We propose a computed tomography (CT) for the incoherent optical system based on a generalized analytic reconstruction method from discrete samples(GARDS), by which an object image defined in a continuous space is reconstructed from discrete images acquired through the imaging system. We apply this method to reconstruct depth structures of micro-specimens using conventional fluorescence microscopes. Also, we discuss the optimal sampling distance in the depth direction through a generalized singular value decomposition of a continuous -to-discrete imaging system. We next apply the GARDS-based CT method to a double-axis microscope, in which two microscopes are set up perpendiculrly to cover a missing frequency band of each microscopic imaging system. We show simulation results which verify the effectiveness of our proposed method.