1. A system configured to determine a configuration for an optical element positioned in a collection aperture during wafer inspection, comprising: a light source configured to generate light that is directed to the wafer; an optical element positioned in a collection pupil plane, wherein the optical element comprises a set of collection apertures; a detector configured to detect light from the wafer that passes through the optical element when the optical element has different configurations thereby generating different images for the different configurations, wherein at least one of the different configurations comprises only a single collection aperture in the set, and wherein at least another of the different configurations comprises two of the collection apertures in the set; and a computer subsystem configured for: constructing one or more additional images from two or more of the different images, wherein the two or more different images used to generate any one of the one or more additional images do not comprise only the different images generated for single collection apertures in the set; determining one or more characteristics of the different images and the one or more additional images; comparing the one or more characteristics of the different images and the one or more additional images; selecting one of the different or additional configurations for the optical element for inspection of the wafer based on results of said comparing; determining phase shift between the light scattered at different directions from the wafer based on the different images; and determining one or more parameters of a phase contrast filter for use in the system during the inspection of the wafer based on the determined phase shift.