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Wireless Capsule Endoscopy (WCE) is a new colour imaging technology that enables close examination of the interior of the entire small intestine. Typically, the WCE operates for ~8 hours and captures ~40,000 useful images. The images are viewed as a video sequence, which generally takes a doctor over an hour to analyse. In order to activate certain key features of the software provided with the capsule, it is necessary to locate and annotate the boundaries between certain gastrointestinal (GI) tract regions (stomach, intestine and colon) in the footage. In this paper we propose a method of automatically discriminating stomach, intestine and colon tissue in order to significantly reduce the video assessment time. We use hue saturation chromaticity histograms which are compressed using a hybrid transform, incorporating the Discrete Cosine Transform (DCT) and Principal Component Analysis (PCA). The …