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We have demonstrated a technique to calculate the EMG instantaneous median frequency to assess muscle fatigue during a dynamic exercise commonly prescribed in patients with ACL deficiency. We used Cohen-Posch time-frequency representations to improve upon the variability of the instantaneous median frequency estimates derived using Cohen Class transformations. The technique was applied to surface EMG data recorded from the quadriceps and hamstring muscles of a control subject and a patient with ACL deficiency during a repetitive squat exercise. Instantaneous median frequency values were derived for the knee-extension phases of the exercise. Ensemble average and standard deviation of the instantaneous median frequency were computed for the portion of the cycle associated with the lowest variability of the mechanics.