Brain function is dictated by its circuitry, but currently we know comparatively little about how the mammalian brain is connected: only 10% of all mesoscale connections in the most studied mammal (rat) have been catalogued and only perhaps one third have been probed at all. To address this knowledge gap, this dissertation is focused on the development of a semi-automated pipeline to enable high-throughput neuroanatomy in mouse, and the use of that pipeline to assemble the first brain-wide connectivity map in mouse. The pipeline was assembled in its entirety as part of this dissertation work, in a top-down design approach of five principle subsystems: (1) Tracer Injection; (2) Brain Fixation and Freezing; (3) Brain Sectioning; (4) Section Staining; (5) Whole-slide Section Imaging and Data Analysis. For each subsystem, conventional neuroanatomy techniques were innovated to facilitate pipeline integration and maximize efficiency. Key innovations include: computer guided stereotactic neurosurgery using a skull scan, a method of freezing mouse brains in stereotaxic coordinates and tape-transfer assisted cryosectioning. Along with whole-slide imaging, these innovations allow for accurate injections to be placed throughout the regions of the brain, in a uniformed manner, across thousands of animals and for the brain of each animal to be finely sampled and imaged in its entirety. The result is an unprecedented view of each injection and each brain, made available to the community through a public web portal. Instead of a few images per experiment, that are published in literature, all the sections of a given experiment (~500 per brain) can be accessed through this portal by anyone. All brains have roughly the same number of sections and span the entire brain. Comparing specific structures in all brains is possible. This work has the potential to transform neuroanatomy in the same way that the Allen Mouse Brain Atlas changed rodent neurogenetics.