Optical testing in adverse environments, ophthalmology and applications where characterization by curvature is leveraged all have a common goal: accurately estimate wavefront shape. This dissertation investigates wavefront sensing techniques as applied to optical testing based on gradient and curvature measurements. Wavefront sensing involves the ability to accurately estimate shape over any aperture geometry, which requires establishing a sampling grid and estimation scheme, quantifying estimation errors caused by measurement noise propagation, and designing an instrument with sufficient accuracy and sensitivity for the application. Starting with gradient-based wavefront sensing, a zonal least-squares wavefront estimation algorithm for any irregular pupil shape and size is presented, for which the normal matrix equation sets share a pre-defined matrix. A Gerchberg–Saxton iterative method is employed to reduce the deviation errors in the estimated wavefront caused by the pre-defined matrix across discontinuous boundary. The results show that the RMS deviation error of the estimated wavefront from the original wavefront can be less than λ/130~ λ/150 (for λ equals 632.8nm) after about twelve iterations and less than λ/100 after as few as four iterations. The presented approach to handling irregular pupil shapes applies equally well to wavefront estimation from curvature data. A defining characteristic for a wavefront estimation algorithm is its error propagation behavior. The error propagation coefficient can be formulated as a function of the eigenvalues of the wavefront estimation-related matrices, and such functions are established for each of the basic estimation geometries (i.e. Fried, Hudgin and Southwell) with a serial numbering scheme, where a square sampling grid array is sequentially indexed row by row. The results show that with the wavefront piston-value fixed, the odd-number grid sizes yield lower error propagation than the even-number grid sizes for all geometries. The Fried geometry either allows sub-sized wavefront estimations within the testing domain or yields a two-rank deficient estimation matrix over the full aperture; but the latter usually suffers from high error propagation and the waffle mode problem. Hudgin geometry offers an error propagator between those of the Southwell and the Fried geometries. For both wavefront gradient-based and wavefront difference-based estimations, the Southwell geometry is shown to offer the lowest error propagation with the minimum-norm least-squares solution. Noll’s theoretical result, which was extensively used as a reference in the previous literature for error propagation estimate, corresponds to the Southwell geometry with an odd-number grid size. For curvature-based wavefront sensing, a concept for a differential Shack-Hartmann (DSH) curvature sensor is proposed. This curvature sensor is derived from the basic Shack-Hartmann sensor with the collimated beam split into three output channels, along each of which a lenslet array is located. Three Hartmann grid arrays are generated by three lenslet arrays. Two of the lenslets shear in two perpendicular directions relative to the third one. By quantitatively comparing the Shack-Hartmann grid coordinates of the three channels, the differentials of the wavefront slope at each Shack-Hartmann grid point can be obtained, so the Laplacian curvatures and twist terms will be available. The acquisition of the twist terms using a Hartmann-based sensor allows us to uniquely determine the principal curvatures and directions more accurately than prior methods. Measurement of local curvatures as opposed to slopes is unique because curvature is intrinsic to the wavefront under test, and it is an absolute as opposed to a relative measurement. A zonal least-squares-based wavefront estimation algorithm was developed to estimate the wavefront shape from the Laplacian curvature data, and validated. An implementation of the DSH curvature sensor is proposed and an experimental system for this implementation was initiated. The DSH curvature sensor shares the important features of both the Shack-Hartmann slope sensor and Roddier’s curvature sensor. It is a two-dimensional parallel curvature sensor. Because it is a curvature sensor, it provides absolute measurements which are thus insensitive to vibrations, tip/tilts, and whole body movements. Because it is a two-dimensional sensor, it does not suffer from other sources of errors, such as scanning noise. Combined with sufficient sampling and a zonal wavefront estimation algorithm, both low and mid frequencies of the wavefront may be recovered. Notice that the DSH curvature sensor operates at the pupil of the system under test, therefore the difficulty associated with operation close to the caustic zone is avoided. Finally, the DSH-curvature-sensor-based wavefront estimation does not suffer from the 2π-ambiguity problem, so potentially both small and large aberrations may be measured.

Wavefront controller optimization is important in achieving the best possible image quality for adaptive optics systems on the current generation of large and very large aperture telescopes. This will become even more critical when we consider the demands of the next generation of extremely large telescopes currently under development. These telescopes will be capable of providing resolution which is significantly greater than the current generation of optical/IR telescopes. However, reaching the full resolving potential of these instruments will require a careful analysis of all disturbance sources, then optimizing the wavefront controller to provide the best possible image quality given the desired science goals and system constraints. Along with atmospheric turbulence and sensor noise, structural vibration will play an important part in determining the overall image quality obtained. The next generation of very large aperture telescopes currently being developed will require assessing the effects of structural vibration on closed loop AO system performance as an integral part of the overall system design. Telescope structural vibrations can seriously degrade image quality, resulting in actual spot full width half maximum (FWHM) and angular resolution much worse than the theoretical limit. Strehl ratio can also be significantly degraded by structural vibration as energy is dispersed over a much larger area of the detector. In addition to increasing telescope diameter to obtain higher resolution, there has also been significant interest in adaptive optics systems which observe at shorter wavelength from the near infrared to visible (VNIR) wavelengths, at or near 0.7 microns. This will require significant reduction in the overall wavefront residuals as compared with current systems, and will therefore make assessment and optimization of the wavefront controller even more critical for obtaining good AO system performance in the VNIR regime.

This paper presents the early-stage simulation results of linear dark field control (LDFC) as a new approach to maintaining a stable dark hole within a stellar post-coronagraphic PSF. In practice, conventional speckle nulling is used to create a dark hole in the PSF, and LDFC is then employed to maintain the dark field by using information from the bright speckle field. The concept exploits the linear response of the bright speckle intensity to wavefront variations in the pupil, and therefore has many advantages over conventional speckle nulling as a method for stabilizing the dark hole. In theory, LDFC is faster, more sensitive, and more robust than using conventional speckle nulling techniques, like electric field conjugation, to maintain the dark hole. In this paper, LDFC theory, linear bright speckle characterization, and first results in simulation are presented as an initial step toward the deployment of LDFC on the UA Wavefront Control testbed in the coming year.

MagAO is the adaptive optics instrument at the Magellan Clay telescope at Las Campanas Observatory, Chile. MagAO has a 585-actuator adaptive secondary mirror and 1000-Hz pyramid wavefront sensor, operating on natural guide stars from R-magnitudes of -1 to 15. MagAO has been in on-sky operation for 166 nights since installation in 2012. MagAO's unique capabilities are simultaneous imaging in the visible and infrared with VisAO and Clio, excellent performance at an excellent site, and a lean operations model. Science results from MagAO include the first ground-based CCD image of an exoplanet, demonstration of the first accreting protoplanets, discovery of a new wide-orbit exoplanet, and the first empirical bolometric luminosity of an exoplanet. We describe the status, report the AO performance, and summarize the science results. New developments reported here include color corrections on red guide stars for the wavefront sensor; a new field stop stage to facilitate VisAO imaging of extended sources; and eyepiece observing at the visible-light diffraction limit of a 6.5-m telescope. We also discuss a recent hose failure that led to a glycol coolant leak, and the recovery of the adaptive secondary mirror (ASM) after this recent (Feb. 2016) incident.

En complément aux méthodes traditionnelles d’observation et de stimulation en neuroscience, l’optogénétique, combinant l’expression ciblée de protéines photosensibles dans les neurones et l’utilisation de nouvelles techniques de microscopies, a connu un essor important ces dernières années. Ce nouveau procédé permet d’enregistrer de manière non invasive les signaux fonctionnels de circuits intacts tels que les changements de potentiel de membrane ou de concentration intracellulaire de calcium mais également de moduler l’excitabilité des neurones. Pour illuminer ces protéines photosensibles, de nouvelles méthodes de microscopie ont été développées. En particulier, afin d’obtenir une résolution spatiale optimale au sein d’un tissu biologique, il devient nécessaire d’utiliser l’illumination bi-photonique et d’utiliser des techniques permettant la mise en forme du faisceau lumineux pour s’adapter à la morphologie des circuits ou même des neurones étudiés.Au cours de ma thèse, j’ai développé une combinaison de méthodes optiques (associant le contraste de phase généralisé avec la focalisation temporelle) afin d’activer le canal cationique channelrhodopsin-2 en excitation bi-photonique. Ce travail a démontré, pour la première fois, l’activation simultanée de potentiels d’action dans plusieurs cellules tout en conservant une résolution axiale à l’échelle cellulaire (~10 μm).La mise en forme du faisceau lumineux semble très avantageuse pour améliorer la spécificité de l’activation. Il restait à démontrer que les faisceaux ainsi modulés conservaient leur intégrité spatiale en se propageant à l’intérieur de tissus biologiques diffusants. J’ai donc étudié la propagation de faisceaux lasers modulés par les techniques du contraste de phase généralisé et de l’holographie numérique en combinaison avec la focalisation temporelle. L’utilisation de la focalisation temporelle permet aux volumes d’excitation de rester confinés sur l’axe de propagation comme observé précédemment, mais aussi de reconstruire un profil d’excitation en profondeur dans le tissu, qui correspond au profile généré sans milieu diffusant. Cet effet est plus important pour le contraste de phase généralisé que pour l’holographie numérique et se dégrade en fonction de la profondeur à laquelle l’activation a lieu. J’ai démontré pour la première fois, l’activation en profondeur (> 200 μm) de neurones grâces à ces méthodes.Enfin, j’ai testé les mêmes techniques d’illumination sur d’autres protéines photosensibles, telles que la C1V1 et l’halorhodopsin. Après avoir établi les spectres d’activation afin de trouver la longueur d’onde optimale pour l’activation bi-photonique, j’ai exprimé ces protéines dans des tranches de cerveaux. Les deux protéines requièrent une activation à 1040 nm à la limite du laser Ti:Sapphire utilisé dans de nombreux laboratoires biologiques. La C1V1 a généré des courants similaires à la ChR2 en terme d’amplitude tout en conservant la lente cinétique de fermeture caractéristique de ce canal. L’halorhodopsin, quant à elle, reste difficile à activer avec de faibles courants et ne permet pas une inhibition sélective de trains de potentiels d’action. Ce problème est probablement dû à un faible taux d’expression observé dans les neurones étudiés et serait peut-être résolu en changeant de construction virale. / Optogenetics relies on the genetically targeted expression of light sensitive proteins in specific cell populations. This novel field has had a large impact in neuroscience, allowing both monitoring and stimulating the activity of specific neuronal populations, in intact brain preparations. Optogenetic tools have been used to record functional signals, such as changes in membrane potential or intracellular calcium concentration, as well as to modulate the excitability of neurons. To fully exploit the potentiality of optogenetics, new microscopy techniques have been developed to optimize illumination of photo-active compounds in situ. In particular, an important effort has been directed towards improving the spatial and temporal resolution of light stimulation, in order to match the dynamics of physiological processes. In this frame, the use of two-photon excitation becomes necessary to ensure penetration of light in scattering biological tissues, as well as confining the excitation volume and improve the specificity of illumination. My thesis was dedicated to the development and use of advanced optical methods for two-photon excitation of optogenetic tools. In a first project, we combined optical approaches (generalized phase contrast and temporal focusing) to perform two-photon activation of neurons expressing the light-sensitive cationic channel channelrhodopsin-2 (ChR2). Our work demonstrated for the first time the simultaneous generation of action potentials in multiple neurons, while maintaining a micrometric axial and lateral resolution. These results pointed out the advantages of light sculpting to increase both the specificity and the flexibility of photo-stimulation.In order to investigate the potential of this technique for efficient in-depth stimulation, we therefore studied the propagation through scattering biological media of laser beams generated by two different light patterning techniques, generalized phase contrast and digital holography in combination with temporal focusing. We demonstrated that temporal focusing enabled the excitation volumes to maintain micrometric axial confinement, as well as to maintain well defined patterns deep inside tissues. We also demonstrated for the first time the activation of ChR2 at depth over 200 μm.Finally, the last part of my PhD was focused on testing light patterning methods for the activation of two other photosensitive proteins, the excitatory channel C1V1 and the inhibitory pump, halorhodopsin.

Neste trabalho foi desenvolvido um novo método voltado para a caracterização de lentes térmicas em materiais fotônicos, utilizados como meios ativos no desenvolvimento de lasers. Este método baseia-se em interferometria por padrão de speckle eletrônico (ESPI), utilizando dois lasers de diodo multímodo sintonizados a diferentes freqüências. Com o ajuste desta diferença, foi possível escolher uma resolução apropriada para medirmos as variações geradas no raio de curvatura da frente de onda, relacionados ao efeito térmico. Para os nossos experimentos escolhemos uma amostra vítrea de aluminato de cálcio dopado com 4% de érbio; e potências de bombeio incidentes de até 1,76 mW do laser de bombeio. Os lasers de diodo foram sintonizados para ter um intervalo de contorno por volta de 120 m. Com o aumento da potência absorvida pela amostra, observamos a diminuição da curvatura da frente de onda incidente na CCD, devido ao aumento da potência da lente térmica gerada. Através de uma análise paraxial dos feixes, foi feita uma aproximação para obtermos os valores das lentes para cada configuração, apresentando comprimentos focais de 131,39 mm a 42,76 mm. / In this work we will develop a new method focused on the caracterization of thermal lenses effect in photonic materials used as active media in lasers design. This method is based on electronic speckle pattern interferometry (ESPI) using two multimode diode lasers tuned to different frequencies. Adjusting this difference we can achieve an appropriate resolution to measure the variability generated within the curvature radius of the wavefront due to thermal lens effect. For our experiments we chose a vitreous sample of calcium aluminate doped with 4% erbium and incident pump powers ranging to 1.76mW. The diode lasers were tuned to have a contour interval of around 120m. With addition in power absorbed by the sample, we observed a decrease in the curvature radius incident on the camera due to increased power of the thermal lens generated. Through a paraxial of the wavefront, an approach was made to obtain the values of the lenses for each configuration, with focal lengths ranging from 131.39 mm to 42.76 mm.

This work explores remote sensing of planetary atmospheres and their circumstellar surroundings. The terrestrial ionosphere is a highly variable space plasma embedded in the thermosphere. Generated by solar radiation and predominantly composed of oxygen ions at high altitudes, the ionosphere is dynamically and chemically coupled to the neutral atmosphere. Variations in ionospheric plasma density impact radio astronomy and communications. Inverting observations of 83.4 nm photons resonantly scattered by singly ionized oxygen holds promise for remotely sensing the ionospheric plasma density. This hypothesis was tested by comparing 83.4 nm limb profiles recorded by the Remote Atmospheric and Ionospheric Detection System aboard the International Space Station to a forward model driven by coincident plasma densities measured independently via ground-based incoherent scatter radar. A comparison study of two separate radar overflights with different limb profile morphologies found agreement between the forward model and measured limb profiles. A new implementation of Chapman parameter retrieval via Markov chain Monte Carlo techniques quantifies the precision of the plasma densities inferred from 83.4 nm emission profiles. This first study demonstrates the utility of 83.4 nm emission for ionospheric remote sensing. Future visible and ultraviolet spectroscopy will characterize the composition of exoplanet atmospheres; therefore, the second study advances technologies for the direct imaging and spectroscopy of exoplanets. Such spectroscopy requires the development of new technologies to separate relatively dim exoplanet light from parent star light. High-contrast observations at short wavelengths require spaceborne telescopes to circumvent atmospheric aberrations. The Planet Imaging Concept Testbed Using a Rocket Experiment (PICTURE) team designed a suborbital sounding rocket payload to demonstrate visible light high-contrast imaging with a visible nulling coronagraph. Laboratory operations of the PICTURE coronagraph achieved the high-contrast imaging sensitivity necessary to test for the predicted warm circumstellar belt around Epsilon Eridani. Interferometric wavefront measurements of calibration target Beta Orionis recorded during the second test flight in November 2015 demonstrate the first active wavefront sensing with a piezoelectric mirror stage and activation of a micromachine deformable mirror in space. These two studies advance our ``close-to-home'' knowledge of atmospheres and move exoplanetary studies closer to detailed measurements of atmospheres outside our solar system.

A new type of adaptive optics (AO) based on the principles of digital holography (DH) is proposed and developed for the use in wide-field and confocal retinal imaging. Digital holographic adaptive optics (DHAO) dispenses with the wavefront sensor and wavefront corrector of the conventional AO system. DH is an emergent imaging technology that gives direct numerical access to the phase of the optical field, thus allowing precise control and manipulation of the optical field. Incorporation of DH in an ophthalmic imaging system can lead to versatile imaging capabilities at substantially reduced complexity and cost of the instrument. A typical conventional AO system includes several critical hardware pieces: spatial light modulator, lenslet array, and a second CCD camera in addition to the camera for imaging. The proposed DHAO system replaces these hardware components with numerical processing for wavefront measurement and compensation of aberration through the principles of DH. We first design an image plane DHAO system which is basically simulating the process the conventional AO system and replacing the hardware pieces and complicated control procedures by DH and related numerical processing. In this original DHAO system, CCD is put at the image plane of the pupil plane of the eye lens. The image of the aberration is obtained by a digital hologram or guide star hologram. The full optical field is captured by a second digital hologram. Because CCD is not at the conjugate plane of the sample, a numerical propagation is necessary to find the image of the sample after the numerical aberration compensation at the CCD plane. The theory, simulations and experiments using an eye model have clearly demonstrated the effectiveness of the DHAO. This original DHAO system is described in Chapter 2. Different from the conventional AO system, DHAO is a coherent imaging modality which gives more access to the optical field and allows more freedom in the optical system design. In fact, CCD does not have to be put at the image plane of the CCD. This idea was first explored by testing a Fourier transform DHAO system (FTDHAO). In the FTDHAO, the CCD can directly record the amplitude point spread function (PSF) of the system, making it easier to determine the correct guide star hologram. CCD is also at the image plane of the target. The signal becomes stronger than the image plane DHAO system, especially for the phase aberration sensing. Also, the numerical propagation is not necessary. In the FTDHAO imaging system, the phase aberration at the eye pupil can be retrieved by an inverse Fourier transform (FT) of the guide star hologram and the complex amplitude of the full field optical field at the eye pupil can be obtained by an inverse FT of the full field hologram. The correction takes place at the eye pupil, instead of the CCD plane. Taking FT of the corrected field at the eye pupil, the corrected image can be obtained. The theory, simulations, and experiments on FTDHAO are detailed in chapter 3. The successful demonstration of FTDHAO encourages us to test the feasibility of putting CCD at an arbitrary diffraction plane in the DHAO system. Through theoretical formulation by use of paraxial optical theory, we developed a correction method by correlation for the general optical system to perform the DHAO. In this method, a global quadratic phase term has to be removed before the correction operation. In the formulation, it is quite surprising to find that the defocus term can be eliminated in the correlation operation. The detailed formulations, related simulations, and experimental demonstrations are presented in Chapter 4. To apply the DHAO to the confocal retinal imaging system, we first transformed the conventional line-scanning confocal imaging system into a digital form. That means each line scan is turned into a digital hologram. The complex amplitude of the optical field from each slice of the sample and aberration of the optical system can be retrieved by digital holographic process. In Chapter 5, we report our experiments on this digital line-scanning confocal imaging system. This digital line-scanning confocal image absorbs the merits of the conventional line-scanning confocal imaging system and DH. High-contrast intensity images with low coherent noise, and the optical sectioning capability are made available due to the confocality. Phase profiles of the samples become accessible thanks to DH. The quantitative phase map is even better than that from the wide field DH. We then explore the possibility of applying DHAO to this newly developed digital line-scanning confocal imaging system. Since optical field of each line scan can be achieved by the DH, the aberration contained in this field can be eliminated if we are able to obtain the phase aberration. We have demonstrated that the phase aberration can be obtained by a guide star hologram in the wide field DHAO systems. We then apply this technique to acquire the aberration at the eye pupil, remove this aberration from the optical fields of the line scans and recover the confocal image. To circumvent the effect of phase aberration on the line illumination, a small collimated laser beam is shone on the cylindrical lens. Thus the image is solely blurred by the second passage through the aberrator. This way, we can clearly demonstrate the effect of DHAO on the digital line-scanning confocal image system. Simulations and experiments are presented in chapter 6, which clearly demonstrates the validity of this idea. Since line-scanning confocal imaging system using spatially coherent light sources has proven an effective imaging tool for retinal imaging, the presented digital adaptive optics line-scanning confocal imaging system is quite promising to become a compact digital adaptive optics laser scanning confocal ophthalmoscope.

Clinical wavefront-guided corneal ablation has been now the most technologically advanced method to reduce the dependence of glasses and contact lenses. It has the potential not only to eliminate spherocylindrical errors but also to reduce higher-order aberrations (HOA). Recent statistics show that more than 96% of the patients who received laser in situ keratomileusis (LASIK) treatment reported their satisfaction about the improvement on vision, six months after the surgery. However, there are still patients complaining that their vision performance did not achieve the expectation or was even worse than before surgery. The reasons causing the unexpected post-surgical outcome include undercorrection, overcorrection, induced HOA, and other postoperative diseases, most of which are caused by inaccurate ablation besides other pathological factors. Therefore, to find out the method to optimize the LASIK procedures and provide a higher surgical precision has become increasingly important. A proper method to calculate ablation profile and an effective way to control the laser beam size and shape are key aspects in this research to resolve the problem. Here in this Master of Philosophy degree thesis, the author has performed a meticulous study on the existing methods of ablation profile calculation and investigated the efficiency of wavefront only ablation by a computer simulation applying real patient data. Finally, the concept of a refractive surgery system with dynamical beam shaping function is sketched, which can theoretically overcome the disadvantages of traditional procedures with a finite laser beam size.

The degradation of astronomical images caused by atmospheric turbulence will be much more severe in the next generation of terrestrial telescopes and its compensation will require deformable mirrors with up to tens-of-thousands of actuators. Current designs for these correctors consist of scaling up the proven technologies of flexible optical plates deformed under the out-of-plane action of linear actuators. This approach will lead to an exponential growth of cost with the number of actuators, and in very complex mechanisms. This thesis proposes a new concept of optical correction which is modular, robust, lightweight and low-cost and is based on the bimorph in-plane actuation. The adaptive mirror consists of segmented identical hexagonal bimorph mirrors allowing to indefinitely increase the degree of correction while maintaining the first mechanical resonance at the level of a single segment and showing an increase in price only proportional to the number of segments. Each bimorph segment can be mass-produced by simply screen-printing an array of thin piezoelectric patches onto a silicon wafer resulting in very compact and lightweight modules and at a price essentially independent from the number of actuators. The controlled deformation of a screen-printed bimorph mirror was experimentally achieved with meaningful optical shapes and appropriate amplitudes; its capability for compensating turbulence was evaluated numerically. The generation of continuous surfaces by an assembly of these mirrors was numerically simulated and a demonstrator of concept consisting of 3 segments was constructed.