In this paper, we present a complete processing pipeline for focused plenoptic cameras. In particular, we propose 1) a new algorithm for microlens center calibration fully in the Fourier domain, 2) a novel algorithm for depth map computation using a stereo focal stack, and 3) a depth-based rendering algorithm that is able to refocus at a particular depth or to create all-in-focus images. The proposed algorithms are fast, accurate, and do not need to generate subaperture images or epipolar plane images which is capital for focused plenoptic cameras. Also, the resolution of the resulting depth map is the same as the rendered image. We show results of our pipeline on Georgiev's dataset and real images captured with different Raytrix cameras.