  A method is presented to quantify resolution as a function of depth in
features of morphologically complex 3D samples. Applying the method to the
brain of Drosophila, resolution is measured at increasing depth throughout the
central brain region. The results quantify improvements in image quality when
using two-photon microscopy compared to confocal. It is also demonstrated how
resolution improvements through tuning a single parameter, laser power, can be
measured objectively. Since the metric is interpretable as the average
resolution within a feature, it is suitable for comparing results across
optical systems, and can be used to inform the design of biological experiments
requiring resolution of structures at a specific scale.
