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Major advances in the understanding in the biological sciences have been achieved by the precision automation of repetitive analytical procedures. The requirements for precision are pushed to the extreme when considering the analysis of cell function at the single cell level. Such analyses may include examination of gene expression, protein synthesis, and metabolic activity. The repetitive nature of performing measurement of these parameters requires not only effective signal transduction and amplification, significant attention to system integration and automation is paramount to instrument development objectives. Here we present the systems integration and software development for a multi-spectral imaging and phosphorescence lifetime measurement tool. This tool represents and early engineering prototype of one subsystem of an integrated automation pipeline comprising robotics for microwell-array movement, microwell-array sealing for metabolic rate measurements, control of experimental protocol sequencing and real-time imaging of dynamic experiments. A graphical user interface and underlying control software allows for flexible construction of experimental procedures. The engineering prototype has demonstrated experimental operation times up to 10 times faster than previous manual methods.