In WinLTP, stimulus artifacts can be removed or blanked out, as shown by the Analyze Whole Train figure.  Stimulus artifact blanking is useful 1) for determining the area or peak amplitude of a whole train which could be seriously distorted by the stimulus artifact, 2) for determining the peak amplitudes of individual EPSPs when the stimulus artifacts are riding on top of the previous EPSP, and 3) when trying to fit exponential curves to the decay phase of closely spaced EPSCs when the artifact for the next EPSC occurs during this decay phase.

WinLTP has three methods of blanking the stimulus artifact, the Average, Slope and Hold method. In the figure below, the gray lines show the original voltage trajectories with the stimulus artifacts going negative in this example.  The blue lines show the voltage trajectories after stimulus artifact blanking.  The blue line voltages are the ones analyzed by WinLTP, not the gray line voltages.

In the Average method, a horizontal voltage line is taken half way between the last voltage point before blanking begins and the first voltage point after blanking stops (Fig. 12.1A).

In the Slope method, a sloped voltage line is taken between the last voltage point before blanking begins and the first voltage point after blanking stops (Fig. 12.1B).

In the Hold method, a horizontal voltage line is taken as the last voltage point before blanking begins, which is useful for very large, long duration artifacts (Fig. 12.1C).

For more information see Section 4.5.2 in the online WinLTP Manual.

A Average
B Slope
C Hold