The Eurasian blackcap, a small migratory songbird, now has the first high-resolution three-dimensional map of its brain. Researchers used advanced imaging to create a detailed digital atlas that is freely available to scientists worldwide.
Brain atlases are digital, high-resolution 3D maps that show the exact locations and shapes of different brain structures. They help scientists compare results across studies, align their own data to a common reference, and better understand functions such as learning, memory, and navigation. The new atlas for the Eurasian blackcap was built from eight male birds using serial two-photon tomography. This imaging method takes many thin, precisely aligned slices through the whole brain at a very fine scale of two by two by five micrometres. The separate brain scans were then aligned and averaged to form a single representative template. Experts manually labelled 44 distinct brain regions, including areas involved in song, senses, and processing the Earth’s magnetic field.
The atlas has been added to the open-source BrainGlobe platform, which provides tools for automatic registration of data, cell detection, and mapping. It can even be used with old microscope slides stored for years.
First digital atlas for a migratory bird brain
This resource is expected to speed up research into how birds navigate thousands of miles using the Earth’s magnetic field. In the same study, scientists discovered a previously unknown direct connection between brain areas sensitive to magnetic fields and the nidopallium caudolaterale, a region similar to the decision-making prefrontal cortex in mammals. The link helps explain how birds make navigation decisions.
The atlas supports studies of magnetoreception, migration, and navigation. It also lays the groundwork for creating similar maps for other species. Work has already started on a zebra finch atlas to study vocal learning. The entire process uses open-source software, making it possible for other laboratories to build atlases from different imaging methods, including light-sheet microscopy. Future updates will incorporate new labelling techniques that highlight specific genes or proteins.
The availability of this atlas is expected to improve consistency between studies and accelerate understanding of the neuronal mechanisms behind long-distance bird migration.
This research is published in Current Biology.