In general, a formal specification for hardware-software integration is imperative for systematic design of automated systems. This specification requires a critical understanding of hardware and software systems at various levels of abstraction. The objective of the research we present is to develop a framework that serves as a specification for the implementation of an integrated system for the analysis of cell function - a classic application for laboratory automation. The proposed framework addresses a specific set of integrated system requirements comprising the placement of single cells in analysis locations, the analyses of these cells throughout application of external stimuli, and post stimuli end-point analyses of these same cells. The same framework can be directly extended to automate cell-to-cell and tissue analyses. It has been developed using principles from Unified Modeling Language (UML) to maximize potential for integration with other standard laboratory automation systems. The research presented provides the foundation for efficient use of UML with the proposed framework, and serves as an exemplar for others pursuing similar laboratory automation challenges.