We describe a stable method for calibrating digital waveforms and eye diagrams by use of the measurement system response function and its regularized inverse. The function describing the system response includes the response of the oscilloscope and any associated cables and test fixtures. We demonstrate the effectiveness of the method by performing a statistical analysis of the calculated eye height and eye width obtained from a controlled experiment consisting of multiple cable lengths, bit rates, and oscilloscope samplers. We also demonstrate our approach by measuring the transmission through a test device consisting of a short length of cable, a ball-grid array socket, and complicated circuit board.