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.
