Recent studies have shown high correlation between pulmonary perfusion mapping with impedance contrast enhanced Electrical Impedance Tomography (EIT) and standard perfusion imaging methods such as Computed Tomography (CT) and Single Photon Emission Computerized Tomography (SPECT). EIT has many advantages over standard imaging methods as it is highly portable and non-invasive. Contrast enhanced EIT uses hypertonic saline bolus instead of nephrotoxic contrast medium that are utilized by CT and nuclear Ventilation/Perfusion (V/Q) scans. However, current implementation of contrast enhanced EIT requires induction of an apnea period for perfusion measurement, rendering it disadvantageous compared with current gold standard imaging modalities. In the present paper, we propose the use of a wavelet denoising algorithm to separate perfusion signal from ventilation signal such that no interruption in patient's ventilation would be required. Furthermore, right lung to left lung perfusion ratio and ventilation ratio are proposed to assess the mismatch between ventilation and perfusion for detection of Pulmonary Embolism (PE). The proposed methodology was validated on an ovine model (n=3, 83.7±7.7 kg) with artificially induced PE in the right lung. The results showed a difference in right lung to left lung perfusion ratio between baseline and diseased states in all cases with all paired t-tests between baseline and PE yielding p <; 0.01, while the right lung to left lung ventilation ratio remained unchanged in two out of three experiments. Statistics were pooled from multiple repetitions of measurements per experiment.