Here are some suggestions for overcoming the problem of stimulation artifact when applying a stimulation voltage to a muscle.
Have the ground between the stimulating electrodes and the recording electrodes.
The recording electrodes should be placed orthogonal to the stimulating electrodes.
Apply the highest possible low pass filter on the amplifier. This will allow the amplifier to recover faster.
During analysis, the find peak function should be used to look for EMG activity between the electrical stimuli. For example, if the stimuli are 100 msec apart and it takes 10 msec for the amplifier to recover from the stimulus a find peak from 10 to 99 msec after the interval can be used.
The stimulus artifact may never be removed completely because it is so intense. But this will not be much of an issue since the EMG signal you need for analysis falls between the spikes in the signal caused by the stimulator.
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