Reference Space

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.

Structure Tree

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 StructureTree class provides an interface for interacting with a structure tree.

To download a structure tree, use the allensdk.api.queries.ontologies_api.OntologiesApi class as seen in this example

Annotation Volumes

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.

To download a nrrd formatted annotation volume at a specified isometric resolution, use the allensdk.api.queries.mouse_connectivity_api class. There is an example in the notebook.

ReferenceSpace Class

The allensdk.core.reference_space.ReferenceSpace class contains methods for working with our reference spaces. Some use cases might include:

• Building an indicator mask for one or more structures
• Viewing the annotation
• Querying the structure graph

Please see the example notebook for more code samples.