Adaptive Optics (AO) has revealed as a very promising technique for high-resolution microscopy, where the presence of optical aberrations can easily compromise the image quality. Typical AO systems however, are almost impossible to implement on commercial microscopes. We propose a simple approach by using a Multi-actuator Adaptive Lens (MAL) that can be inserted right after the objective and works in conjunction with an image optimization software allowing for a wavefront sensorless correction. We presented the results obtained on several commercial microscopes among which a confocal microscope, a fluorescence microscope, a light sheet microscope and a multiphoton microscope.@en

Optical coherence tomography (OCT) is a technique for non-invasive imaging based on low coherence interferometry. Its main application is found in ophthalmology, where it is used for 3D in vivo imaging of the cornea and the retina. OCT has evolved over the past decade as one of the most important ancillary tests in ophthalmic practice, providing great diagnostic value for disease screening and monitoring. In retinal OCT imaging, the lateral resolution is not determined by the pupil size, but instead it is limited by optical wavefront aberrations of the cornea and lens. These aberrations reduce the OCT image resolution and lower the signal to noise ratio. To obtain high quality OCT images the optical aberrations can be removed using adaptive optics (AO). In general, AO consists of an adaptive optical element and a wavefront sensor. The adaptive element, such as a deformable mirror, is used to reshape the wavefront and remove the undesired aberrations. The wavefront sensor measures the aberrations by reconstructing the phase of the wavefront, which is used to determine the correction on the wavefront applied by the deformable mirror. However, the use of a wavefront sensor has some disadvantages. It requires light being directed out of the imaging path onto the wavefront sensor. This leads to a loss of signal in the imaging path and can result in non-common optical path errors in the aberrations estimation procedure. Additionally, the use of a deformable mirror and a wavefront sensor leads to a bulky and expensive OCT setup. The work presented in this thesis has the goal of reducing the cost and bulkiness of an AO-OCT system. First, we investigate the influence of optical wavefront aberrations to the OCT signal strength. The establishment of the relation between aberrations and the OCT signal strength is key to estimating and correcting the aberrations based on single OCT scans. By using Fresnel optical wave propagation and determining the fiber coupling efficiency, we find that the OCT transfer function, i.e. the function that expresses the relation between the aberrations and OCT signal strength, is quasi-convex. We determine both analytically and experimentally the transfer function for both reflective and scattering media, such as a mirror and Scotch tape sample. Additionally, if the OCT system and its optical properties are well-known we demonstrate a method to correct a defocus aberration in one step. Second, we use the OCT transfer function to develop and determine an efficient wavefront sensorless (WFSL) AO optimization procedure. WFSL-AO methods aim to correct the aberrations without using a wavefront sensor, but instead base the determination of the wavefront on the imaging signal itself. This eliminates the use of the wavefront sensor, its extra cost and its disadvantages from an AO-OCT setup. To keep up with the OCT imaging rate, which is of the order of several tens of kHz, the algorithm has to be computationally efficient. Furthermore, there are no analytic derivatives available for the optimization and the OCT signal is very noisy. Finally, the derivative-free optimization algorithm also has to be able to determine the aberrations accurately when dealing with a minimum number of noisy measurements. We developed the Data-based Online Nonlinear extremum-seeker (DONE) algorithm. Every iteration, the DONE algorithm updates a surrogate function, which is based on random Fourier expansions (RFE) of the OCT transfer function, with a new OCT signal measurement. The optimum of the RFE surrogate function is then found with a well-known (quasi-Newton) optimization method. We demonstrate the effectiveness of the DONE algorithm compared to other optimization algorithms for WFSL-AO on biological and non-biological samples. We conclude that DONE has a smaller convergence error, while maintaining similar or faster convergence speeds compared to the other algorithms. Third, we demonstrate a fully functional WFSL-AO OCT setup for retinal imaging. We use a state-of-the-art deformable lens with 18 actuators, rather than a deformable mirror, which leads to a smaller and more integrated WFSL-AO setup. The WFSL-AO OCT setup is successfully used for in vivo retinal OCT imaging and demonstrates that the DONE algorithm can remove the ocular wavefront aberrations with the deformable lens during in vivo OCT imaging. By developing a new algorithm and exploring the options for adaptive components, we have succeeded in retinal WFSL-AO OCT. In a broader perspective, we show that the DONE algorithm is suitable for other applications than WFSL-AO OCT. We demonstrate that the DONE derivative-free optimization algorithm is robust towards noisy measurements for applications in robotics, microscopy and optical beam forming networks.@en

In recent years we have seen a rise in the amount of fitness tracking and self monitoring devices. These devices which often work in conjunction with a smartphone are becoming more accurate and are becoming widely adopted. This trend goes hand in hand with Electronic Health Care (e-health): the shift of health care to the digital domain. E-health would allow patients to measure their medical condition at home, allowing a diagnosis to be made based on measurements taken over a longer period of time, while reducing the work performed by a doctor. Measurements are  tored in the cloud, simplifying the way in which they can be shared with healthcare providers and possibly research  nstitutions. Modernizing healthcare this way should give the patient more insight and control over his/her healthcare and  medical data. Furthermore the amount of visits required to the hospital can be reduced, an endeavor which can be demanding for many less fit for elderly individuals. However, handling medical data this way causes concern for privacy. Often the data handled by these devices is very  sensitive and could easily be used to identify the user and monitor many of their behaviours. In order to achieve privacy there are several approaches. One way is to enforce involved parties through legislation to use the data for specific purposes only. However, this relies on the party being semi-trusted and does not guarantee safety in case of a data-breach.  In this work the way in which the integration of wearables into the medical domain is currently taking place and how privacy and security is handled will be explored. Furthermore we will show the current state of research regarding improving this security. @en

Optical Coherence Tomography (OCT) has revolutionized modern ophthalmology, providing depth resolved images of the retinal layers in a system that is suited to a clinical environment. A limitation of the performance and utilization of the OCT systems has been the lateral resolution. Through the combination of wavefront sensorless adaptive optics with dual variable optical elements, we present a compact lens based OCT system that is capable of imaging the photoreceptor mosaic. We utilized a commercially available variable focal length lens to correct for a wide range of defocus commonly found in patient eyes, and a multi-actuator adaptive lens after linearization of the hysteresis in the piezoelectric actuators for aberration correction to obtain near diffraction limited imaging at the retina. A parallel processing computational platform permitted real-time image acquisition and display. The Data-based Online Nonlinear Extremum seeker (DONE) algorithm was used for real time optimization of the wavefront sensorless adaptive optics OCT, and the performance was compared with a coordinate search algorithm. Cross sectional images of the retinal layers and en face images of the cone photoreceptor mosaic acquired in vivo from research volunteers before and after WSAO optimization are presented. Applying the DONE algorithm in vivo for wavefront sensorless AO-OCT demonstrates that the DONE algorithm succeeds in drastically improving the signal while achieving a computational time of 1 ms per iteration, making it applicable for high speed real time applications.@en

The use of adaptive lenses instead of deformable mirrors can simplify the implementation of an adaptive optics system. The recently introduced Multi-actuator Adaptive Lens (MAL) can be used in closed loop with a wavefront sensor to correct for time-variant wavefront aberrations. The MAL can guarantee a level of correction and a response time similar to the ones obtained with deformable mirrors. The adaptive lens is based on the use of piezoelectric actuators and, without any obstruction or electrodes in the clear aperture, can guarantee a fast response time, less than ∼10ms. Our tests show that the MAL can be used both in combination with a wavefront sensor in a "classical" adaptive optics closed loop, or in a wavefront sensorless configuration. The latter has allowed us to design more compact and simple imaging systems for different microscopy platforms. We will show that the Multi-actuator Adaptive Lens has been successfully used for in-vivo OCT ophthalmic imaging in both mice and humans, as well as confocal and two photon microscopy. We tested and compared different optimization strategies such as coordinate search and the DONE algorithm. The results suggest that the MAL optimization can correct for eye aberrations with a pupil of 5mm or sample induced aberrations in microscopy.@en

The quality of fluorescence microscopy images is often impaired by the presence
of sample induced optical aberrations. Adaptive optical elements such as deformable mirrors or spatial light modulators can be used to correct aberrations. However, previously reported techniques either require special sample preparation, or time consuming optimization procedures for the correction of static aberrations. This paper reports a technique for optical sectioning fluorescence microscopy capable of correcting dynamic aberrations in any fluorescent sample during the acquisition. This is achieved by implementing adaptive optics in a non conventional confocal microscopy setup, with multiple programmable confocal apertures, in which out of focus light can be separately detected, and used to optimize the correction performance with a sampling frequency an order of magnitude faster than the imaging rate of the system. The
paper reports results comparing the correction performances to traditional image optimization algorithms, and demonstrates how the system can compensate for dynamic changes in the aberrations, such as those introduced during a focal stack acquisition though a thick sample.@en

In this report, which is an international collaboration of OCT, adaptive optics, and control research, we demonstrate the data-based online nonlinear extremum-seeker (DONE) algorithm to guide the image based optimization for wavefront sensorless adaptive optics (WFSL-AO) OCT for in vivo human retinal imaging. The ocular aberrations were corrected using a multi-actuator adaptive lens after linearization of the hysteresis in the piezoelectric actuators. The DONE algorithm succeeded in drastically improving image quality and the OCT signal intensity, up to a factor seven, while achieving a computational time of 1 ms per iteration, making it applicable for many high speed applications. We demonstrate the correction of five aberrations using 70 iterations of the DONE algorithm performed over 2.8 s of continuous volumetric OCT acquisition. Data acquired from an imaging phantom and in vivo from human research volunteers are presented.

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Adaptive optics has been successfully applied to cellular resolution imaging of the retina, enabling visualization of the characteristic mosaic patterns of the outer retina. Wavefront sensorless adaptive optics (WSAO) is a novel technique that facilitates high resolution ophthalmic imaging; it replaces the Hartmann-Shack Wavefront Sensor with an image-driven optimization algorithm and mitigates some the challenges encountered with sensor-based designs. However, WSAO generally requires longer time to perform aberrations correction than the conventional closed-loop adaptive optics. When used for in vivo retinal imaging applications, motion artifacts during the WSAO optimization process will affect the quality of the aberration correction. A faster converging optimization scheme needs to be developed to account for rapid temporal variation of the wavefront and continuously apply corrections. In this project, we investigate the Databased Online Nonlinear Extremum-seeker (DONE), a novel non-linear multivariate optimization algorithm in combination with in vivo human WSAO OCT imaging. We also report both hardware and software updates of our compact lens based WSAO 1060nm swept source OCT human retinal imaging system, including real time retinal layer segmentation and tracking (ILM and RPE), hysteresis correction for the multi-actuator adaptive lens, precise synchronization control for the 200kHz laser source, and a zoom lens unit for rapid switching of the field of view. Cross sectional images of the retinal layers and en face images of the cone photoreceptor mosaic acquired in vivo from research volunteers before and after WSAO optimization are presented. @en

This paper analyzes data-based online nonlinear extremum-seeker (DONE), an online optimization algorithm that iteratively minimizes an unknown function based on costly and noisy measurements. The algorithm maintains a surrogate of the unknown function in the form of a random Fourier expansion. The surrogate is updated whenever a new measurement is available, and then used to determine the next measurement point. The algorithm is comparable with Bayesian optimization algorithms, but its computational complexity per iteration does not depend on the number of measurements. We derive several theoretical results that provide insight on how the hyperparameters of the algorithm should be chosen. The algorithm is compared with a Bayesian optimization algorithm for an analytic benchmark problem and three applications, namely, optical coherence tomography, optical beam-forming network tuning, and robot arm control. It is found that the DONE algorithm is significantly faster than Bayesian optimization in the discussed problems while achieving a similar or better performance.@en

In this manuscript, we present a lens setup for large defocus and astigmatism correction. A deformable defocus lens and two rotational cylindrical lenses are used to control the defocus and astigmatism. The setup is calibrated using a simple model that allows the calculation of the lens inputs so that a desired defocus and astigmatism are actuated on the eye. The setup is tested by determining the feedforward prediction error, imaging a resolution target, and removing introduced aberrations.@en