DeepMapi: a Fully Automatic Registration Method for Mesoscopic Optical Brain Images Using Convolutional Neural Networks

The extreme complexity of mammalian brains requires a comprehensive deconstruction of neuroanatomical structures. Scientists normally use a brain stereotactic atlas to determine the locations of neurons and neuronal circuits. However, different brain images are normally not naturally aligned even when they are imaged with the same setup, let alone under the differing resolutions and dataset sizes used in mesoscopic imaging. As a result, it is difficult to achieve high-throughput automatic registration without manual intervention. Here, we propose a deep learning-based registration method called DeepMapi to predict a deformation field used to register mesoscopic optical images to an atlas. We use a self-feedback strategy to address the problem of imbalanced training sets (sampling at a fixed step size in nonuniform brains of structures and deformations) and use a dual-hierarchical network to capture the large and small deformations. By comparing DeepMapi with other registration methods, we demonstrate its superiority over a set of ground truth images, including both optical and MRI images. DeepMapi achieves fully automatic registration of mesoscopic micro-optical images, even macroscopic MRI datasets, in minutes, with an accuracy comparable to those of manual annotations by anatomists.