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.