AN OPEN-SOURCE THREE-DIMENSIONAL DIGITAL BRAIN ATLAS OF THE MIGRATORY EURASIAN BLACKCAP

Birds are nature’s foremost long-distance navigators, utilizing the Earth’s magnetic field—among other natural orientation cues—to traverse thousands of kilometers. While several brain regions are implicated in magnetic field information processing, the absence of a standardized, high-resolution 3D reference atlas has hindered the comparison of data across laboratories. To address this, we present the first open-source, digital, 3D brain atlas for the magnetoreceptive migratory Eurasian blackcap (Sylvia atricapilla). Using serial-section two-photon tomography, we imaged whole bird brains to create an average template at an isotropic 25-μm voxel size followed by expert segmentation. The first version of this atlas features 43 annotated areas, encompassing principal compartments, anatomical subdivisions common across avian species, and specific sensory regions (visual, trigeminal, vestibular) implicated in magnetic field processing. Importantly, the atlas is integrated with the BrainGlobe Atlas API, ensuring compatibility with a suite of open-source computational neuroanatomy tools. We demonstrate its utility through the automated localization of injection sites and cell populations, providing a unified coordinate space that facilitates the precise alignment of experimental data. By democratizing computational neuroanatomy for migratory species, this resource enables researchers to accurately compare findings across studies, accelerating our understanding of the neural mechanisms underlying long-distance navigation. This 3D framework serves as a living reference, designed to be continuously updated by the community to foster collaboration and reproducibility in avian neuroscience.