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Active electro-optical systems benefit from stronger signal returns than their passive counterparts by providing scalable illumination power in otherwise limited ambient light. From an imaging standpoint this means higher signal-to-noise ratios for tracking purposes, leading to higher probabilities of detection, classification, recognition and identification of potentially distant objects. By creating an artificial beacon, active illumination also enables wavefront sensing where there is no natural beacon available to act as a reference source. In either application, however, actively illuminating an object of opportunity gives rise to a unique form of multiplicative noise known as speckle. A speckle pattern exhibits spatial variations in both amplitude and phase that result from diffuse scattering off an optically rough surface. Image quality suffers greatly from the presence of fully developed speckle, as the noise in such an image is on the order of the signal level itself. In the case of wavefront sensing, speckle contaminates measurements such that phase aberrations from the object become indistinguishable from those in the atmosphere. Mitigating speckle generally involves increasing the number of degrees of freedom in a speckle field, whether by manipulating coherence or polarization or system dynamics. The latter option allows access to a rich trade space for studying speckle mitigation on a wave-optics simulation basis. With that in mind, this work begins by exploring how different modes of object motion translate to varying degrees of speckle decorrelation in both the pupil and image planes of an optical system. Next, it derives scaling laws that describe the positional uncertainty associated with speckle to quantify active tracking performance. Adapting these scaling laws to the geometry of a Shack–Hartmann wavefront sensor then gives an indication of its open-loop performance limitations, while applying decorrelation theory extends the analysis to cover p

Coherent X-ray imaging techniques, such as in-line holography, exploit the high brilliance provided by diffraction-limited storage rings to perform imaging sensitive to the electron density through contrast due to the phase shift, rather than conventional attenuation contrast. Thus, coherent X-ray imaging techniques enable high-sensitivity and low-dose imaging, especially for low-atomic-number (Z) chemical elements and materials with similar attenuation contrast. Here, the first implementation of in-line holography at the NanoMAX beamline is presented, which benefits from the exceptional focusing capabilities and the high brilliance provided by MAX IV, the first operational diffractionlimited storage ring up to approximately 300 eV. It is demonstrated that in-line holography at NanoMAX can provide 2D diffraction-limited images, where the achievable resolution is only limited by the 70 nm focal spot at 13 keV X-ray energy. Also, the 3D capabilities of this instrument are demonstrated by performing holotomography on a chalk sample at a mesoscale resolution of around 155 nm. It is foreseen that in-line holography will broaden the spectra of capabilities of MAX IV by providing fast 2D and 3D electron density images from mesoscale down to nanoscale resolution., QC 20220131

Coherent X-ray imaging techniques, such as in-line holography, exploit the high brilliance provided by diffraction-limited storage rings to perform imaging sensitive to the electron density through contrast due to the phase shift, rather than conventional attenuation contrast. Thus, coherent X-ray imaging techniques enable high-sensitivity and low-dose imaging, especially for low-atomic-number (Z) chemical elements and materials with similar attenuation contrast. Here, the first implementation of in-line holography at the NanoMAX beamline is presented, which benefits from the exceptional focusing capabilities and the high brilliance provided by MAX IV, the first operational diffraction-limited storage ring up to approximately 300 eV. It is demonstrated that in-line holography at NanoMAX can provide 2D diffraction-limited images, where the achievable resolution is only limited by the 70 nm focal spot at 13 keV X-ray energy. Also, the 3D capabilities of this instrument are demonstrated by performing holotomography on a chalk sample at a mesoscale resolution of around 155 nm. It is foreseen that in-line holography will broaden the spectra of capabilities of MAX IV by providing fast 2D and 3D electron density images from mesoscale down to nanoscale resolution.

High-order harmonic generation (HHG) provides the basis for attosecond light sources delivering coherent pulses in the extreme ultraviolet spectral region. Such light sources are employed for a variety of applications within imaging, attosecond spectroscopy, and high-precision frequency metrology. However, the rather low efficiency of the HHG process, which implies a limited pulse energy and repetition rate, places restrictions on many applications. In this thesis, the scaling of different parameters controlling the generation conditions for HHG in gases is analyzed. A general scaling model is developed, which allows scaling of the pulse energy and repetition rate of attosecond sources over many orders of magnitude, while maintaining temporal and spatial pulse characteristics. The scaling model is applied to different attosecond beam lines, which were developed and built as part of this thesis work. This includes a high-repetition rate (200\,kHz) beam line used for photoelectron emission microscopy applications, and an intense harmonic beam line delivering pulses with up to 3 µJ in the extreme ultraviolet, which was used for coherent imaging as well as for nonlinear spectroscopy applications. In addition, microscopic sub-cycle control mechanisms based on multi-color field synthesis are studied, as well as noncollinear generation geometries. It is shown that a noncollinear geometry can be used to angularly streak attosecond pulse trains, allowing access to single pulses within the train. This technique is of interest for attosecond pump-probe measurements as well as for isolated attosecond pulse generation inside an optical cavity, a scheme that promises attosecond pulses at unprecedented power levels and repetition rates.

We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrodinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated., QC 20110907

We present a new approach to simulate electron cryo-microscope images of biological specimens. The framework for simulation consists of two parts; the first is a phantom generator that generates a model of a specimen suitable for simulation, the second is a transmission electron microscope simulator. The phantom generator calculates the scattering potential of an atomic structure in aqueous buffer and allows the user to define the distribution of molecules in the simulated image. The simulator includes a well defined electron-specimen interaction model based on the scalar Schrodinger equation, the contrast transfer function for optics, and a noise model that includes shot noise as well as detector noise including detector blurring. To enable optimal performance, the simulation framework also includes a calibration protocol for setting simulation parameters. To test the accuracy of the new framework for simulation, we compare simulated images to experimental images recorded of the Tobacco Mosaic Virus (TMV) in vitreous ice. The simulated and experimental images show good agreement with respect to contrast variations depending on dose and defocus. Furthermore, random fluctuations present in experimental and simulated images exhibit similar statistical properties. The simulator has been designed to provide a platform for development of new instrumentation and image processing procedures in single particle electron microscopy, two-dimensional crystallography and electron tomography with well documented protocols and an open source code into which new improvements and extensions are easily incorporated., authorCount :5

Very high resolution imaging systems, regardless of wavelength, require large apertures with a high resolution, low sidelobe level and high gain. These apertures are often considered to be technically and economically infeasible. We investigated the efficacy of using very sparse arrays of randomly placed small antenna elements in imaging systems. The properties of these arrays are established in antenna theory. What we have done is to make the first demonstration of their application in imaging systems. Computer simulation studies were made for coherent, partially coherent, and incoherent imaging. These were done using various conditions, including variable signal-to-noise ratio and phase aberration, but with monochromatic illumination. We showed that, for incoherent imaging, a large degree of thinning down to 6% of the number of full array elements (4096) produces image quality comparable to that produced by the full array. For broad-band polychromatic incoherent imaging, even larger degrees of thinning, down to 3% were similarly effective. The fractional degree of thinning allowable for incoherent imaging in principle is inversely proportional to the square root of the number of elements in the full array, which number is equivalent to the number of elements resolved in the full array.

Thesis (Ph. D.)--University of Rochester. The Institute of Optics, 2021., Coherent optical interferometry has a long history of enabling extremely precise measurements at length scales of less than the wavelength of light used in the interferometer. It is the ability of these systems to measure both the relative phase and amplitude information of the optical field that makes them so useful. As the name would imply, measuring phase and amplitude is accomplished by interfering two or more beams of light. Interferometric techniques have been adopted for use in both imaging/sensing technologies. For imaging systems under ideal conditions, the ability to measure both phase and amplitude information in one transverse plane allows for the calculation of that field’s phase and amplitude distribution in any other transverse plane. However, the presence of atmospheric turbulence unpredictably alters the index of refraction in the propagation medium thereby adversely affecting the reliability of calculation of phase and amplitude in other transverse planes. To address this problem, we demonstrate iterative sharpness maximization (ISM) correction of anisoplanatic turbulence effects in simulated range-compressed holography (RCH) fields and their corresponding range images. Our turbulence correction estimated four phase screens placed along the path of optical propagation using nonlinear optimizations aided by the method of sieves technique. We conducted a study of range images created from simulated single speckle realization 3D RCH fields subjected to twenty different turbulence profiles at five different strengths of turbulence, D/r0 = 7, 14, 21, 28, and 36. Range images showed significant improvement for all strengths of turbulence. To assist in correction, we introduced a novel constraint limiting the spread of energy in the corrected pupil. Corrected range images were qualitatively very similar to unaberrated range images in all but the most severe turbulence case, D/r0 = 36. Additionally, our algorithm was tested for fields affected by shot nois

Thesis (Ph. D.)--University of Rochester. Dept. of Electrical and Computer Engineering, 2010., The resolution of an imaging system is limited by the wavelength and numerical aperture of the system. Structured illumination imaging has been applied in microscopy to resolve spatial frequencies that conventionally lie outside the passband of the imaging system. The object is imaged with a sinusoidally patterned illumination, rather than the customary uniform illumination. This produces aliased moiré patterns which carry high frequency information in the image. These aliasing effects shift the traditionally inaccessible portions of the object’s spatial frequencies into the passband of the system making superresolution imaging possible. Structured illumination has also been used to obtain axially sectioned images on similar lines as the superresolution imaging with somewhat modified image processing. The applications of interest in this thesis are ophthalmoscopy and any moving microscopy application. The human retina is made up of millions of cells. Imaging the human retina in vivo is necessary for the study of structure and function of retinal physiology, and the detection, diagnosis and study of retinal diseases. In vivo retinal imaging with adaptive optics has shown the potential to resolve individual cells noninvasively. Cells such as cones, blood vessels and retinal pigment epithelial cells can now be routinely imaged in the human retina in vivo. The resolution of adaptive optics retinal imaging systems is fundamentally limited by the size of the pupil of the eye. The pupil aperture cannot increase beyond a certain point even with dilating drops. This restricts retinal imaging to structures larger than about 2 microns. In order to image finer features such as rods, foveal cones, ganglion cell axons and dendrites, it is necessary to use superresolution imaging. Similar incentives and restrictions for imaging moving specimens makes superresolution attractive to other forms of microscopy as well. However, prior work in the area of structured illumination imaging