posterior vagal trunk (>1840)vtrphBrain Maps 4.0 - Rat brain Atlas
spinal medial forebrain bundle (Swanson, 2015)mfbsBrain Maps 4.0 - Rat brain Atlas
renal plexus (Drake, 1707)replBrain Maps 4.0 - Rat brain Atlas
marginal mandibular branch of facial nerve (>1840)fntmBrain Maps 4.0 - Rat brain Atlas
habenular nuclei (>1840)HBrain Maps 4.0 - Rat brain Atlas
lateral septal nucleus caudal (caudodorsal) part ventral zone medial region dorsal domain (Risold & Swanson, 1997a)LSc.v.m.dBrain Maps 4.0 - Rat brain Atlas
lesser splanchnic nerve (Haller, 1762)lespBrain Maps 4.0 - Rat brain Atlas
subiculum ventral part stratum radiatum (>1840)SUBv-srBrain Maps 4.0 - Rat brain Atlas
septohippocampal nucleus (>1840)SHBrain Maps 4.0 - Rat brain Atlas
middle cervical ganglion (Haller, 1762)GMCBrain Maps 4.0 - Rat brain Atlas
crus 1 fissure 2 (>1840)cr1f2Brain Maps 4.0 - Rat brain Atlas
nerve to soleus (>1840)nsoBrain Maps 4.0 - Rat brain Atlas
lateral hypothalamic area middle group lateral tier ventral region parvicellular region (Swanson, 2004)LHApcBrain Maps 4.0 - Rat brain Atlas
ventral spinothalamic tract (>1840)sttvBrain Maps 4.0 - Rat brain Atlas
medullary reticular nucleus dorsal part (>1840)MDRNdBrain Maps 4.0 - Rat brain Atlas
fimbria principal part (Swanson, 2018)fiBrain Maps 4.0 - Rat brain Atlas
posterior thalamic complex (>1840)POBrain Maps 4.0 - Rat brain Atlas
area 8 (Brodmann, 1909)8Brain Maps 4.0 - Rat brain Atlas
medial geniculate complex ventral part (>1840)MGvBrain Maps 4.0 - Rat brain Atlas
spinal root of accessory nerve rootlets (>1840)sXIrBrain Maps 4.0 - Rat brain Atlas
pontine dorsal tegmental tract (Swanson, 2015)dttpBrain Maps 4.0 - Rat brain Atlas
midbrain reticular nucleus (>1840)MRNBrain Maps 4.0 - Rat brain Atlas
striatal fundus (>1840)FSBrain Maps 4.0 - Rat brain Atlas
area 9 (Brodmann, 1909)9Brain Maps 4.0 - Rat brain Atlas
hypoglossal nerve rootlets (>1840)XIIrlBrain Maps 4.0 - Rat brain Atlas
esophageal plexus (Haller, 1762)espBrain Maps 4.0 - Rat brain Atlas
spinal segment of spino-olivary tract (Swanson, 2018)sotsBrain Maps 4.0 - Rat brain Atlas
Ammon’s horn field CA1 (Lorente de Nó, 1934)CA1Brain Maps 4.0 - Rat brain Atlas
intercalated amygdalar nuclei (>1840)IABrain Maps 4.0 - Rat 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 documentation.