The BioFlux System (Figure 1) enables flow-based assays for applications such as cellular adhesion, platelet studies, stem cell research and microbial biofilms. This wide variety of uses for the BioFlux requires versatility in selecting data acquisition strategies for each experiment. BioFlux enables a wide variety of optical data collection techniques. This Application Note will describe some of the optical properties of the BioFlux Plates and present examples of some common imaging modalities acquired with the BioFlux System. An overview of microscopy basics and optimization strategies with the BioFlux is presented at the end.