ALLEN REFERENCE

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ATLASES AND VIEWING TOOLS

This is the online help for the ALLEN Reference Atlas: Interactive Atlas Viewer.
The Interactive Atlas Viewer is an application from which you can view annotated versions of Nissl sections from several Allen Brain Atlas 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 AtlasThis Reference Atlas includes a sagittal and a coronal atlas. The sagittal atlas contains 21 sections spaced at 200 microns and is annotated for 71 structures. The coronal atlas contains 132 sections spaced at 100 microns and is annotated for over 800 structures (including cortical layers)

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

This Reference Atlas includes seven developmental stages drawn by These anatomical reference atlases illustrate the developing mouse brain, covering seven stages of embryonic (E) and postnatal (P) development. Dr. Luis Puelles .

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Human Brain Atlas

Allen Institute anatomists have created a neuroanatomic reference guide to provide a spatial context for both the microarray and ISH samples available in the Human Brain Atlasused a custom developmental taxonomy for annotation of the Allen Developing Mouse Brain Reference Atlases.

BrainSpan Atlas of the Developing Human BrainAllen Institute anatomists have created Reference Atlases at two prenatal and an adult developmental stage to provide a spatial context for the microarray, RNASeq and ISH data available in the 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 C57Bl6 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.