An open-source three-dimensional digital brain atlas of a migratory bird, the Eurasian blackcap

Birds are among nature's foremost navigators, utilizing the Earth's magnetic field as one of their most important orientation cues to successfully travel between breeding and wintering grounds. Although migratory birds are key models for studying brain areas involved in magnetic field information processing, there is a lack of a high-resolution, 3D reference atlas to standardize research across studies. Here, we present the first freely available, digital, isotropic 25-μm voxel size 3D bird brain atlas. It is based on light microscopy images from eight male Eurasian blackcaps (Sylvia atricapilla), a night-migratory songbird central to magnetoreception and navigation research. We detail the atlas development process from whole-brain serial-section two-photon tomography to the creation of an average template and subsequent segmentation. The first atlas version comprises 44 segmented brain areas, including principal brain compartments, prominent anatomical subdivisions shared across all bird species, regions of the song system, and sensory regions-visual, trigeminal, and vestibular-implicated in magnetic field processing. The atlas is accessible via the standardized BrainGlobe Atlas API, making it compatible with a suite of computational neuroanatomy tools. This integration enables the accurate localization and comparison of implanted devices, injection sites, and cell populations across whole brains or individual slices. Providing a common coordinate space, this atlas serves as a reference that can be continuously updated with new annotations and facilitates alignment of future experimental data. We demonstrate its utility by registering viral tracing data to reveal a direct projection from the magneto-processing area "Cluster N" to the multi-integrational, "prefrontal" nidopallium caudolaterale.