The field of stem cell science is one with enormous potential for impact in both therapeutic applications and in understanding human development and homeostasis. It is increasingly appreciated that stem cells and stem cell behavior are governed by a complex, interwoven network of environmental signals with variable spatial and temporal presentation. While conventional molecular and cellular biology techniques have provided a fundamental foundation for stem cell investigation, advances in the adaptability and through-put of future laboratory work flows will be necessary to address questions in this ever-expanding parameter space. The goal of this dissertation, therefore, has been to instantiate just such a platform, and provide proof of concept evidence as to its utility in stem cell investigations. Design considerations and pipeline engineering are discussed, and data collected with the system in benchmarking, dose-response, and combinatorial experimental formats are provided to illustrate the experimental work the platform enables.