FACSAria II flow cytometry system features a fluidics design that supports aseptic set-up and cleaning, nozzle sizes that allow sorting of a range of particles, and a 375 nm near UV laser option to expand the instruments range of applications. Software includes a Cytometer Set-up and Tracking, which automates quality control and experiment set-up. Design is based on a true fixed-alignment flow cell that is gel-coupled to the collection optics. This minimizes start-up time, improves experiment-to-experiment reproducibility, and increases the sensitivity and resolution needed for multi-color applications.