The advent of highly-coherent x-ray light sources, such as those now available world-wide in modern third-generation synchrotrons and increasingly available in free-electron lasers, is driving the need for improved analytical and experimental techniques which exploit the coherency of the generated light. As the light illuminating a sample approaches full coherence, a simple Fourier transform describes the diffraction pattern generated by the scattered light in the far field; because the Fourier transform of an object is unique, coherent scattering can directly probe local structure in the scattering object instead of bulk properties. In this dissertation, we exploit the coherence of Advanced Light Source beamline 12.0.2 to build three types of novel coherent scattering microscopes. First, we extend the techniques of coherent diffractive imaging and Fourier transform holography, which uses iterative computational methods to invert oversampled coherent speckle patterns, into reflection geometry. This proof-of-principle experiment demonstrates a method by which reflection Bragg peaks, such as those from the orbitally-ordered phase of complex metal oxides, might eventually be imaged. Second, we apply a similar imaging method to the x-ray beam itself to directly image the mutual coherence function with only a single diffraction pattern. This technique supersedes the double-slit experiments commonly seen in the scattering literature to measure the mutual intensity function by using a set of apertures which effectively contains all possible double slit geometries. Third, we show how to evaluate the speckle patterns taken from a labyrinthine domain pattern for "hidden" rotational symmetries. For this measurement, we modify the iterative algorithms used to invert speckle patterns to generate a large number of domain configurations with the same incoherent scattering profile as the candidate pattern and then use these simulations as the basis for a statistical inference of the degree of ordering in the domain configuration. We propose extending this measurement to position-resolved speckle patterns, creating a symmetry-sensitive microscope. The three new techniques described herein may be employed at current and future light sources.

O microscópio é um instrumento de grande relevância para o contexto científico. Dentre as variadas montagens desse instrumento óptico, os microscópios sem lentes têm chamado atenção por serem robustos, reduzidos em tamanho e custo, e ainda possibilitarem imagens com amplo campo de visão (usualmente da ordem de algumas dezenas de mm2). Dentro dessa categoria, existem os microscópios holográficos in-line, os quais obtêm a imagem da amostra a partir da reconstrução numérica de um holograma adquirido por um sensor digital de imagem. Este trabalho tem o objetivo de construir um desses microscópios para observar amostras semitransparentes. O microscópio desenvolvido ao longo deste trabalho tem sua iluminação baseada no uso de um LED associado a um pinhole, cuja finalidade é aumentar a coerência temporal da luz. Com isso, a iluminação proveniente do pinhole percorre uma distância de aproximadamente 10 cm até atingir a amostra, posicionada sobre uma lâmina de vidro. À uma distância mínima da amostra, está posicionado um sensor CMOS, responsável pela aquisição do padrão de interferência da parcela da luz que foi transmitida sem desvio pela amostra e da parte da luz que foi difratada por ela. Esse padrão de intensidade, chamado holograma, é reconstruído numericamente de modo a obter uma boa imagem do objeto-alvo. A reconstrução da imagem medida é feita considerando a propagação da luz de volta ao plano de do objeto e, depois, estimando a fase referente à luz incidente no sensor no instante da medida. Essa primeira etapa resulta na imagem da amostra com a influência de um artefato muito conhecido na holografia: a imagem gêmea. Enquanto a reconstrução de fase reconstrói a imagem de uma forma mais completa, reduzindo a influência de tais artefatos. A reconstrução de fase é feita com o método multialturas, o qual faz uso de mais de uma imagem medida, com distâncias diferentes entre a amostra e o sensor, como entrada para o algoritmo desenvolvido. Utilizando um sensor de 10 MP (3856 x 2764 pixels), com o pixel de 1,67 μm, construímos um microscópio holográfico sem lentes com um campo de visão de quase 30 mm2 e resolução de aproximadamente 3 μm. / The microscope is an instrument of great relevance in the scientific context. Among various assembly of this optic instrument, the lensless microscope have had drawing attention by been robust, with small size and low cost and, in addiction, enable imaging with a large field of view (usually about tens of mm2). Inside this category, there is the in-line holographic microscopes, which achieve the sample image from the numerical reconstruction of a hologram acquired by an image digital sensor. This study have the objective of develop one of these microscopes to image semitransparent samples. The microscope developed over this study has its illumination based on the use of an LED associated with a pinhole, whose purpose is to increase the light temporal coherence. Therefore, illumination from the pinhole goes 10 cm until reach the sample, positioned over the glass slide. From a minimal distance of the sample, a CMOS sensor is positioned, which is responsible to acquire the interference pattern of the transmitted light with the diffracted light. This intensity pattern, called hologram, is numerically reconstructed in order to get a great image of target object. The reconstruction of the measured image is performed considering the back propagation of the light to the object plane and, then, estimating the phase related to the incident light over the sensor at the time of the measurement. This first step results in a sample image influenced by an artifact well-known in the holography: the twin-image. Whereas phase reconstruction reconstruct the image more fully, reducing the artifact influence. Phase reconstruction is performed using the multiheigh method, which uses more than one measured image, with different distances between the sample and sensor, as input to the developed algorithm. Using a 10 MP (3856 x 2764 pixels) sensor, with a pixel size of 1.67 μm, we built a lensless holographic microscope with a field of view near of 30 mm2 and resolution of approximately 3 μm.

Current methodologies for characterization of tympanic membranes (TMs) have some limitations. They: are qualitative rather than quantitative, consist of single point mobility measurements, or only include one-dimensional deformation measurements. Furthermore, none of the current clinical tools for diagnosis of hearing losses have the capability to measure the shape of TM, which is very useful for anatomical or pathological investigations. The multi-wavelength lensless digital holography system (MLDHS) reported in this work consists of laser delivery (LD), optical head (OH), and computing platform (CP) subsystems, with capabilities of real-time, non-contact, full-field of view measurements. One version of the LD houses two tunable near-infrared external-cavity diode lasers with central wavelengths of 780.24nm and 779.74nm respectively, an acousto-optic modulator, and a laser-to-fiber mechanism. The output of the LD is delivered to an ultra-fast MEMS-based fiber optic switch and the light beam is directed to the OH, which is arranged to perform imaging and measurements by phase-shifting holography. The second LD version subsystem contains one tunable near-infrared diode laser in the range from 770nm to 789nm, an anamorphic prism pair, an acousto-optic modulator, a half-wave plate, and a fiber coupler assembly. The output of the LD is delivered to the OH directly. The OH is designed by 3D optical ray tracing simulations in which components are rotated at specific angles to overcome reflection issues. A high-resolution digital camera with pixel size of 6.7μm by 6.7μm in the OH is used for image recording at high-rates while the CP acquires and processes images in either time-averaged or double-exposure modes. The choice of working version depends on the requirements of the measurement and the sample under test. MLDHS can obtain shape and one-dimensional deformations along one optical axis (z-axis). In order to recover 3D deformations, assumptions based on elasticity theory are prerequisites for the calculations: (a) the TM is analyzed as a thin shell; (b) shape before and after deformation is considered nearly the same since acoustic pressure typically introduces nanometer scale deformations; and (c) normal vectors remain perpendicular to the deformed mid-plane of the TM. Another part of this Thesis is the design and prototyping of the MLDHS, which translates this holographic platform into a simple and compact holographic instrument for measurements of the visible tympanic-membrane motions in live patients. Therefore, the OH subsystem needs to be light and portable, as it can be mounted on a robotic arm be near the ear canal, while the LD subsystem needs to be stable and safely protected. Preliminary results of acoustically induced 3D deformations and shape measurements by a single instrument that demonstrate the capabilities of the devices developed in this Thesis are presented.

O microscópio é um instrumento de grande relevância para o contexto científico. Dentre as variadas montagens desse instrumento óptico, os microscópios sem lentes têm chamado atenção por serem robustos, reduzidos em tamanho e custo, e ainda possibilitarem imagens com amplo campo de visão (usualmente da ordem de algumas dezenas de mm2). Dentro dessa categoria, existem os microscópios holográficos in-line, os quais obtêm a imagem da amostra a partir da reconstrução numérica de um holograma adquirido por um sensor digital de imagem. Este trabalho tem o objetivo de construir um desses microscópios para observar amostras semitransparentes. O microscópio desenvolvido ao longo deste trabalho tem sua iluminação baseada no uso de um LED associado a um pinhole, cuja finalidade é aumentar a coerência temporal da luz. Com isso, a iluminação proveniente do pinhole percorre uma distância de aproximadamente 10 cm até atingir a amostra, posicionada sobre uma lâmina de vidro. À uma distância mínima da amostra, está posicionado um sensor CMOS, responsável pela aquisição do padrão de interferência da parcela da luz que foi transmitida sem desvio pela amostra e da parte da luz que foi difratada por ela. Esse padrão de intensidade, chamado holograma, é reconstruído numericamente de modo a obter uma boa imagem do objeto-alvo. A reconstrução da imagem medida é feita considerando a propagação da luz de volta ao plano de do objeto e, depois, estimando a fase referente à luz incidente no sensor no instante da medida. Essa primeira etapa resulta na imagem da amostra com a influência de um artefato muito conhecido na holografia: a imagem gêmea. Enquanto a reconstrução de fase reconstrói a imagem de uma forma mais completa, reduzindo a influência de tais artefatos. A reconstrução de fase é feita com o método multialturas, o qual faz uso de mais de uma imagem medida, com distâncias diferentes entre a amostra e o sensor, como entrada para o algoritmo desenvolvido. Utilizando um sensor de 10 MP (3856 x 2764 pixels), com o pixel de 1,67 μm, construímos um microscópio holográfico sem lentes com um campo de visão de quase 30 mm2 e resolução de aproximadamente 3 μm. / The microscope is an instrument of great relevance in the scientific context. Among various assembly of this optic instrument, the lensless microscope have had drawing attention by been robust, with small size and low cost and, in addiction, enable imaging with a large field of view (usually about tens of mm2). Inside this category, there is the in-line holographic microscopes, which achieve the sample image from the numerical reconstruction of a hologram acquired by an image digital sensor. This study have the objective of develop one of these microscopes to image semitransparent samples. The microscope developed over this study has its illumination based on the use of an LED associated with a pinhole, whose purpose is to increase the light temporal coherence. Therefore, illumination from the pinhole goes 10 cm until reach the sample, positioned over the glass slide. From a minimal distance of the sample, a CMOS sensor is positioned, which is responsible to acquire the interference pattern of the transmitted light with the diffracted light. This intensity pattern, called hologram, is numerically reconstructed in order to get a great image of target object. The reconstruction of the measured image is performed considering the back propagation of the light to the object plane and, then, estimating the phase related to the incident light over the sensor at the time of the measurement. This first step results in a sample image influenced by an artifact well-known in the holography: the twin-image. Whereas phase reconstruction reconstruct the image more fully, reducing the artifact influence. Phase reconstruction is performed using the multiheigh method, which uses more than one measured image, with different distances between the sample and sensor, as input to the developed algorithm. Using a 10 MP (3856 x 2764 pixels) sensor, with a pixel size of 1.67 μm, we built a lensless holographic microscope with a field of view near of 30 mm2 and resolution of approximately 3 μm.

Fluorescence microscopy has revolutionized medicine and biological science with its ability to study the behavior and chemical expressions of living cells. Fluorescent probes can label cell components or cells of a particular type. Clinically the impact of fluorescence imaging can be seen in the diagnosis of cancers, AIDS, and other blood related disorders. Although fluorescence imaging devices have been established as a vital tool in medicine, the size, cost, and complexity of fluorescence microscopes limits their use to central laboratories. The work described in this thesis overcomes these limitations by developing a low cost integrated fluorescence microscope so single use fluorescence microscopy assays can be developed. These assays will enable at-home testing, diagnostics in resource limited settings, and improved emergency medicine.

Due to the ever-increasing demands of highly integrated optical devices in imaging, spectroscopy, communications, and so on, there is a compelling need to design and characterize novel compact photonic components. The traditional approaches to realizing compact optical devices typically result in large footprints and sizable optical thicknesses. Moreover, they offer few degrees of freedom (DOF), hampering on-demand functionalities, on-chip integration, and scalability. This thesis will address the design and development of ultracompact diffractive devices for imaging and spectroscopy, utilizing advanced machine learning techniques and optimization algorithms. I first present the inverse design of ultracompact dual-focusing lenses and broad-band focusing spectrometers based on adaptive diffractive optical networks (a-DONs), which combine optical diffraction physics and deep learning capabilities for the inverse design of multi-layered diffractive devices. I designed two-layer diffractive devices that can selectively focus incident radiation over well-separated spectral bands at desired distances and also optimized a-DON-based focusing spectrometers with engineered angular dispersion for desired bandwidth and nanometer spectral resolution. Furthermore, I introduced a new approach based on a-DONs for the engineering of diffractive devices with arbitrary k-space, which produces improved imaging performances compared to contour-PSF approaches to lens-less computational imaging. Moreover, my method enables control of sparsity and isotropic k-space in pixelated screens of dielectric scatterers that are compatible with large-scale photolithographic fabrication techniques. Finally, by combining adjoint optimization with the rigorous generalized Mie theory, I developed and characterize functionalized compact devices, which I called "photonic patches," consisting of ~100 dielectric nanocylinders that achieve predefined functionalities such as beam steering, Fresnel zone focusing, local density of states (LDOS) enhancement, etc. My method enables the inverse design of ultracompact focusing spectrometers for on-chip planar integration. Leveraging multiple scattering of light in disordered random media, I additionally demonstrated a novel approach to on-chip spectroscopy driven by high-throughput multifractal (i.e., multiscale) media, resulting in sub-nanometer spectral resolution at the 50×50 µm²-scale footprint.

State-of-the art Fourier transform holography (FTH) techniques use x-ray magnetic circular dichroism (XMCD) as a contrast mechanism for element-specfi c imaging of magnetic domains. With the soft x-ray Nanoscience beamline at Diamond Light Source in the UK, and the Dragon beamline at the European Synchrotron Radiation Facility (ESRF) in France, the possibility of new methods to study nanostructured magnetic systems has been demonstrated. The ability to record images without the use of lenses, in varying magnetic fi elds and with high spatial resolution down to 30 nm has been used to study in-plane magnetism of 50 nm thin permalloy (NiFe alloy) nanoelements. The holographic technique used extended reference objects rather than conventional pinhole references, which allowed a high flexibility on the direction of magnetisation that is probed. The element specific nature of the imaging, with the additional choice in the directions of magnetisation that are probed has been used to study dipolar interactions in a hard/Ta/soft [Co/Pt]30/Ta/Py multi-layered system. Images of the out-of-plane magnetised domains of [Co/Pt]30 were found to bare strong spatial resemblance to the in-plane domains of the permalloy. The domain structure is thought to be magnetostatically imprinted into permalloy during the growth stage of the lm, where stray elds generated by the adjacent Co/Pt multilayer influence the formation of domains in the permalloy. Strong resemblance between the two layers could be found at remanence within a pristine sample, however the similarities disappear after the sample was exposed to a saturating magnetic field. This disagreed with micromagnetic simulations performed in The Object Oriented MicroMagnetic Framework (OOMMF) program, and an explanation for the observations has been sought in the growth process of the multi-layered fi lm, with conditions that are diffi cult to recreate in the model. Optical holography has been used for preliminary insight into implementing a method of FTH in a reflective geometry at soft x-rays wavelength. With scattering chambers at BESSY II in Germany and at the Stanford Synchrotron Radiation Lightsource (SSRL) in California the possibility of reducing scattered noise in a hologram recorded in a reflective geometry has been investigated. Studies into specular and dif use reflections have been performed optically however the use of extended references alone may alleviate the current problem at x-ray wavelengths which lie in the weak signal given by a reflective point-like reference source.

abstract: Cameras have become commonplace with wide-ranging applications of phone photography, computer vision, and medical imaging. With a growing need to reduce size and costs while maintaining image quality, the need to look past traditional style of cameras is becoming more apparent. Several non-traditional cameras have shown to be promising options for size-constraint applications, and while they may offer several advantages, they also usually are limited by image quality degradation due to optical or a need to reconstruct a captured image. In this thesis, we take a look at three of these non-traditional cameras: a pinhole camera, a diffusion-mask lensless camera, and an under-display camera (UDC). For each of these cases, I present a feasible image restoration pipeline to correct for their particular limitations. For the pinhole camera, I present an early pipeline to allow for practical pinhole photography by reducing noise levels caused by low-light imaging, enhancing exposure levels, and sharpening the blur caused by the pinhole. For lensless cameras, we explore a neural network architecture that performs joint image reconstruction and point spread function (PSF) estimation to robustly recover images captured with multiple PSFs from different cameras. Using adversarial learning, this approach achieves improved reconstruction results that do not require explicit knowledge of the PSF at test-time and shows an added improvement in the reconstruction model’s ability to generalize to variations in the camera’s PSF. This allows lensless cameras to be utilized in a wider range of applications that require multiple cameras without the need to explicitly train a separate model for each new camera. For UDCs, we utilize a multi-stage approach to correct for low light transmission, blur, and haze. This pipeline uses a PyNET deep neural network architecture to perform a majority of the restoration, while additionally using a traditional optimization approach which is then fused in a learned manner in the second stage to improve high-frequency features. I show results from this novel fusion approach that is on-par with the state of the art. / Dissertation/Thesis / Masters Thesis Electrical Engineering 2020

Techniques for fast, 3D, quantitative microscopy are of great interest in many fields. In this context, in-line digital holography has significant potential due to its relatively simple setup (lensless imaging), its three-dimensional character and its temporal resolution. The goal of this thesis is to improve existing hologram reconstruction techniques by employing an "inverse problems" approach. For applications of objects with parametric shapes, a greedy algorithm has been previously proposed which solves the (inherently ill-posed) inversion problem of reconstruction by maximizing the likelihood between a model of holographic patterns and the measured data. The first contribution of this thesis is to reduce the computational costs of this algorithm using a multi-resolution approach (FAST algorithm). For the second contribution, a "matching pursuit" type of pattern recognition approach is proposed for hologram reconstruction of volumes containing parametric objects, or non-parametric objects of a few shape classes. This method finds the closest set of diffraction patterns to the measured data using a diffraction pattern dictionary. The size of the dictionary is reduced by employing a truncated singular value decomposition to obtain a low cost algorithm. The third contribution of this thesis was carried out in collaboration with the laboratory of fluid mechanics and acoustics of Lyon (LMFA). The greedy algorithm is used in a real application: the reconstruction and tracking of free-falling, evaporating, ether droplets. In all the proposed methods, special attention has been paid to improvement of the accuracy of reconstruction as well as to reducing the computational costs and the number of parameters to be tuned by the user (so that the proposed algorithms are used with little or no supervision). A Matlab® toolbox (accessible on-line) has been developed as part of this thesis

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