Mapping out the complex vascular network in the brain is critical for understanding the transport of oxygen, nutrition, and signaling molecules. The vascular network can also provide us with clues to the relationship between neural activity and blood oxygen-related signals. Advanced high-throughput 3D imaging instruments such as the Knife-Edge Scanning Microscope (KESM) are enabling the imaging of the full vascular network in small animal brains (e.g., the mouse) at sub-micrometer resolution. The amount of data per brain (for KESM) is on the order of 2TB, thus it is a major challenge just to visualize it at full resolution. In this paper, we present an enhanced image processing pipeline for KESM mouse vascular network data set, and a parallel multi-scale tile generation system for web-based pseudo-3D rendering. The system allows full navigation of the data set at all resolution scales. We expect our approach to help in broader dissemination of large-scale, high-resolution 3D microscopy data.