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Brain regions

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Brain region name
Acronym
Atlas
layer III of area 13mA13m3Allen Developing Human Brain Atlas
layer IV of area 13mA13m4Allen Developing Human Brain Atlas
layer V of area 13mA13m5Allen Developing Human Brain Atlas
layer VI of area 13mA13m6Allen Developing Human Brain Atlas
caudal subdivision of area 14A14cAllen Developing Human Brain Atlas
layer I of area 14cA14c1Allen Developing Human Brain Atlas
layer II of area 14cA14c2Allen Developing Human Brain Atlas
layer III of area 14cA14c3Allen Developing Human Brain Atlas
layer IV of area 14cA14c4Allen Developing Human Brain Atlas
layer V of area 14cA14c5Allen Developing Human Brain Atlas
layer VI of area 14cA14c6Allen Developing Human Brain Atlas
rostral subdivision of area 14A14rAllen Developing Human Brain Atlas
layer I of area 14rA14r1Allen Developing Human Brain Atlas
layer II of area 14rA14r2Allen Developing Human Brain Atlas
layer III of area 14rA14r3Allen Developing Human Brain Atlas
layer IV of area 14rA14r4Allen Developing Human Brain Atlas
layer V of area 14rA14r5Allen Developing Human Brain Atlas
layer VI of area 14rA14r6Allen Developing Human Brain Atlas
primary auditory cortex (core)A1CAllen Developing Human Brain Atlas
rostral portion of A1CA1CrAllen Developing Human Brain Atlas
layer I of rostral primary auditory cortexA1Cr1Allen Developing Human Brain Atlas
layer II of rostral primary auditory cortexA1Cr2Allen Developing Human Brain Atlas
layer III of rostral primary auditory cortexA1Cr3Allen Developing Human Brain Atlas
layer IV of rostral primary auditory cortexA1Cr4Allen Developing Human Brain Atlas
layer V of rostral primary auditory cortexA1Cr5Allen Developing Human Brain Atlas
layer VI of rostral primary auditory cortexA1Cr6Allen Developing Human Brain Atlas
caudal subdivision of area 20A20cAllen Developing Human Brain Atlas
layer I of area 20cA20c1Allen Developing Human Brain Atlas
layer II of area 20cA20c2Allen Developing Human Brain Atlas
layer III of area 20cA20c3Allen Developing Human Brain Atlas
layer IV of area 20cA20c4Allen Developing Human Brain Atlas
layer V of area 20cA20c5Allen Developing Human Brain Atlas
layer VI of area 20cA20c6Allen Developing Human Brain Atlas
intermediate subdivision of area 20A20iAllen Developing Human Brain Atlas
layer I of area 20iA20i1Allen Developing Human Brain Atlas
layer II of area 20iA20i2Allen Developing Human Brain Atlas
layer III of area 20iA20i3Allen Developing Human Brain Atlas
layer IV of area 20iA20i4Allen Developing Human Brain Atlas
layer V of area 20iA20i5Allen Developing Human Brain Atlas
layer VI of area 20iA20i6Allen Developing Human Brain Atlas
rostral subdivision of area 20A20rAllen Developing Human Brain Atlas
layer I of area 20rA20r1Allen Developing Human Brain Atlas
layer II of area 20rA20r2Allen Developing Human Brain Atlas
layer III of area 20rA20r3Allen Developing Human Brain Atlas
layer IV of area 20rA20r4Allen Developing Human Brain Atlas
layer V of area 20rA20r5Allen Developing Human Brain Atlas
layer VI of area 20rA20r6Allen Developing Human Brain Atlas
caudal subdivision of area 21A21cAllen Developing Human Brain Atlas
layer I of area 21cA21c1Allen Developing Human Brain Atlas
layer II of area 21cA21c2Allen Developing Human Brain Atlas
layer III of area 21cA21c3Allen Developing Human Brain Atlas
layer IV of area 21cA21c4Allen Developing Human Brain Atlas
layer V of area 21cA21c5Allen Developing Human Brain Atlas
layer VI of area 21cA21c6Allen Developing Human Brain Atlas
intermediate subdivision of area 21A21iAllen Developing Human Brain Atlas
layer I of area 21iA21i1Allen Developing Human Brain Atlas
layer II of area 21iA21i2Allen Developing Human Brain Atlas
layer III of area 21iA21i3Allen Developing Human Brain Atlas
layer IV of area 21iA21i4Allen Developing Human Brain Atlas
layer V of area 21iA21i5Allen Developing Human Brain Atlas
layer VI of area 21iA21i6Allen Developing Human Brain Atlas
rostral subdivision of area 21A21rAllen Developing Human Brain Atlas
layer I of area 21rA21r1Allen Developing Human Brain Atlas
layer II of area 21rA21r2Allen Developing Human Brain Atlas
layer III of area 21rA21r3Allen Developing Human Brain Atlas
layer IV of area 21rA21r4Allen Developing Human Brain Atlas
layer V of area 21rA21r5Allen Developing Human Brain Atlas
layer VI of area 21rA21r6Allen Developing Human Brain Atlas
layer I of area 22cA22c1Allen Developing Human Brain Atlas
layer II of area 22cA22c2Allen Developing Human Brain Atlas
layer III of area 22cA22c3Allen Developing Human Brain Atlas
layer IV of area 22cA22c4Allen Developing Human Brain Atlas
layer V of area 22cA22c5Allen Developing Human Brain Atlas
layer VI of area 22cA22c6Allen Developing Human Brain Atlas
layer I of area 22iA22i1Allen Developing Human Brain Atlas
layer II of area 22iA22i2Allen Developing Human Brain Atlas
layer III of area 22iA22i3Allen Developing Human Brain Atlas
layer IV of area 22iA22i4Allen Developing Human Brain Atlas
layer V of area 22iA22i5Allen Developing Human Brain Atlas
layer VI of area 22iA22i6Allen Developing Human Brain Atlas
caudal division of 22p (area 22pc)A22pcAllen Developing Human Brain Atlas
layer I of area 22pcA22pc1Allen Developing Human Brain Atlas
layer II of area 22pcA22pc2Allen Developing Human Brain Atlas
layer III of area 22pcA22pc3Allen Developing Human Brain Atlas
layer IV of area 22pcA22pc4Allen Developing Human Brain Atlas
layer V of area 22pcA22pc5Allen Developing Human Brain Atlas
layer VI of area 22pcA22pc6Allen Developing Human Brain Atlas
intermediate division of 22p (area 22pi)A22piAllen Developing Human Brain Atlas
layer I of area 22piA22pi1Allen Developing Human Brain Atlas
layer II of area 22piA22pi2Allen Developing Human Brain Atlas
layer III of area 22piA22pi3Allen Developing Human Brain Atlas
layer IV of area 22piA22pi4Allen Developing Human Brain Atlas
layer V of area 22piA22pi5Allen Developing Human Brain Atlas
layer VI of area 22piA22pi6Allen Developing Human Brain Atlas
rostral division of 22p (area 22pr)A22prAllen Developing Human Brain Atlas
layer I of area 22prA22pr1Allen Developing Human Brain Atlas
layer II of area 22prA22pr2Allen Developing Human Brain Atlas
layer III of area 22prA22pr3Allen Developing Human Brain Atlas
layer IV of area 22prA22pr4Allen Developing Human Brain Atlas
layer V of area 22prA22pr5Allen Developing Human Brain Atlas

1 2 3 4 5 … 33 34 3316 Brain regions

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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.