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The mouse reference brain in 3D

Wang, Q. et al. Cell 181, 936–953 (2020).

Many image datasets of the mouse brain require registration to a reference atlas; for example, for annotation or comparison between datasets. The Allen Mouse Brain Common Coordinate Framework serves this purpose and is now presented in its third version (CCFv3). CCFv3 is based on 1,675 mouse brains, which were stained with various histological techniques, and has an isotropic resolution of 10 micrometers, thereby surpassing existing reference brain atlases. In contrast to previous atlases, CCFv3 is parcellated in 3D, which avoids irregular borders between its 658 annotated structures. Furthermore, the parcellation is based on multiple image modalities, ensuring unprecedented accuracy. The reference brain atlas and its underlying datasets can be viewed in the dedicated interactive Atlas Viewer, while the data are also available for download. CCFv3 can be accessed at

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Correspondence to Nina Vogt.

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Vogt, N. The mouse reference brain in 3D. Nat Methods 17, 655 (2020).

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