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The Allen Mouse Brain Atlas includes a full-color, high-resolution anatomic reference atlas accompanied by a systematic, hierarchically organized taxonomy of mouse brain structures.

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.

Use the image below to select a section through the brain. The bregma zero coordinate is marked by the grey circle. Click on a button to view the corresponding section, or use the numbered guide in the frame below.

Use the image below to select a section through the brain. Click on a button to view the corresponding section, or use the numbered guide in the frame below. Scroll down for more background on this atlas.

Here, we present the Allen Mouse Brain Common Coordinate Framework (CCFv3) as such a resource. We constructed an average template brain at 10 μm voxel resolution by interpolating high resolution in-plane serial two-photon tomography images with 100 μm z-sampling from 1,675 young adult C57BL/6J mice.

The High Resolution Mouse Brain Atlas at Harvard Medical School provides detailed images and information about the mouse brain for research purposes.

The Allen Developing Mouse Brain Atlas includes a full-color, high-resolution anatomic reference atlas at seven timepoints accompanied by a systematic developmental taxonomy of mouse brain structures.

Mar 9, 2025 · View labeled high-resolution cross-sections of mouse brains. Also we include a tutorial that gives detailed instructions for creating your own mouse brain atlas. to provide online realtime access to the slides which form the Mouse Brain Library.

Mar 24, 2025 · For the continuous sections of the whole mouse brain, we grouped the brain section data based on the interval from the appearance to the disappearance of major brain regions in the brain section (e.g. the 123 brain sections of mouse #1 were divided into 12 compartments). We then merged the Seurat objects of brain sections in each group separately.

section (made perpendicular to the midline, as if you're slicing a loaf of bread) the medial/lateral and dorsal/ventral planes can be seen. The image below shows the 3 different planes (axial, coronal, and sagittal) in which a brain can be sectioned: