Allen Brain Reference Atlases

The Allen Institute for Brain Science has generated multiple reference atlases, to use with our online datasets or as stand-alone resources. Refer to our Citation Policy for information on how you may use these images in your work.

Adult Mouse
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.

The 2D coronal reference atlas is created from a 3D volumetric reference atlas, annotated symmetrically using an average of data merged from 1,675 brain specimens. It provides spatial context and a common coordinate framework for mapping data in the Allen Mouse Connectivity Atlas, the Allen Cell Types Database (mouse), and the Allen Brain Observatory.

132 virtual planes at 100 µm intervals

The 2D coronal reference atlas is annotated on Nissl sections collected from a single adult male C57Bl6 mouse, postnatal day 56. It provides the spatial context for in situ hybridization-based gene expression in the Allen Mouse Brain Atlas.

132 coronal sections at 100 µm intervals

The 2D sagittal reference atlas is annotated on Nissl sections collected from a single adult male C57Bl6 mouse, postnatal day 56. It provides the spatial context for in situ hybridization-based gene expression in the Allen Mouse Brain Atlas.

21 sagittal sections at 200 µm intervals
Adult Human
These anatomical reference atlases illustrate the adult human brain, using modified Brodmann or gyral annotation.

The 2D coronal reference atlas is annotated on Nissl sections from a 34-year-old female based on a modified Brodmann nomenclature. It provides spatial context for gene expression in the Allen Human Brain Atlas and the BrainSpan Atlas of the Developing Human Brain.

106 coronal sections at 0.4 - 3.4 mm intervals

The 2D coronal reference atlas is annotated on Nissl sections from a 34-year-old female, by gyrus. It provides spatial context for gene expression in the Allen Human Brain Atlas and the BrainSpan Atlas of the Developing Human Brain.

106 coronal sections at 0.4 - 3.4 mm intervals
Developing Mouse
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.

The 2D sagittal reference atlas is annotated on Nissl sections collected from a single adult male C57Bl6 mouse, postnatal day 56 (P56). It provides the spatial context for in situ hybridization-based gene expression in the Allen Developing Mouse Brain Atlas.

21 sagittal sections at 200 µm intervals

The 2D sagittal reference atlas is annotated on Nissl sections collected from a single adult male C57Bl6 mouse, postnatal day 14 (P14). It provides the spatial context for in situ hybridization-based gene expression in the Allen Developing Mouse Brain Atlas.

39 sagittal sections at 125 µm intervals

The 2D sagittal reference atlas is annotated on Nissl sections collected from a single adult male C57Bl6 mouse, postnatal day 4 (P4). It provides the spatial context for in situ hybridization-based gene expression in the Allen Developing Mouse Brain Atlas.

23 sagittal sections at 160 µm intervals

The 2D sagittal reference atlas is annotated on Nissl sections collected from a single adult male C57Bl6 mouse, embryonic day 18.5 (E18.5) or Theiler stage 26 (TS26). It provides the spatial context for in situ hybridization-based gene expression in the Allen Developing Mouse Brain Atlas.

19 sagittal sections at 120 µm intervals

The 2D sagittal reference atlas is annotated on Nissl sections collected from a single adult male C57Bl6 mouse, embryonic day 15.5 (E15.5) or Theiler stage 24 (TS24). It provides the spatial context for in situ hybridization-based gene expression in the Allen Developing Mouse Brain Atlas.

16 sagittal sections at 120 µm intervals

The 2D sagittal reference atlas is annotated on Nissl sections collected from a single adult male C57Bl6 mouse, embryonic day 13.5 (E13.5) or Theiler stage 21 (TS21). It provides the spatial context for in situ hybridization-based gene expression in the Allen Developing Mouse Brain Atlas.

15 sagittal sections at 100 µm intervals

The 2D sagittal reference atlas is annotated on Nissl sections collected from a single adult male C57Bl6 mouse, embryonic day 11.5 (E11.5) or Theiler stage 19 (TS19). It provides the spatial context for in situ hybridization-based gene expression in the Allen Developing Mouse Brain Atlas.

28 sagittal sections at 40 µm intervals
Developing Human
These anatomical reference atlases illustrate the developing human brain, covering two embryonic stages.

The 2D sagittal reference atlas is annotated on Nissl sections collected from an embryo at 15 weeks post-conception (15 pcw). It provides the spatial context for gene expression in the BrainSpan Atlas of the Developing Human Brain.

46 coronal sections at 0.5 to 1.0 mm intervals

The 2D sagittal reference atlas is annotated on Nissl sections collected from an embryo at 21 weeks post-conception (21 pcw). It provides the spatial context for gene expression in the BrainSpan Atlas of the Developing Human Brain.

81 coronal sections from the cerebrum at 0.5 to 1.2 mm intervals

The 2D sagittal reference atlas is annotated on Nissl sections collected from an embryo at 21 weeks post-conception (21 pcw). It provides the spatial context for gene expression in the BrainSpan Atlas of the Developing Human Brain.

41 transverse sections from the brainstem at 0.25 to 0.5 mm intervals
Mouse Spinal Cord
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.

The 2D sagittal reference atlas is annotated on Nissl sections collected from a juvenile male C57Bl6 mouse, postnatal day 4 (P4). It provides the spatial context for in situ hybridization-based gene expression in Allen Mouse Spinal Cord Atlas.

34 transverse sections at 2 mm intervals
Note: Image viewer functionality may not be supported in current web browsers

The 2D sagittal reference atlas is annotated on Nissl sections collected from an adult male C57Bl6 mouse, postnatal day 56 (P56). It provides the spatial context for in situ hybridization-based gene expression in Allen Mouse Spinal Cord Atlas.

34 transverse sections at 2 mm intervals
Note: Image viewer functionality may not be supported in current web browsers