Selected properties of a microplate comprising a plurality of sample wells are obtained by repetitively performing focusing functions to determine sequentially a well surface z-position and then a plate bottom z-position for a corresponding current x-y position based on an intensity indicative of a best focus of the well surface and the plate bottom respectively. The well surface z-position and the plate bottom z-position corresponding to each of the plurality of x-y positions are determined by repeating the steps of positioning the objective lens, performing the focusing function to determine the well surface z-position, and performing the focusing function for the plate bottom z-position. The well surface z-positions and the plate bottom z-positions at the plurality of x-y positions are used to generate data to determine the selected properties of the microplate.