A method of navigational calibration for an x-ray inspection system, the method characterized by comprising: mounting a calibration phantom on a moveable stage, wherein a first surface of the calibration phantom is generally planar and includes an optically visible pattern illustrated thereon, the pattern including: a plurality of polygons of different sizes, wherein a first polygon of the plurality of polygons is inset and centered within a second polygon of the plurality of polygons; a center mark at a center of the calibration phantom; and a vertex mark at a vertex of one of the plurality of polygons; wherein a physical location of the vertex mark is offset from a physical location of the center mark by a predetermined first offset distance in a first direction and a predetermined second offset distance in a second direction, and wherein the first and second directions lie in the plane of the first surface and are orthogonal to one another; generating a graphical user interface including a sequence of images of a field of view of an optical video camera and a crosshair overlaid upon the sequence of images; outputting the GUI for display; moving the moveable stage to a first location, wherein the calibration phantom is within the field of view of the video camera such that the crosshair center is aligned with the center mark within the GUI; determining a calibration ratio defined as a physical length per pixel or as a ratio of a physical dimension and a measured number of pixels within the sequence of images when the moveable stage is at the first location; receiving the physical location of the vertex mark; moving the moveable stage from the first position to a second position by moving the first offset distance in the first direction and moving the second offset distance in the second direction; measuring, at the second location, respective first pixel differences in the first and second directions between a pixel location of the predetermined vertex mark within the GUI and a pixel location of the crosshair center within the GUI; and outputting a calibration status based upon a comparison between the first pixel differences in the first and second directions and a threshold value. mounting a calibration phantom on a moveable stage, wherein a first surface of the calibration phantom is generally planar and includes an optically visible pattern illustrated thereon, the pattern including: a plurality of polygons of different sizes, wherein a first polygon of the plurality of polygons is inset and centered within a second polygon of the plurality of polygons; a center mark at a center of the calibration phantom; and a vertex mark at a vertex of one of the plurality of polygons; wherein a physical location of the vertex mark is offset from a physical location of the center mark by a predetermined first offset distance in a first direction and a predetermined second offset distance in a second direction, and wherein the first and second directions lie in the plane of the first surface and are orthogonal to one another; a plurality of polygons of different sizes, wherein a first polygon of the plurality of polygons is inset and centered within a second polygon of the plurality of polygons; a center mark at a center of the calibration phantom; and a vertex mark at a vertex of one of the plurality of polygons; wherein a physical location of the vertex mark is offset from a physical location of the center mark by a predetermined first offset distance in a first direction and a predetermined second offset distance in a second direction, and wherein the first and second directions lie in the plane of the first surface and are orthogonal to one another; generating a graphical user interface including a sequence of images of a field of view of an optical video camera and a crosshair overlaid upon the sequence of images; outputting the GUI for display; moving the moveable stage to a first location, wherein the calibration phantom is within the field of view of the video camera such that the crosshair center is aligned with the center mark within the GUI; determining a calibration ratio defined as a physical length per pixel or as a ratio of a physical dimension and a measured number of pixels within the sequence of images when the moveable stage is at the first location; receiving the physical location of the vertex mark; moving the moveable stage from the first position to a second position by moving the first offset distance in the first direction and moving the second offset distance in the second direction; measuring, at the second location, respective first pixel differences in the first and second directions between a pixel location of the predetermined vertex mark within the GUI and a pixel location of the crosshair center within the GUI; and outputting a calibration status based upon a comparison between the first pixel differences in the first and second directions and a threshold value.