FAQ: How can I get a printed or PDF version of the [mouse, human brain] reference atlas?

Many people find the digital reference atlases generated by the Allen Institute to be useful tools for educational, programmatically-accessible visualization and analysis. But some people want to use a ‘classically printed’ atlas, on paper or in a PDF. Are these available? This post explains how to produce printable versions of the human and mouse brain reference atlases. A Forum post explaining how to download SVG files from the API is here.

Allen Mouse Brain Atlas:
In 2008, Wiley published a spiral-bound version of the first Allen Reference Atlas: A Digital Color Brain Atlas of the C57BL/6J Male Mouse, by Dong, H. W. (John Wiley and Sons, 2008 with CD-ROM. ISBN 978‐0‐470‐05408‐6). This atlas is no longer in print, but is referenced in a review by Dan Goldowitz, among other places. Copies of this coveted atlas occasionally appear in second-use marketplaces such as Amazon and textbook clearinghouses. The Allen Institute does not provide copies of this book, and queries about past or future availability should be addressed to the publisher.

Since that release, multiple revisions have been made to the Allen Mouse Brain Atlas, available in digital formats. These versions are accessible at brain-map.org, under Reference Atlases, the API or Allen Mouse Brain Atlas. Individual atlas plates can be downloaded programmatically; instructions are here. Or, through the browser by launching the viewer (or from ‘thumbnail’ images), navigating to the upper right hand corner control icons, select ‘Atlas’ from the dropdown and then select ‘Download Image’ from the stacked line icon.

Allen Human Brain Atlas
The Allen Human Brain Atlas was published in 2016 by Wiley as a special issue that is available in print through the Journal of Comparative Anatomy: Comprehensive cellular‐resolution atlas of the adult human brain, by Ding, S.-L. (https://doi.org/10.1002/cne.24080).
Like the mouse brain atlas, reference images (for adult and developing human brain) can be accessed programmatically through the API or downloaded directly through the online reference atlas browser, using the same controls as described for mouse, above. More information about tools for navigating the human brain reference atlases are available in the Help section.

Detailed descriptions on mouse and human brain reference atlas creation, annotation and associated publications are available through the Technical Documentation links for each atlas. Learn more about digital 3D reference atlases in other posts on the Forum: