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Compares an extended conventional filter technique for automated detection and analysis of rapid eye movements (REM) in neonates, using amplitude, synchrony, velocity, and coherence threshold criteria, with a matched filtering technique using the morphology of the REM waveform. Analyses of both simulated and real data were carried out. Automated REM tabulations are compared with visual scoring by a trained observer. Both preterm and fullterm neonates were used to test these methods. Both the advantages and disadvantages of these two techniques are discussed as compared with conventional methods which use only amplitude and synchrony threshold criteria. The major advantage of the extended conventional over the conventional method, as well as the matched filtering over the extended conventional technique, is the increased REM detection rate for ten minute intervals of artifact-free sleep. More accurate methods of automated REM detection that can be applied over extended monitoring periods are still needed.