...
Now run a loop with pulseJacker enabled: 'Enable' pulseJacker and put ephys on 'External'. Use the loopGUI to configure three acquisitions. The loopGui should be set to CPU timing mode, with an interval longer (by >0.5 sec) than the trace length in the ephys GUI (or stimulator, as appropriate). The iteration number should be set to the total number of sweeps desired. For example, to acquire all the sweeps for 3 positions in pulseJacker, this should be 3. To do them all twice, 6 iterations (and so forth). The position on the pulseJacker should also be 1, to start at the first pulse. To see all sweeps in the Acqusition window as they are acquired accumulate press the 'hold on' button in the toolbar (all the way on the right).
...