Coherent Diffractive Imaging Using Randomly Coded Masks

Coherent diffractive imaging (CDI) provides new opportunities for high resolution X-ray imaging with simultaneous amplitude and phase contrast. Extensions to CDI broaden the scope of the technique for use in a wide variety of experimental geometries and physical systems. Here, we experimentally demonstrate a new extension to CDI that encodes additional information through the use of a series of randomly coded masks. The information gained from the few additional diffraction measurements removes the need for typical object-domain constraints; the algorithm uses prior information about the masks instead. The experiment is performed using a laser diode at 532.2 nm, enabling rapid prototyping for future X-ray synchrotron and even free electron laser experiments. Diffraction patterns are collected with up to 15 different masks placed between a CCD detector and a single sample. Phase retrieval is performed using a convex relaxation routine known as "PhaseCut" followed by a variation on Fienup's input-output algorithm. The reconstruction quality is judged via calculation of phase retrieval transfer functions as well as by an object-space comparison between reconstructions and a lens-based image of the sample. The results of this analysis indicate that with enough masks (in this case 3 or 4) the diffraction phases converge reliably, implying stability and uniqueness of the retrieved solution

Nanoscale EUV Microscopy on a Tabletop: A General Transmission and Reflection Mode Microscope Based on Coherent Diffractive Imaging with High Harmonic Illumination

A new scientific frontier exists at the intersection of the nanoscale and the ultrafast. In order to explore this frontier, new tools with unique capabilities for imaging with nanometer spatial and femtosecond temporal resolution are critical. This thesis describes the development of such a tool, combining coherent diffractive imaging (CDI) with an extreme ultraviolet (EUV) high harmonic generation (HHG) light source to produce a compact, accessible, high-resolution microscope. Here, this microscope is used to demonstrate 22 nm resolution in transmission, a record for any full-field tabletop light-based microscope. Further, this microscope is used to demonstrate the most general reflection mode implementation of CDI to date, enabling image reconstruction at any angle of incidence. Chapter 2 describes the optimization of the HHG source for use with CDI. A pulse shaper is implemented to produce transform-limited pulses at 800 nm for increased HHG conversion efficiency. Furthermore, the long-term stability of the HHG source is improved by an order of magnitude through the pointing stabilization of the kHz driving laser. Chapter 3 develops the ideas necessary for the data processing techniques that enable general reflection mode CDI. Chapter 4 describes enhancements to the microscope to produce images with record 22 nm resolution in addition to extension of the microscope to image more complex, transmissive samples. Chapter 5 presents the most general implementation of reflection mode CDI to date. In chapter 6, the route towards dynamic femtosecond imaging of complex nanosystems is outlined, which includes potential for simultaneous hyperspectral EUV imaging across multiple absorption edges

Machine Learning Based Alignment For LCLS-II-HE Optics

The hard X-ray instruments at the Linac Coherent Light Source are in the design phase for upgrades that will take full advantage of the high repetition rates that will become available with LCLS-II-HE. The current X-ray Correlation Spectroscopy instrument will be converted to the Dynamic X-ray Scattering instrument, and will feature a meV-scale high-resolution monochromator at its front end with unprecedented coherent flux. With the new capability come many engineering and design challenges, not least of which is the sensitivity to long-term drift of the optics. With this in mind, we have estimated the system tolerance to angular drift and vibration for all the relevant optics ($\sim$10 components) in terms of how the central energy out of the monochromator will be affected to inform the mechanical design. Additionally, we have started planning for methods to correct for such drifts using available (both invasive and non-invasive) X-ray beam diagnostics. In simulations, we have demonstrated the ability of trained Machine Learning models to correct misalignments to maintain the desired central energy and optical axis within the necessary tolerances. Additionally, we exhibit the use of Bayesian Optimization to minimize the impact of thermal deformations of crystals as well as beam alignment from scratch. The initial results are very promising and efforts to further extend this work are ongoing

Ptychographic hyperspectral spectromicroscopy with an extreme ultraviolet high harmonic comb

We demonstrate a new scheme of spectromicroscopy in the extreme ultraviolet (EUV) spectral range, where the spectral response of the sample at different wavelengths is imaged simultaneously. It is enabled by applying ptychographical information multiplexing (PIM) to a tabletop EUV source based on high harmonic generation, where four spectrally narrow harmonics near 30 nm form a spectral comb structure. Extending PIM from previously demonstrated visible wavelengths to the EUV/X-ray wavelengths promises much higher spatial resolution and more powerful spectral contrast mechanism, making PIM an attractive spectromicroscopy method in both the microscopy and the spectroscopy aspects. Besides the sample, the multicolor EUV beam is also imaged in situ, making our method a powerful beam characterization technique. No hardware is used to separate or narrow down the wavelengths, leading to efficient use of the EUV radiation

Sex Hormone-Binding Globulin Levels Are Inversely Associated With Nonalcoholic Fatty Liver Disease in HIV-Infected and -Uninfected Men.

BackgroundNonalcoholic fatty liver disease (NAFLD) is a leading cause of liver disease worldwide. Elevated sex hormone-binding globulin (SHBG) levels have been observed in the setting of HIV and may protect against some metabolic disorders. We aimed to investigate whether higher SHBG levels may protect against NAFLD in men with/without HIV.MethodsNAFLD was assessed using noncontrast computed tomography in 530 men in the Multicenter AIDS Cohort Study (MACS) who drank <3 alcoholic drinks/d and were uninfected with chronic hepatitis C or B (340HIV+, 190HIV-). Morning serum samples were tested for SHBG, total testosterone (TT), and adiponectin. Multivariable logistic regression was used to assess associations between HIV, SHBG, TT, adiponectin, and NAFLD.ResultsMedian SHBG was highest among HIV+/NAFLD- men and lowest among HIV-/NAFLD+ men. Adjusted for demographics, HIV, visceral adiposity, HOMA-IR, TT, and PNPLA3 genotype, higher SHBG was associated with lower odds of NAFLD (odds ratio [OR], 0.52 per doubling; 95% confidence interval [CI], 0.34-0.80). In separate multivariable models without SHBG, HIV (OR, 0.46; 95% CI, 0.26-0.79) and higher adiponectin (OR, 0.66 per doubling; 95% CI, 0.49-0.89) were associated with lower NAFLD odds, whereas TT was not significantly associated (OR, 0.74 per doubling; 95% CI, 0.53-1.04). Adjusting for SHBG attenuated the associations of HIV (OR, 0.61; 95% CI, 0.34-1.08) and adiponectin (OR, 0.74; 95% CI, 0.54-1.02) with NAFLD.ConclusionsSHBG levels were higher among HIV+ men, were independently associated with lower NAFLD, and could partially explain the associations of HIV and higher adiponectin with lower NAFLD in our cohort. These findings suggest that SHBG may protect against NAFLD, supporting further prospective and mechanistic studies

The Impact of HAART on the Respiratory Complications of HIV Infection: Longitudinal Trends in the MACS and WIHS Cohorts

Objective: To review the incidence of respiratory conditions and their effect on mortality in HIV-infected and uninfected individuals prior to and during the era of highly active antiretroviral therapy (HAART). Design: Two large observational cohorts of HIV-infected and HIV-uninfected men (Multicenter AIDS Cohort Study [MACS]) and women (Women's Interagency HIV Study [WIHS]), followed since 1984 and 1994, respectively. Methods: Adjusted odds or hazards ratios for incident respiratory infections or non-infectious respiratory diagnoses, respectively, in HIV-infected compared to HIV-uninfected individuals in both the pre-HAART (MACS only) and HAART eras; and adjusted Cox proportional hazard ratios for mortality in HIV-infected persons with lung disease during the HAART era. Results: Compared to HIV-uninfected participants, HIV-infected individuals had more incident respiratory infections both pre-HAART (MACS, odds ratio [adjusted-OR], 2.4; 95% confidence interval [CI], 2.2-2.7; p<0.001) and after HAART availability (MACS, adjusted-OR, 1.5; 95%CI 1.3-1.7; p<0.001; WIHS adjusted-OR, 2.2; 95%CI 1.8-2.7; p<0.001). Chronic obstructive pulmonary disease was more common in MACS HIV-infected vs. HIV-uninfected participants pre-HAART (hazard ratio [adjusted-HR] 2.9; 95%CI, 1.02-8.4; p = 0.046). After HAART availability, non-infectious lung diseases were not significantly more common in HIV-infected participants in either MACS or WIHS participants. HIV-infected participants in the HAART era with respiratory infections had an increased risk of death compared to those without infections (MACS adjusted-HR, 1.5; 95%CI, 1.3-1.7; p<0.001; WIHS adjusted-HR, 1.9; 95%CI, 1.5-2.4; p<0.001). Conclusion: HIV infection remained a significant risk for infectious respiratory diseases after the introduction of HAART, and infectious respiratory diseases were associated with an increased risk of mortality. © 2013 Gingo et al

Ultrafast Structural Dynamics along the β − γ Phase Transition Path in MnAs

International audienceWe investigate the orthorhombic distortion and the structural dynamics of epitaxial MnAs layers on GaAs(001) using static and time-resolved x-ray diffraction. Laser-induced intensity oscillations of Bragg reflections allow us to identify the optical phonon associated with orthorhombic distortion and to follow its softening along the path towards an undistorted phase of hexagonal symmetry. The frequency of this mode falls in the THz range, in agreement with recent calculations. Incomplete softening suggests that the $\beta-\gamma$ transformation deviates from a purely second-order displacive transition

Simultaneous Bright- and Dark-Field X-ray Microscopy at X-ray Free Electron Lasers

The structures, strain fields, and defect distributions in solid materials underlie the mechanical and physical properties across numerous applications. Many modern microstructural microscopy tools characterize crystal grains, domains and defects required to map lattice distortions or deformation, but are limited to studies of the (near) surface. Generally speaking, such tools cannot probe the structural dynamics in a way that is representative of bulk behavior. Synchrotron X-ray diffraction based imaging has long mapped the deeply embedded structural elements, and with enhanced resolution, Dark Field X-ray Microscopy (DFXM) can now map those features with the requisite nm-resolution. However, these techniques still suffer from the required integration times due to limitations from the source and optics. This work extends DFXM to X-ray free electron lasers, showing how the $10^{12}$ photons per pulse available at these sources offer structural characterization down to 100 fs resolution (orders of magnitude faster than current synchrotron images). We introduce the XFEL DFXM setup with simultaneous bright field microscopy to probe density changes within the same volume. This work presents a comprehensive guide to the multi-modal ultrafast high-resolution X-ray microscope that we constructed and tested at two XFELs, and shows initial data demonstrating two timing strategies to study associated reversible or irreversible lattice dynamics