A method for operating an imaging system, the method comprising: collecting a two-dimensional image of a portion of a substrate on a positioning stage via a digital camera in the imaging system by moving the positioning stage in a first path of travel under an objective lens component of the imaging system that is normal to the optical axis of the objective lens component, wherein the image spans multiple rows of pixels of a sensor element in the camera; while the camera is collecting the image of the portion of the substrate, performing steps comprising: changing an angle of a scan mirror that is disposed in the optical path between the objective lens component and the camera so that the image of the portion of the substrate is kept still with respect to the camera while the positioning stage is moving; scanning a line of light generated by a line generator across the portion of the substrate by changing an angle of an illumination mirror, thereby exposing first one or more rows of pixels spanned by the image while keeping in the dark second one or more rows of pixels spanned by the image; and reading out the first one or more rows of pixels while continuing to scan the line of light across the portion of the substrate thereby exposing the second one or more rows of pixels. collecting a two-dimensional image of a portion of a substrate on a positioning stage via a digital camera in the imaging system by moving the positioning stage in a first path of travel under an objective lens component of the imaging system that is normal to the optical axis of the objective lens component, wherein the image spans multiple rows of pixels of a sensor element in the camera; while the camera is collecting the image of the portion of the substrate, performing steps comprising: changing an angle of a scan mirror that is disposed in the optical path between the objective lens component and the camera so that the image of the portion of the substrate is kept still with respect to the camera while the positioning stage is moving; scanning a line of light generated by a line generator across the portion of the substrate by changing an angle of an illumination mirror, thereby exposing first one or more rows of pixels spanned by the image while keeping in the dark second one or more rows of pixels spanned by the image; and reading out the first one or more rows of pixels while continuing to scan the line of light across the portion of the substrate thereby exposing the second one or more rows of pixels. changing an angle of a scan mirror that is disposed in the optical path between the objective lens component and the camera so that the image of the portion of the substrate is kept still with respect to the camera while the positioning stage is moving; scanning a line of light generated by a line generator across the portion of the substrate by changing an angle of an illumination mirror, thereby exposing first one or more rows of pixels spanned by the image while keeping in the dark second one or more rows of pixels spanned by the image; and reading out the first one or more rows of pixels while continuing to scan the line of light across the portion of the substrate thereby exposing the second one or more rows of pixels.