As the brain has a high degree of functional specialization and is highly integrated at various hierarchies, it is necessary to investigate anatomical and functional brain networks unbiasedly and independently of any foreseen hypothesis to elucidate the pathophysiology of brain diseases. To address the issue, we have developed a highly scalable and high-speed imaging system (block-FAce Serial microscopy Tomography, FAST) and methods to compare structures and neural activity among individual animal groups. Using these methods, we are examining anatomical structure and neuronal activity changes in animal disease models and those administered with therapeutic drugs. In this symposium, I will introduce our recent progress and discuss the directions of future research that would contribute to a better understanding of brain systems and disorders.