Hi Andrei. I have used flow cytometry on 96 well microplates, but for cell proliferation studies. You just have to put samples and set up an acquisition protocol depending upon number of events to be acquired or acquisition time. I have worked with BD LSR Fortessa flow cytometer for the same. Other platforms like BD FACS Calibur, LSR-II, Canto II are few other systems offering similar applications.

Thank U Ravi! We have a Canto II and I already asked for the prices on the 96 well platform update! Cheers!