Mouse - Allen Mouse Brain volumetric atlas 2012

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About this atlas

The Allen Reference Atlas is created by the Allen Institute for Brain Science. There are two variants of 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.

The volumetric atlas also features in Allen Brain Institute's stand-alone software package BrainExplorer.

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]

• Nissl: Nissl
  • ../../templates/ABA12/source/Atlas2014.nii.gz; filesize 30187 kB; shape [456x528x320]
  • ../../templates/ABA12/source/Atlas2014_downsample2.nii.gz; filesize 3903 kB; shape [228x264x160]
• labels: labels
  The label index mapper converts label indices to acronyms, full names, and rgb-values.
  • ../../templates/ABA12/source/Annotation2014.nii.gz; filesize 7362 kB; shape [456x528x320]
  • ../../templates/ABA12/source/Annotation2014_downsample2.nii.gz; filesize 1369 kB; shape [228x264x160]
• 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.
  • ../../templates/ABA12/source/coronal_svg.zip; filesize 7829 kB
• wholebrain_mesh: surface mesh of the entire brain
  • ../../templates/ABA12/wholebrain.x3d; filesize 5308 kB