Flow cytometer systems are provided that mitigate aerosols generated during operation of a flow cytometer. A flow cytometer system can include various combinations of: a flow cytometer instrument base, a flow cytometer, and a biosafety hood (BSH). In some embodiments, a subject flow cytometer system includes a flow cytometer instrument base, a flow cytometer, and a BSH. In some embodiments, a subject flow cytometer system includes a flow cytometer instrument base and a flow cytometer. In some cases, a BSH includes an aerosol management system, which provides a redundant air filtration system. Also provided are components of a flow cytometer system (e.g., a BSH configured to attach to a flow cytometer instrument base, a flow cytometer instrument base configured to attach to a BSH, etc.). Also provided are methods, including methods of performing a flow cytometric procedure using a flow cytometer system and methods of decontaminating a flow cytometer system.
