The invention includes an apparatus for controlling a microscope stage assembly having a rod for moving the stage in two directions. An ECU of the control system calculates a first estimated intake air amount according to a valve lift, a cam phase, and a compression ratio, calculates a second estimated intake air amount according to the flow rate of air detected by an air flow sensor. It comprises processing trays plurally stacked in a state of each supporting at least one semiconductor wafer individually and a coupling mechanism for integrally coupling the processing trays in a state where the processing trays are plurally stacked and separating the processing trays at an arbitrary location. By doing so, it is possible to easily compare images with different depths of field, and it is possible to simultaneously photograph images with different depths of field. Step includes performing at each individual rotation the sub-step of fitting the modelled blade displacements at each frequency to the zeroed blade displacements for successive rotations which include that individual rotation.