A system, method and virtual tool for size estimation of in-vivo objects includes receiving and displaying a two-dimensional image of in-vivo objects obtained by in-vivo imaging device; receiving indication of a selected area representing a point of interest from the user via a user input device; estimating depth of a plurality of image pixels around the selected area; calculating three-dimensional coordinates representation of the plurality of image points, based on the estimated depths; casting a virtual tool of a known size onto the three-dimensional representation; and projecting the virtual tool onto the two-dimensional image to create a cursor having a two-dimensional shape on the displayed image.