12The Allen Institute recently built a set of high-throughput experimental pipelines to 13 collect comprehensive in vivo surveys of physiological activity in the visual cortex of awake, 14head-fixed mice. Developing these large-scale, industrial-like pipelines posed many scientific, 15operational, and engineering challenges. Here we describe our strategies for collecting 16standardized, multi-modal in vivo datasets across many instrumental platforms over long 17 periods of time. Our goal of creating a cross-platform reference space to which all pipeline 18 datasets were mapped required development of 1) a robust headframe, 2) a reproducible 19clamping system, and 3) data-collection systems that are built, and maintained, around precise 20 alignment with a reference artifact. When paired with our pipeline clamping system, the Allen 21Brain Observatory headframe exceeded deflection and reproducibility requirements. All 22 headframe, surgical tooling, and clamp design documentation have been made freely available 23 as an open resource to the scientific community. 24 65