ALLEN REFERENCE ATLASES AND VIEWING TOOLS

This is the online help for the ALLEN Reference Atlases and the web-based tools that can be used to access them.  The reference atlases are neuroanatomical guides to accompany Allen Institute data and are also useful as stand-alone resources.

Allen Mouse Brain Atlas

These anatomical reference atlases illustrate the adult mouse brain in coronal and sagittal planes of section. They are the spatial framework for datasets such as in situ hybridization, cell projection maps, and in vitro cell characterization.

Human Brain Atlas

These anatomical reference atlases illustrate the adult human brain, using modified Brodmann or gyral annotation.

Developing Mouse Brain Atlas

These anatomical reference atlases illustrate the developing mouse brain, covering seven stages of embryonic (E) and postnatal (P) development. Dr. Luis Puelles used a custom developmental taxonomy for annotation of the Allen Developing Mouse Brain Reference Atlases.

BrainSpan Atlas of the Developing Human Brain

These anatomical reference atlases illustrate the developing human brain, covering two embryonic stages.

Mouse Spinal Cord Reference Atlases

These anatomical reference atlases illustrate the mouse spinal cord in adult and juvenile C57BL/6J mouse. They provide a spatial map for the Allen Mouse Spinal Cord Atlases of gene expression. Dr. Charles Watson and Dr, Gulgun Kayalioglu created a custom taxonomy for annotation of the spinal cord, covering cervical, thoracic, lumbar, sacral, and coccygeal segments.

Reference Atlas Viewing Tools

Each reference atlas can be explored using a set of custom, web-based visualization tools.  This section provides additional information about how to use the tools to help understand the online data or to explore neuroanatomy.