Brain region mappings.

Four mappings are currently available within the IBL, these are:

  • Allen Atlas - total of 1328 annotation regions provided by Allen Atlas.

  • Beryl Atlas - total of 308 annotation regions determined by Nick Steinmetz for the brain wide map, mainly at the level of major cortical areas, nuclei/ganglia. Thus annotations relating to layers and nuclear subregions are absent.

  • Cosmos Atlas - total of 10 annotation regions determined by Nick Steinmetz for coarse analysis. Annotations include the major divisions of the brain only.

  • Swanson Atlas - total of 319 annotation regions provided by the Swanson atlas (FIXME which one?).


  • Name - The full anatomical name of a brain region.

  • Acronymn - A shortened version of a brain region name.

  • Index - The index of the of the brain region within the ordered list of brain regions.

  • ID - A unique numerical identifier of a brain region. These are typically integers that therefore take up less space than storing the region names or acronyms.

  • Mapping - A function that maps one ordered list of brain region IDs to another, allowing one to control annotation granularity and brain region hierarchy, or to translate brain region names from one atlas to another. The default mapping is identity. See [atlas package documentation](./ibllib.atlas.html#mappings) for other mappings.

  • Order - Each structure is assigned a consistent position within the flattened graph. This value is known as the annotation index, i.e. the annotation volume contains the brain region order at each point in the image.

FIXME Document the two structure trees. Which Website did they come from, and which publication/edition?