1. A method for segmenting an image stream captured within a gastrointestinal tract by an in vivo device inserted into said gastrointestinal tract, said device comprising an imager and being designed to pass through said gastrointestinal tract and to capture a stream of images thereof, the method comprising: receiving a first image and a second image of the image stream captured using said imager during a single pass of the device through the gastrointestinal tract, wherein the first image and the second image correspond to first and second chronological points in a time scale of the image stream, respectively; computing, using a computer, average pixel color values of the first image and of the second image; detecting, using a computer, a transition between organs of the gastrointestinal tract based on a change in the average pixel color values; and segmenting the image stream at the points in the time scale of the image stream that correspond to transitions between the organs of the gastrointestinal tract.