1. A method for automatic generation of a model of an organ, the organ imaged by an in vivo capsule comprising an imager, the method comprising: capturing, via the in vivo capsule, light-based images in-vivo; generating, by a computer data processor, an initial organ model being a three-dimensional hollow geometric shell representing an inner surface of an organ within a body, the initial organ model based on a predetermined estimated structure of the imaged organ; receiving, by the computer data processor, a user indication of an image captured while the in vivo capsule images a first point of interest to a user identified in the imaged organ; determining a position and orientation of the in vivo capsule upon capturing the indicated image of the first point of interest; based on the position and orientation of the in vivo capsule, updating, by the computer data processor, the initial model to a customized model, such that a location in the customized model corresponding to the position of the point of interest in vivo reflects the organ size and organ location within the body; and based on the customized model and images captured by the in vivo capsule, constructing, by the computer data processor, a three-dimensional visualization of the organ including the images for display to the user.