Brain regions

marginal zone of spinal cord (>1840)MZBrain Maps 4.0 - Rat brain Atlas
cerebral nuclei segment of striatotegmental fascicle (Swanson, 2018)stgcBrain Maps 4.0 - Rat brain Atlas
dorsal median sulcus of spinal cord (>1840)dmssBrain Maps 4.0 - Rat brain Atlas
lateral hypothalamic area anterior group retrochiasmatic area (>1840)RCHBrain Maps 4.0 - Rat brain Atlas
inferior cervical ganglion (Vieussens, 1684)GICBrain Maps 4.0 - Rat brain Atlas
tegmental medial forebrain bundle (Swanson, 2015)mfbtBrain Maps 4.0 - Rat brain Atlas
visceral area layers 1-6 (>1840)VISC1-6Brain Maps 4.0 - Rat brain Atlas
supraoptic decussations (>1840)supBrain Maps 4.0 - Rat brain Atlas
cerebellar vermis lobules II,III (>1840)LII,IIIBrain Maps 4.0 - Rat brain Atlas
hypothalamic mammillothalamic tract (Swanson, 2018)mtthBrain Maps 4.0 - Rat brain Atlas
secondary somatomotor areas (>1840)MOsBrain Maps 4.0 - Rat brain Atlas
posterior labial nerves (>1840)plaBrain Maps 4.0 - Rat brain Atlas
longitudinal pontine fibers (Arnold, 1838b)lpfBrain Maps 4.0 - Rat brain Atlas
dentate gyrus molecular layer (>1840)DGmoBrain Maps 4.0 - Rat brain Atlas
right colic plexus (>1840)rcplBrain Maps 4.0 - Rat brain Atlas
lateral cutaneous nerve of calf (>1840)lcncBrain Maps 4.0 - Rat brain Atlas
trigeminal sulcus (Swanson, 2018)tgsBrain Maps 4.0 - Rat brain Atlas
intermediolateral nucleus (>1840)IMLBrain Maps 4.0 - Rat brain Atlas
anteromedial visual area (Espinoza & Thomas, 1983)VISamBrain Maps 4.0 - Rat brain Atlas
parasubiculum (>1840)PARBrain Maps 4.0 - Rat brain Atlas
interposed nucleus (>1840)IPBrain Maps 4.0 - Rat brain Atlas
medullary reticular nucleus (>1840)MDRNBrain Maps 4.0 - Rat brain Atlas
inferior colliculus (Haller, 1762)ICBrain Maps 4.0 - Rat brain Atlas
superior hypogastric plexus (Tiedemann, 1822)shplBrain Maps 4.0 - Rat brain Atlas
cerebral nuclei segment of pallidothalamic fascicle (Swanson, 2018)pthfcBrain Maps 4.0 - Rat brain Atlas
pontine medial longitudinal fascicle (Swanson, 2015)mlfpBrain Maps 4.0 - Rat brain Atlas
spinal root of accessory nerve central rootlets (Swanson, 2018)sXIcBrain Maps 4.0 - Rat brain Atlas
primary somatosensory area upper limb field layers 1-6 (>1840)SSp-ul1-6Brain Maps 4.0 - Rat brain Atlas
nerve to tensor tympani (Arnold, 1834)ntyBrain Maps 4.0 - Rat brain Atlas
tegmental cervicothalamic tract (Swanson, 2018)cetttgBrain Maps 4.0 - Rat brain Atlas
nucleus reuniens caudal division median part (Risold et al., 1997)REcmBrain Maps 4.0 - Rat brain Atlas
midbrain nucleus of trigeminal nerve (>1840)MEVBrain Maps 4.0 - Rat brain Atlas
opening of cerebral aqueduct (>1840)AQoBrain Maps 4.0 - Rat brain Atlas
spinal nucleus of trigeminal nerve oral part caudal dorsomedial part (>1840)SPVOcdmBrain Maps 4.0 - Rat brain Atlas
magnocellular reticular nucleus (>1840)MARNBrain Maps 4.0 - Rat brain Atlas
tuberomammillary nucleus (>1840)TMBrain Maps 4.0 - Rat brain Atlas
inferior testicular nerves (>1840)itenBrain Maps 4.0 - Rat brain Atlas
olive (Tiedemann, 1821)olBrain Maps 4.0 - Rat brain Atlas
mediodorsal thalamic nucleus lateral part (>1840)MDlBrain Maps 4.0 - Rat brain Atlas
lateral septal nucleus rostral (rostroventral) part medial zone ventral region (Risold & Swanson, 1997a)LSr.m.vBrain Maps 4.0 - Rat brain Atlas
ventral lateral geniculate nucleus lateral zone (>1840)LGvlBrain Maps 4.0 - Rat brain Atlas
vascular organ of lamina terminalis (>1840)OVBrain Maps 4.0 - Rat brain Atlas
lateral hypothalamic area middle group lateral tier ventral region medial zone (Swanson, 2004)LHAvmBrain Maps 4.0 - Rat brain Atlas
collateral branch of intercostal nerves (Davies et al., 1931)inccBrain Maps 4.0 - Rat brain Atlas
principal lateral olfactory tract (Swanson, 2018)lotpBrain Maps 4.0 - Rat brain Atlas
area 35 (Brodmann, 1909)35Brain Maps 4.0 - Rat brain Atlas
retina (Herophilus, 335-263 BC)RBrain Maps 4.0 - Rat brain Atlas
lateral hypothalamic area middle group lateral tier tuberal nucleus intermediate part (Swanson, 2004)TUiBrain Maps 4.0 - Rat brain Atlas
spinotelencephalic tract (Swanson, 2018)steltBrain Maps 4.0 - Rat brain Atlas
cerebellar vermis lingula (Malacarne, 1776)LINGBrain Maps 4.0 - Rat brain Atlas
bed nucleus of accessory olfactory tract (Scalia & Witans, 1975)BABrain Maps 4.0 - Rat brain Atlas
endbrain terminal stria (Swanson, 2015)steBrain Maps 4.0 - Rat brain Atlas
ventral median fissure of spinal cord (>1840)vmfsBrain Maps 4.0 - Rat brain Atlas
parabrachial nucleus lateral division internal part (>1840)PBliBrain Maps 4.0 - Rat brain Atlas
longitudinal tectal sulcus (>1840)ltsBrain Maps 4.0 - Rat brain Atlas
muscular branches of medial plantar nerve (>1840)mplnmBrain Maps 4.0 - Rat brain Atlas
Ammon’s horn field CA2 stratum radiatum (>1840)CA2srBrain Maps 4.0 - Rat brain Atlas
cerebral cortex (Swanson, 2000a)CTXBrain Maps 4.0 - Rat brain Atlas
simple fissure (Swanson, 1992)sifBrain Maps 4.0 - Rat brain Atlas
atrial plexuses (>1840)atplBrain Maps 4.0 - Rat brain Atlas
choroid plexus of lateral ventricle (Vicq d’Azyr, 1784)chplBrain Maps 4.0 - Rat brain Atlas
subthalamic fascicle (>1840)stfBrain Maps 4.0 - Rat brain Atlas
pontine ventral spinocerebellar tract (Swanson, 2015)vsctpBrain Maps 4.0 - Rat brain Atlas
epibranchial placodes (>1840)ebpBrain Maps 4.0 - Rat brain Atlas
paramedian fissure (>1840)pmfBrain Maps 4.0 - Rat brain Atlas
suboccipital nerve (Winslow, 1733)socnBrain Maps 4.0 - Rat brain Atlas
lesser petrosal nerve (>1840)lpnBrain Maps 4.0 - Rat brain Atlas
paraventricular hypothalamic nucleus magnocellular division posterior magnocellular part lateral zone (>1840)PVHpmlBrain Maps 4.0 - Rat brain Atlas
tegmental mammillary peduncle (Swanson, 2018)mptgBrain Maps 4.0 - Rat brain Atlas
body of lateral ventricle (Bell, 1803b)VLbBrain Maps 4.0 - Rat brain Atlas
mammillary body (Ludwig, 1799)MBOBrain Maps 4.0 - Rat brain Atlas
superior salivatory nucleus (>1840)SSNBrain Maps 4.0 - Rat brain Atlas
retrosplenial area ventral part zone a layers 1-6 (>1840)RSPv.a1-6Brain Maps 4.0 - Rat brain Atlas
ectorhinal area layers 1-6 (>1840)ECT1-6Brain Maps 4.0 - Rat brain Atlas
anterolateral visual area layers 1-6 (>1840)VISal1-6Brain Maps 4.0 - Rat brain Atlas
nucleus reuniens rostral division anterior part (Risold et al., 1997)REraBrain Maps 4.0 - Rat brain Atlas
median eminence external lamina (>1840)MEexBrain Maps 4.0 - Rat brain Atlas
tegmental central tegmental tract (Swanson, 2015)ctttBrain Maps 4.0 - Rat brain Atlas
tegmental superior cerebellar peduncle (Swanson, 2015)scptBrain Maps 4.0 - Rat brain Atlas
hypoglossal triangle (>1840)htBrain Maps 4.0 - Rat brain Atlas
periaqueductal gray medial division (Beitz, 1985)PAGmBrain Maps 4.0 - Rat brain Atlas
nerve to inferior oblique (>1840)IIIioBrain Maps 4.0 - Rat brain Atlas
hypothalamic part of third ventricle principal part (Swanson, 2018)V3hBrain Maps 4.0 - Rat brain Atlas
subiculum dorsal part pyramidal layer (>1840)SUBd-spBrain Maps 4.0 - Rat brain Atlas
area 33 (Brodmann, 1909)33Brain Maps 4.0 - Rat brain Atlas
ventrolateral hypothalamic tract (Swanson, 2004)vltBrain Maps 4.0 - Rat brain Atlas
ventral root (>1840)vrtBrain Maps 4.0 - Rat brain Atlas
anteromedial thalamic nucleus ventral part (Canteras & Swanson, 1992a)AMvBrain Maps 4.0 - Rat brain Atlas
medullary gracile fascicle (Swanson, 2015)grfmBrain Maps 4.0 - Rat brain Atlas
tegmental habenulo-interpeduncular tract (Swanson, 2015)hittgBrain Maps 4.0 - Rat brain Atlas
ventral premammillary nucleus (>1840)PMvBrain Maps 4.0 - Rat brain Atlas
thoracic part of spinal cord (>1840)SP-TBrain Maps 4.0 - Rat brain Atlas
vestibular nerve central root (>1840)vVIIIcBrain Maps 4.0 - Rat brain Atlas
lateral hypothalamic area middle group perifornical tier subfornical region (Swanson, 2004)LHAsfBrain Maps 4.0 - Rat brain Atlas
primary somatosensory area trunk field layers 1-6 (>1840)SSp-tr1-6Brain Maps 4.0 - Rat brain Atlas
lateral hypothalamic area middle group lateral tier tuberal nucleus subventromedial part (Swanson, 2004)TUsvBrain Maps 4.0 - Rat brain Atlas
communicating branches of sympathetic trunk (>1840)sytcBrain Maps 4.0 - Rat brain Atlas
medullary segment of spinal tract of trigeminal nerve (Swanson, 2015)sptVmBrain Maps 4.0 - Rat brain Atlas
third ventricle pineal recess (>1840)V3piBrain Maps 4.0 - Rat brain Atlas
parabrachial nucleus lateral division central part (>1840)PBlcBrain 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.