1. An imaging system for generating an image of a sub-surface feature of an object through a surface of the object, the system comprising: an illumination array, the illumination array comprising a plurality of illumination sources positioned around the sub-surface feature of the object, wherein each of the illumination sources directs illumination in an imaging wavelength range towards the surface at an angle relative to the normal of the surface; an imaging device comprising an objective; a computer system in communication with the illumination array, the computer system comprising at least one processor and operatively associated memory, wherein the computer is programmed to: calculate an optimized illumination pattern of the plurality of illumination sources for imaging the sub-surface feature, wherein the calculating comprises: receiving a first result set, wherein the first result set comprises a plurality of illumination patterns; for each of the plurality of illumination patterns of the first result set: receiving an image of the sub-surface feature of the object with the illumination pattern activated; and based on the image, calculating a fitness function value; determine that none of the fitness function values for any of the plurality of illumination patterns of the first result set exceed a threshold value; and generating a next result set comprising a second plurality of illumination patterns, wherein the generating is based at least in part on the first result set and the fitness function values for the plurality of illumination patterns of the first result; activate the optimized illumination pattern; and instruct the imaging device to capture an image of the sub-surface feature with the imaging device based on reflected illumination from the optimized illumination pattern.