Mapping the mesoscopic brain of mammals, including mice and macaques, significantly advances our understanding of brain structure, function, and associated diseases. Recent advancements in microscopic imaging techniques have made it possible to rapidly capture and reconstruct the entire macaque brain in three dimensions at micrometer resolution. Despite this progress, analyzing the vast data volumes—amounting to hundreds of terabytes—remains a formidable challenge due to the scarcity of automated data analysis tools. In this presentation, we introduce several AI-driven automated processing methods designed to address critical bottlenecks, such as enhancing axial resolution and tracing neurons. These methods are not only accurate and efficient but also seamlessly integrate into existing data processing pipelines for comprehensive whole-brain mapping.