Wavefront coding is a technique that combines optical phase elements and digital signal processing in order to increase the effective depth of focus of optical systems. The success of wavefront coding lies in the design of a suitable phase mask placed at the system's aperture. This element allows for image formation invariant under the effects of different second-order optical aberrations. In optical systems limited by temporally or spatially varying high-order aberrations, the use of wavefront coding has not been fully demonstrated. Here we propose the choice of Jacobi-Fourier shaped phase masks to produce sharp and clear retinal images of living eyes. To demonstrate the potential use of the technique, we analyze the performance of the Jacobi-Fourier phase masks through experimental simulations to alleviate aberrations for different eye aberrations. We will show that the best mask choice is robust to noise while keeping acceptable resolution and reducing image artefacts.