Allen Institute atlases and data are registered, when possible, to one of several common reference spaces. Working in such a space allows you to easily compare data across subjects and experimental modalities.
This page documents how to use the Allen SDK to interact with a reference space. For more information and a list of reference spaces, see the API documentation.
Brain structures in our reference spaces are arranged in trees. The leaf nodes of the tree describe the very fine anatomical divisions
of the space, while nodes closer to the root correspond to gross divisions. The
class provides an interface for interacting with a structure tree.
An annotation volume is a 3d raster image that segments the reference space into structures. Each voxel in the annotation volume is assigned an integer value that describes the finest structure to which that point in space definitely belongs.
allensdk.core.reference_space.ReferenceSpace class contains methods for working with our reference spaces. Some use cases might include:
Please see the example notebook for more code samples.