An imaging system on which a calibration method is practiced includes: a light source; a substrate for supporting an object; a patterning mask that generates a substantially periodic spatial pattern on the object; a phase shifter that adjusts the relative position of the patterning mask and object to shift the position of the pattern on the object; a detector that detects images of the object; and an analyzer that analyzes at least three images of the object, each of which represents a different spatial shift of the pattern, the analyzer being configured to remove the spatial pattern from the images to generate an optically sectioned image of the object. The calibration method includes: calibrating the position of the mask relative to the substrate via a phase-voltage technique; calibrating the position of the mask relative to the substrate via a merit function technique; and operating the calibrated imaging system.