Mouse brain Atlas

High Resolution Mouse Brain
Scalable Brain Atlas Coronal3d

About this atlas

  1. The manually annotated 'reference' atlas, published on the web and in print: H.W. Dong, The Allen Reference Atlas, (Book + CD-ROM): A Digital Color Brain Atlas of the C57BL/6J Male Mouse, Wiley, 2008. This atlas has been symmetrized with respect to the midline.
  2. The volumetric atlas, in which each brain region is represented by a set of closed volumes. This atlas is used to initiate coordinate- or structure name based queries into the AGEA gene expression database.

On display here is the second variant of the atlas, in the 2012 realignment. The manually annotated sections can be viewed using the "AllenAtlas" plugin.

Terms of use

The Scalable Brain Atlas does not "own" any of its templates. To ensure that the atlas makers receive proper credit, you must abide by our citation policy.
In brief, always (1) cite each data source that contributed to your analysis, and (2) cite the Scalable Brain Atlas main publication and plugin references where appropriate.The defining citations for this atlas template are:
  1. Lein ES, Hawrylycz MJ, Ao N, et al. (2007) "Genome-wide atlas of gene expression in the adult mouse brain." Nature 445(7124):168-76. [doi 10.1038/nature05453]


The Scalable Brain Atlas provides selected (downsampled) datasets for your convenience. Always check the license terms of the original atlas data source, which may also contain additional and higher resolution data sets.
  • Nissl: Nissl
  • labels: labels
    The label index mapper converts label indices to acronyms, full names, and rgb-values.
  • coronal_svg: Coronal sections of the label volume "Annotation2014_141.nii", converted to Scalable Vector Graphics.
    Brain regions are color-coded by the RGB to Acronym map, which can be chained with the Acronym to Fullname map.
The Scalable Brain Atlas is developed by Rembrandt Bakker and many contributors with financial support from INCF, Radboud University Nijmegen, and others.
Send feedback, report a bug, request a feature, collaborate.

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What is that theory that all humanity is really is a bunch of brains in jars interacting? | Yahoo Answers

The "brain in a jar" idea is usually associated with the philosophical position called solipsism. It goes something like "Since all my sensations of an outside reality are just signals on nerves, how do I know I'm not just a brain in a jar being fed those signals? How do I know what I call reality is real?"

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