Brain regions

striatal part of olfactory tuberculumTuStrAllen Developing Mouse Brain Atlas
intermediate stratum of isADLisADLiAllen Developing Mouse Brain Atlas
mantle zone of r5BIr5BImAllen Developing Mouse Brain Atlas
mantle zone of m1ALm1ALmAllen Developing Mouse Brain Atlas
layer 4 of PRh-EctPRh-Ect-4Allen Developing Mouse Brain Atlas
r1 part of lateral pontine nucleir1LPnAllen Developing Mouse Brain Atlas
r10 part of dorsal parvicellular reticular formationr10DPCRtAllen Developing Mouse Brain Atlas
mantle zone of DgDgmAllen Developing 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
precommissural pretectal domainPcPAllen Developing Mouse Brain Atlas
ventricles, r6 basal platev_r6BAllen Developing Mouse Brain Atlas
AOB, mitral cell layerAMtrAllen Developing 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
r4 part of basointermediate reticular formationr4BIRtAllen Developing Mouse Brain Atlas
prepontine hindbrainPPHAllen Developing Mouse Brain Atlas
ventricular zone of the SpALSpALvAllen Developing Mouse Brain Atlas
lateropallial amygdalopiriform areaLAPAllen Developing Mouse Brain Atlas
ventricles, m2 alar platev_m2AAllen Developing Mouse Brain Atlas
core of SCHSCHcAllen Developing Mouse Brain Atlas
external globus pallidumEPalAllen Developing Mouse Brain Atlas
periventricular stratum of r8Limr8LimpAllen Developing Mouse Brain Atlas
trochlear nerve root4nAllen Developing Mouse Brain Atlas
cerebellar nuclei of CbHCbHNAllen Developing Mouse Brain Atlas
ventricular zone of POPOvAllen Developing Mouse Brain Atlas
mantle zone of SSmAllen Developing Mouse Brain Atlas
anterior tegmental nucleusATgAllen Developing Mouse Brain Atlas
mantle zone of r8Trr8TrmAllen Developing Mouse Brain Atlas
mantle zone of p3Bp3BmAllen Developing Mouse Brain Atlas
intermediate stratum of PalSePalSeiAllen Developing Mouse Brain Atlas
subbrachial nucleus, caudal partSubBCAllen Developing Mouse Brain Atlas
median supracommissural nucleusMnSCAllen Developing Mouse Brain Atlas
ventricular zone of m1Bm1BvAllen Developing Mouse Brain Atlas
p2 portion of the medial terminal nucleus of the accessory optic tractp2MTAllen Developing Mouse Brain Atlas
anterior commissure bedACBedAllen Developing Mouse Brain Atlas
superficial stratum of r8Fr8FsAllen Developing Mouse Brain Atlas
r1 part of basointermediate reticular formationr1BIRtAllen Developing Mouse Brain Atlas
periventricular stratum of r3BLr3BLpAllen Developing Mouse Brain Atlas
ventricles, rhombomere 4v_r4Allen Developing Mouse Brain Atlas
ventricular zone of THyB-DTHyB-DvAllen Developing Mouse Brain Atlas
ventricular zone of PrSPrSvAllen Developing Mouse Brain Atlas
mantle zone of r2Limr2LimmAllen Developing Mouse Brain Atlas
mantle zone of r9BLr9BLmAllen Developing Mouse Brain Atlas
intermediate stratum of AODAODiAllen Developing Mouse Brain Atlas
mantle zone of r11BIr11BImAllen Developing Mouse Brain Atlas
superficial stratum of r3BMr3BMsAllen Developing Mouse Brain Atlas
ventricular zone of the SpAMSpAMvAllen Developing Mouse Brain Atlas
superficial stratum of MPallMPallsAllen Developing Mouse Brain Atlas
superficial stratum of ZICZICsAllen Developing Mouse Brain Atlas
r2 part of basointermediate reticular formationr2BIRtAllen Developing Mouse Brain Atlas
r5 part of dorsal parvicellular reticular formationr5DPCRtAllen Developing Mouse Brain Atlas
periventricular stratum of r2BLr2BLpAllen Developing Mouse Brain Atlas
mantle zone of m2Limm2LimmAllen Developing Mouse Brain Atlas
periventricular stratum of r4Fr4FpAllen Developing Mouse Brain Atlas
cortex of cerebellar hemisphereCbHCxAllen Developing Mouse Brain Atlas
ventricles, alar plate of m1v_m1AAllen Developing Mouse Brain Atlas
r9 alar plater9AAllen Developing Mouse Brain Atlas
mantle zone of SpBMSpBMmAllen Developing Mouse Brain Atlas
ventricular zone of r2Limr2LimvAllen Developing Mouse Brain Atlas
r2 part of principal trigeminal sensory nucleusr2Pr5Allen Developing Mouse Brain Atlas
mantle zone of SeDgSeDgmAllen Developing Mouse Brain Atlas
medial basal reticular formation of m1m1BRtAllen Developing Mouse Brain Atlas
superficial stratum of r4BIr4BIsAllen Developing Mouse Brain Atlas
ventricular zone of StrSeStrSevAllen Developing Mouse Brain Atlas
r9 part of basomedial reticular formationr9BMRtAllen Developing Mouse Brain Atlas
r11 part of ventral parvicellular reticular formationr11VPCRtAllen Developing Mouse Brain Atlas
ventricular zone of r9Fr9FvAllen Developing Mouse Brain Atlas
mantle zone of SeStrSeStrmAllen Developing Mouse Brain Atlas
ventricular zone of r1Trr1TrvAllen Developing Mouse Brain Atlas
r10 part of basomedial reticular formationr10BMRtAllen Developing Mouse Brain Atlas
shell part of DTgDTgSAllen Developing Mouse Brain Atlas
corticoid layer of TuStrTuStr2Allen Developing Mouse Brain Atlas
ventral (liminal) part of the spinal alar plateSpAVAllen Developing Mouse Brain Atlas
periventricular stratum of ITThITThpAllen Developing Mouse Brain Atlas
lateral part of MPOMPOLAllen Developing Mouse Brain Atlas
intermediate stratum of PrS (white matter/subplate)PrSiAllen Developing Mouse Brain Atlas
intermediate stratum of DgSeDgSeiAllen Developing Mouse Brain Atlas
superficial stratum of r3Cor3CosAllen Developing Mouse Brain Atlas
r9 part of the basolateral intermediate zoner9BLIZAllen Developing Mouse Brain Atlas
mantle zone of CACAmAllen Developing Mouse Brain Atlas
intermediate stratum of r8Ver8VeiAllen Developing Mouse Brain Atlas
superficial stratum of THyB-DTHyB-DsAllen Developing Mouse Brain Atlas
r5 roof plater5RAllen Developing Mouse Brain Atlas
mesomere 2 (preisthmus or caudal midbrain)m2Allen Developing Mouse Brain Atlas
ventricular zone of r4Trr4TrvAllen Developing Mouse Brain Atlas
Rexed's layer 6 (basis of dorsal horn)6SpAllen Developing Mouse Brain Atlas
ventricles, basal peduncular hypothalamusv_PHyBAllen Developing Mouse Brain Atlas
ventricles, SpC alar platev_SpAAllen Developing Mouse Brain Atlas
superficial stratum of PCx (cortical plate/marginal zone)PCsAllen Developing Mouse Brain Atlas
optic tractoptAllen Developing Mouse Brain Atlas
ventral posteromedial nucleusVPMAllen Developing Mouse Brain Atlas
periventricular stratum of r5Fr5FpAllen Developing Mouse Brain Atlas
superficial stratum of r6Cor6CosAllen Developing Mouse Brain Atlas
intermediate stratum of r11BLr11BLiAllen Developing Mouse Brain Atlas
OB inner plexiform layerOB-IplAllen Developing Mouse Brain Atlas
ventricular zone of r10Ar10AvAllen Developing Mouse Brain Atlas
ventricles, caudal secondary prosencephalonv_CSPAllen 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.