1. A method of processing images of human gastrointestinal (GI) tract captured using a capsule camera, the method comprising: receiving two images designated as a reference image and a float image, wherein the float image corresponds to a current capsule image and the reference image corresponds to a previously composite image or another captured capsule image prior to the float image; automatically segmenting the float image into one or more first native GI regions if any native GI sample is detected for the float image and one or more first non-GI regions if any non-GI sample is detected for the float image; automatically segmenting the reference image into one or more second native GI regions if any native GI sample is detected for the reference image and one or more second non-GI regions if any non-GI sample is detected for the reference image; registering the float image with respect to the reference image by optimizing a match measure between the reference image and a deformed float image with said one or more first non-GI regions and said one or more second non-GI regions excluded from computing the match measure between the reference image and a deformed float image, wherein the deformed float image is generated by applying a transformation model to the float image to adjust geometric deformation between the float image and the reference image; and generating a composite image by rendering the reference image and the deformed float image in a common coordinate after said registering the float image with respect to the reference image.