The fundamental operation before analyzing bacteria on the microscopic system is optimal focusing. Laboratory technicians implement this process with eye-hand coordination. During auto-focus process avoiding the dependence on technicians, auto-focus functions giving a value about focusing of the images are used in literature. At the end of the auto-focusing based on auto-focus functions, some regions in the in-focus image can be blurred. In this paper auto-focusing based color image fusion is implemented to obtain all of region in-focus image. In this study, firstly an image sequence is captured with moving the microscope stage along Z-axis. The reference image with the highest focus value on the sequence is found. Reference image and several images around the reference image are fused with curvelet transform preferred to obtain curve and line information of image. Moreover, various evaluation criteria are utilized to analyze the performance of the proposed auto-focus approach on different color models.