Developing a brain atlas through deep learning

High-throughput brain image registration methods that are independent of any pre-processing steps, and are robust under mild image transformations, could accelerate the study of region-specific changes in brain development. A deep learning-based method is therefore developed for automated registration through segmenting brain regions of interest with minimal human supervision. Neuroscientists have devoted substantial effort to the creation of standard brain reference atlases for high-throughput registration of anatomical regions of interest. However, the variability in brain size and form across individuals poses a considerable challenge for such reference atlases. To overcome these limitations, we introduce a fully automated deep neural network-based method (named SeBRe) for segmenting brain regions of interest with minimal human supervision. We demonstrate the validity of our method on brain images from different developmental time points of mice, across a range of neuronal markers and imaging modalities. We further assess the performance of our method on images of magnetic resonance-scanned human brains. Our registration method can accelerate brain-wide exploration of region-specific changes in brain development and, by easily segmenting brain regions of interest for high-throughput brain-wide analysis, offer an alternative to existing complex brain registration techniques.