Method for processing eye diagram data from a system under test includes mapping channels of a logic analyzer for eye diagram data signal acquisition to DSO inputs, acquiring signals from the channels, determining if there are additional channels for signal acquisition and in response to the completion of acquisition signals, automatically mapping the additional channels to the DSO inputs and acquiring data signals from the additional channels. The steps are repeated until all selected channels are analyzed. An apparatus includes means for selecting a first plurality of channels for eye diagram signal acquisition and mapping the first plurality of channels to DSO inputs, means for acquiring a first plurality of signals from the first plurality of channels, means for sending a completion of acquisition signal and means for automatically mapping a second plurality of channels for eye diagram signal acquisition to the DSO inputs in response to the completion of acquisition signal. The DSO then sends the eye diagram data to the Logic Analyzer for display.