Aberration-corrected incoherent imaging methods and systems that can acquire a sequence of coherent images and an incoherent image of a specimen, implement an embedded pupil function recovery process in junction with Fourier ptychographic technique to construct an improved resolution image and pupil function of the imaging system using the sequence of coherent images, determine an optical transfer function based on the estimated pupil function, and remove the aberration from the incoherent image using a deconvolution process to generate an aberration-corrected incoherent image.