Our laboratory is uniquely positioned to measure membrane protein organization with a specialized fluorescence method called pulsed interleaved excitation–fluorescence cross-correlation spectroscopy (PIE-FCCS). This method is a two-color, time-correlated single photon counting technique that resolves fluorescence lifetimes, FCS, and FCCS. The pulse arrival times are interleaved so that spectral crosstalk can be removed from the cross-correlation data. PIE-FCCS reduces the likelihood of false positive cross-correlation, especially for heterogeneous systems like the live cell plasma membrane.