A method and system for determining the mineral content of a sample using an electron microscope. The method includes directing an electron beam toward an area of interest of a sample, the area of interest comprising an unknown composition of minerals. The working distance between the backscattered electron detector of the microscope and the area of interest of the sample is determined. Compensation is made for the difference between the working distance and a predetermined working distance in which the predetermined working distance being the working distance that provides desired grayscale values for detected backscattered electrons. One way of compensating for working distance variation is to used an autofocus feature of the microscope to adjust the working distance. Backscattered electrons from the area of interest of the sample are then detected.