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This paper describes the use of color image analysis to automatically discriminate between oesophagus, stomach, small intestine, and colon tissue in wireless capsule endoscopy (WCE). WCE uses ldquopill-camrdquo technology to recover color video imagery from the entire gastrointestinal tract. Accurately reviewing and reporting this data is a vital part of the examination, but it is tedious and time consuming. Automatic image analysis tools play an important role in supporting the clinician and speeding up this process. Our approach first divides the WCE image into subimages and rejects all subimages in which tissue is not clearly visible. We then create a feature vector combining color, texture, and motion information of the entire image and valid subimages. Color features are derived from hue saturation histograms, compressed using a hybrid transform, incorporating the discrete cosine transform and principal component analysis. A second feature combining color and texture information is derived using local binary patterns. The video is segmented into meaningful parts using support vector or multivariate Gaussian classifiers built within the framework of a hidden Markov model. We present experimental results that demonstrate the effectiveness of this method.