A method for combining a plurality of eye images into a plenoptic multifocal image that includes registering the eye images with a plurality of frames into one or more eye image sets with a processor and a memory system, aligning each of the eye images in each of the one or more image sets with a selected reference that resides on the memory system with the processor and determining one or more in-focus regions of the eye images by calculating one or more gradient images while ignoring noise and other imaging artifacts. The method also includes identifying the one or more in-focus regions with highest resolution from the one or more gradient images and selecting one or more corresponding in-focus intensities from the frames to combine into a plenoptic multifocal image with a higher resolution than the eye images, the frames and the one or more eye image sets.
