Adaptive optics for microscopy and photonic engineering
Keywords: Optical Fabrication
Microscopy
Adaptive Optics
Aberrations

Aberrations affect the operation of optical systems, particularly those designed to work at the diffraction limit. These systems include high-resolution microscopes, widely used for imaging in biology and other areas. Similar problems are encountered in photonic engineering, specifically in laser fabrication systems used for the manufacture of fine structures. The work presented in this thesis covers various aspects of adaptive optics developed for applications in microscopes and laser fabrication.
By mathematically modelling a range of idealised fluorescent structures, the effect of different aberrations on their intensity in various microscopes is presented. The effect of random aberrations on the contrast of these different structures is then calculated and the results displayed on idealised images. Images from a two-photon microscope demonstrate the predicted results. The contrast of two structures is compared when imaged first by a conventional microscope and then by the two-photon or confocal sectioning microscopes. The different specimen structures were seen to be affected to varying extents by each aberration mode.
In order to correct for aberrations in microscopy and other photonic applications, adaptive elements such as deformable mirrors are incorporated into the optical setups. An important step is to train the deformable mirror so that it produces appropriate mode shapes to apply a phase to optical wavefronts. One such mirror is modelled using the membrane equation to predict the surface shape when an actuator is applied. Each of these influence functions is combined to produce a set of orthogonal mirror modes, which are used to experimentally produce a set of empirical modes in a two-photon microscope. An alternative method of training a deformable mirror from a spatial light modulator is employed. The focal spot of an optical system is imaged to provide a feedback metric for the mirror to replicate the phase pattern on the spatial light modulator.
A two-photon microscope with adaptive optics is demonstrated by imaging the brains of Drosophila deep within the bulk, correcting for both system and specimen induced aberrations using the deformable mirror with empirical mirror modes applied. A harmonic generation microscope is also used to image both biological and non-biological specimens whilst performing aberration correction with a deformable mirror. Adaptive optical methods are also applied to a laser fabrication system, by constructing a dual adaptive optics setup to correct for aberrations induced when fabricating deep in the bulk of a substrate. The efficiency and fidelity of fabrication in diamond substrate is shown to be significantly increased as a result of the dual aberration correction.
An outstanding problem in microscopy is the effect of spatially variant aberrations. Using measurements from the adaptive microscopes, the extent to which they are present in a range of specimens is quantified. One potential technique to be used to correct for these aberrations is multi-conjugate adaptive optics. Different configurations of a multi-conjugate adaptive optics system are modelled and the improvement on the Strehl ratio of aberrated images quantified for both simulated images and real data. The application of this technique in experimental microscopes is considered.