The Allen Institute recently built a set of high-throughput experimental pipelines to collect comprehensive in vivo surveys of physiological activity in the visual cortex of awake, head-fixed mice. Developing these large-scale, industrial-like pipelines posed many scientific, operational, and engineering challenges. Here we describe our strategies for collecting standardized, multi-modal in vivo datasets across many instrumental platforms over long periods of time. Our goal of creating a cross-platform reference space to which all pipeline datasets were mapped required development of 1) a robust headframe, 2) a reproducible clamping system, and 3) data-collection systems that are built, and maintained, around precise alignment with a reference artifact. When paired with our pipeline clamping system, the Allen Brain Observatory headframe exceeded deflection and reproducibility requirements. All headframe, surgical tooling, and clamp design documentation have been made freely available as an open resource to the scientific community.