Epileptic seizures were experimentally induced in the CA3 region of rat hippocampus in vivo. Recordings of seizure activity were made in both hippocampi as well as anteromedial region of the thalamus in order to analyze the instantaneous activity for synchronous oscillators. A new method is introduced for detecting this synchrony which combines empirical mode decomposition, the Hilbert analytic signal method and eigenvalue decomposition. Effects of targeted deep brain stimulation on multi-site synchrony were assessed as a means to extinguish hypersynchrony during epileptic seizures.