Using the files directly#

Although the API should provide you with the tools you need to work with the atlas (and if they don’t, please raise an issue), you may wish to find the files themselves.

By default, atlases will be downloaded and saved into your home directory in a hidden directory (~/.brainglobe), with one directory per atlas e.g. ~/.brainglobe/allen_mouse_10um_v0.3.

In each atlas directory, there will be the following subdirectories and files:

  • reference.tiff The “template” brain image, i.e., a structural image of the brain (or average of brains) in which the annotations are defined

  • annotation.tiff An image of the same shape as reference.tiff but in which each pixel value corresponds to a unique brain area. A pixel value of 0 typically refers to areas outside the brain

  • hemispheres.tiff (optional) An image of the same shape as reference.tiff but in which each pixel value corresponds to either the left or right hemisphere. They are labelled 0 and 1 respectively. This file is only present for asymmetrical templates

  • meshes A directory of mesh files (as .obj) for each brain region, defined by the unique region ID

  • structures.json A file describing the mapping of brain region ID to region name, and the hierarchy of brain structures

  • metadata.json A file containing the atlas metadata, such as the shape of the images, the anatomical orientation, and the details of the source of the atlas

  • README.txt A human-readable version of the metadata and brain region hierarchies