A system and method for detecting a transition in a stream of images of a gastrointestinal (GI) tract may include selecting images from an in-vivo image stream calculating a segment score for each selected image indicating in which segment of the GI tract the image was captured applying a smoothing function on the scores detecting a global step in the smoothed segment score signal indicating a substantial change in a parameter calculated based on segment score signal values of the segment score signal values detecting a local step indicating a substantial change in a parameter calculated based on segment score signal values of a predetermined interval of the of the segment score signal values combining the local step and the global step and determining a point of transition in the stream from one anatomical segment to another, the point of transition correlating to the combined step.
