A migratory bird brain, the Eurasian blackcap (Sylvia atricapilla), has been mapped for the first time using high-resolution light microscopy. The open-source software tools developed, and the detailed processes published, form a foundation for new brain atlases to be built for any species, providing a valuable resource for neuroscience worldwide. Created by a team from the Sainsbury Wellcome Centre at UCL and the University of Oldenburg, Germany, a paper describing the atlas has been published today (20 April 2026) in Current Biology.
Brain atlases - digital, high-resolution, 3D maps of brain structures - are transforming neuroscience. They improve the ability of researchers to interpret their own data, they enable cross-validation between and within experiments, and they foster collaboration - driving forward studies into learning, memory and cognition.
"A digital open-source brain atlas allows researchers to directly align their own experimental multimodal data to the common coordinate space of the atlas. It enables consistency, meaning researchers around the world can speak the same language when it comes to the brain. We are delighted to bring this resource to the community, and even more excited about building many more atlases for other research communities in the future," said Dr Simon Weiler, Senior Research Fellow at the Sainsbury Wellcome Centre at UCL, and lead author of the study.
The team is already working on creating a similar digital 3D brain atlas of the zebra finch (Taeniopygia guttata), a bird used to study vocal learning.
The new Eurasian blackcap atlas is freely accessible via BrainGlobe for the neuroscience research community and will advance studies of magnetoreception, migration and navigation. The technology means that any brain sample, even historic histology samples that have been stored for years on glass slides, for example, can be mapped onto the atlas.
Birds are among nature's foremost navigators, using the Earth's magnetic field to orient themselves and travel between breeding and wintering grounds. Many species travel thousands of miles with centimetres of precision. In the same publication, the team has revealed a previously unknown direct link between magnetosensitive areas in the brain and the decision-making centre, the nidopallium caudolaterale (equivalent to the prefrontal cortex in mammals), demonstrating how the atlas can assist in characterising novel brain pathways.
"To me, this is a key tool that the migration, navigation, and magnetoreception community has been lacking for decades. It will greatly improve consistency and comparability between studies and related species and will significantly accelerate our understanding of underlying neuronal mechanisms," said Professor Henrik Mouritsen, University of Oldenburg, an author of the study.
To create the atlas, the team at SWC used serial two-photon (STP) tomography to image eight male Eurasian blackcap brains. This advanced imaging technique results in well-aligned 2 x 2 x 5 μm voxel size images of entire brains. The individual 3D images from different brains were then iteratively aligned and averaged to create a representative brain template. Following this, experts at the University of Oldenburg manually annotated the template. This resulted in 44 segmented brain areas, including principal brain compartments, prominent anatomical subdivisions shared across all bird species, regions of the song system, and sensory regions implicated in magnetic field processing. Finally, the atlas was incorporated into the BrainGlobe ecosystem and automatic registration, cell detection and object mapping were demonstrated on experimental data.
"The core aim of BrainGlobe is to democratise computational neuroanatomy. Creating novel atlases is a step in achieving this. All parts of the pipeline are open-source, and over the coming months we will be improving it so that we, and anyone else, can rapidly create new atlases," said Dr Adam Tyson, Head of the Neuroinformatics Unit at the Sainsbury Wellcome Centre at UCL and lead of the BrainGlobe Initiative.
While the team used state-of-the-art STP tomography, other microscopies, including light-sheet images are also suitable for creating atlases. Future advances in whole-brain labelling procedures, paired with STP tomography, will further guide brain area subdivision based on region-specific identification of marker genes or proteins, and the atlas will be regularly updated to incorporate new data.
