Imperfections in image formation, called aberrations, often preclude microscopes from reaching diffraction-limited resolution. Aberrations can be caused either by the microscope itself or by the sample and can be compensated for by using an active element integrated into the beam path which is functioning as a corrector. The optimal settings for this corrector need to be determined without excessive damage to the sample. In particular, for sensitive biological samples, the potential gain for signal and/or resolution needs to be weighed against sample damage. Here I present the development of a special type of optical coherence microscopy (called deep-OCM), which allows the precise determination of the average rat brain refractive index in vivo. The conclusion is that two-photon microscopy is affected by optical aberrations in this sample starting at depths around 200 µm. Deep-OCM is well suited for imaging myelinated nerve fibers. Individual fibers can be visualized in the living brain in unprecedented depths beyond 300 µm. In the second part of this thesis I describe the development and testing of an auto-focuser and auto-stigmator (called MAPFoSt) for a scanning electron microscope to ensure optimal imaging quality after switching samples or during long acquisition series. MAPFoSt determines the three focus and stigmation parameters from only two test images
