Using the files directly

How to access the files outside of the Python API

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. /home/username/.brainglobe/allen_mouse_10um_v0.3).

In each atlas directory, there will be the following sub-directories 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

  • 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