Holographic Particle Image Velocimetry of Ink Jet Streams

Ink jet technology is a rapidly growing and diverse field of research. Ink jets are used to deliver very precise and small (picolitre) volumes of fluid to a surface. Recent advances in ink jet technology demand a better understanding of the dynamics of the fluid during jetting. The aim of this project was to design a method capable of measuring the flow velocities inside ink jet streams. This objective has been achieved by the use of digital holographic particle image velocimetry. The difficulty with measuring flows inside tightly curved samples is that the refractive index change over the boundary leads to an optical distortion and therefore particles cannot be viewed or tracked reliably. Optical distortion is compensated for by taking advantage of the ability to replay a holographically recorded wave. The light scattered by particles is propagated numerically back through the sample’s surface, to form a three-dimensional image in which all refractions at the interface have been accounted for. Three dimensional particle fields are then analysed using custom particle detection and correlation code to extract the displacement of individual particles between exposures, which facilitates the construction of full flow profiles. Holograms were recorded with a simple off-axis holographic microscope, comprising two point sources of divergent light, formed from the same objective lens, acting as the source of illumination and reference light, respectively. Experiments were conducted on continuous ink jet streams of water issuing from a nozzle with 100 µm diameter. For a few millimetres after the nozzle exit, the jet is cylindrical, it then starts to form swells and necks; the swells continue to grow at the expense of the necks until the jet breaks up into a stream of droplets. Measurements of the stream wise component of velocity have been successful in the cylindrical parts of the jet, in swells and in necks greater than 20 µm in diameter. To my knowledge measurements of particle velocities on fluid jets at this scale have not been accomplished previously

Statistics In Diffractive Imaging

This dissertation describes reconstruction techniques in diffractive imaging when the data is exceptionally noisy and when crucial experimental parameters are unmeasured. In particular, this work focuses on two applications of diffractive imaging, single particle imaging with unoriented data and ultrafast magnetic imaging with unmeasured charge distribution, both of which are exciting experiments planned for free electron laser facilities. Concerning single particle imaging, in chapter 2 we introduce the EMC algorithm for reconstructing a particle's 3D diffraction intensity from very many photon-shot-noise limited 2D measurements, when the particle orientation in each measurement is unknown. We coin such an imaging technique cryptotomography. In this chapter, we also study the noise limits beyond which cryptotomography is impossible. This is followed by an experimental demonstration of EMC in chapter 3, where we reconstruct the 3D Fourier intensity distribution of mono-disperse prolate nano-particles using single-shot 2D diffraction patterns collected at DESYs FLASH facility when a bright, coherent, ultrafast X-ray pulse intercepted individual particles of random, unmeasured orientations. This experimental demonstration of cryptotomography extended the Expansion-Maximization-Compression (EMC) framework to accommodate unmeasured fluctuations in photon fluence and loss of data due to saturation or background scatter. In chapter 4 we discuss magnetic imaging. We study, using simulated experiments, the feasibility of phase retrieval in X-ray diffractive imaging of thin-film magnetic domains in the presence of intrinsic charge scattering given only photon-shot-noise limited diffraction data. We also chart out the limits of diffractive imaging when we vary both photon-shot-noise and the intensity of charge-scattering noise. This work is directly relevant to the time-resolved imaging of magnetic dynamics using coherent and ultrafast radiation from Xray free electron lasers

High-Resolution Crystal Truncation Rod Scattering: Application to Ultrathin Layers and Buried Interfaces

In crystalline materials, the presence of surfaces or interfaces gives rise to crystal truncation rods (CTRs) in their X‐ray diffraction patterns. While structural properties related to the bulk of a crystal are contained in the intensity and position of Bragg peaks in X‐ray diffraction, CTRs carry detailed information about the atomic structure at the interface. Developments in synchrotron X‐ray sources, instrumentation, and analysis procedures have made CTR measurements into extremely powerful tools to study atomic reconstructions and relaxations occurring in a wide variety of interfacial systems, with relevance to chemical and electronic functionalities. In this review, an overview of the use of CTRs in the study of atomic structure at interfaces is provided. The basic theory, measurement, and analysis of CTRs are covered and applications from the literature are highlighted. Illustrative examples include studies of complex oxide thin films and multilayers

Signal processing based method for solving inverse scattering problems

The problem of reconstructing an image of the permittivity distribution inside a penetrable and strongly scattering object from a finite number of noisy scattered field measurements has always been very challenging because it is ill-posed in nature. Several techniques have been developed which are either computationally very expensive or typically require the object to be weakly scattering. I have developed here a non-linear signal processing method, which will recover images for both strong scatterers and weak scatterers. This nonlinear or cepstral filtering method requires that the scattered field data is first preprocessed to generate a minimum phase function in the object domain. In 2-D or higher dimensional problems, I describe the conditions for minimum phase and demonstrate how an artificial reference wave can be numerically combined with measured complex scattering data in order to enforce this condition, by satisfying Rouche‘s theorem. In the cepstral domain one can filter the frequencies associated with an object from those of the scattered field. After filtering, the next step is to inverse Fourier transform these data and exponentiate to recover the image of the object under test. In addition I also investigate the scattered field sampling requirements for the inverse scattering problem. The proposed inversion technique is applied to the measured experimental data to recover both shape and relative permittivity of unknown objects. The obtained results confirm the effectiveness of this algorithm and show that one can identify optimal parameters for the reference wave and an optimal procedure that results in good reconstructions of a penetrable, strongly scattering permittivity distribution

Computerized Classification of Surface Spikes in Three-Dimensional Electron Microscopic Reconstructions of Viruses

The purpose of this research is to develop computer techniques for improved three-dimensional (3D) reconstruction of viruses from electron microscopic images of them and for the subsequent improved classification of the surface spikes in the resulting reconstruction. The broader impact of such work is the following. Influenza is an infectious disease caused by rapidly-changing viruses that appear seasonally in the human population. New strains of influenza viruses appear every year, with the potential to cause a serious global pandemic. Two kinds of spikes – hemagglutinin (HA) and neuraminidase (NA) – decorate the surface of the virus particles and these proteins are primarily responsible for the antigenic changes observed in influenza viruses. Identification of the locations of the surface spikes of both kinds in a new strain of influenza virus can be of critical importance for the development of a vaccine that protects against such a virus. Two major categories of reconstruction techniques are transform methods such as weighted backprojection (WBP) and series expansion methods such as the algebraic reconstruction techniques (ART) and the simultaneous iterative reconstruction technique (SIRT). Series expansion methods aim at estimating the object to be reconstructed by a linear combination of some fixed basis functions and they typically estimate the coefficients in such an expansion by an iterative algorithm. The choice of the set of basis functions greatly influences the efficacy of the output of a series expansion method. It has been demonstrated that using spherically symmetric basis functions (blobs), instead of the more traditional voxels, results in reconstructions of superior quality. Our own research shows that, with the recommended data-processing steps performed on the projection images prior to reconstruction, ART (with its free parameters appropriately tuned) provides 3D reconstructions of viruses from tomographic tilt series that allow reliable quantification of the surface proteins and that the same is not achieved using WBP or SIRT, which are the methods that have been routinely applied by practicing electron microscopists. Image segmentation is the process of recognizing different objects in an image. Segmenting an object from a background is not a trivial task, especially when the image is corrupted by noise and/or shading. One concept that has been successfully used to achieve segmentation in such corrupted images is fuzzy connectedness. This technique assigns to each element in an image a grade of membership in an object. Classifications methods use set of relevant features to identify the objects of each class. To distinguish between HA and NA spikes in this research, discussions with biologists suggest that there may be a single feature that can be used reliably for the classification process. The result of the fuzzy connectedness technique we conducted to segment spikes from the background confirms the correctness of the biologists’ assumption. The single feature we used is the ratio of the width of the spike’s head to the width of its stem in 3D space; the ratio appears to be greater for NA than it is for HA. The proposed classifier is tested on different types of 3D reconstructions derived from simulated data. A statistical hypothesis testing based methodology allowed us to evaluate the relative suitability of reconstruction methods for the given classification task

Strain Mapping of Single Nanowires using Nano X-ray Diffraction

Nanowires are explored as basic components for a large range of electronic devices. The nanowire format offersseveral benefits, including reduced material consumption and increased potential for combining materials to formnew novel heterostructures. Several factors, such as mechanical stress from contacting or a lattice mismatch in aheterostructure, can strain and change the lattice tilt. The strain is often intertwined with small gradients ofcomposition. The strain relaxation can differ significantly from bulk due to the small diameters, but the mechanismsare not fully comprehended. X-rays have a penetrating power that makes it possible to investigate embeddedsamples without preparation or slicing. The high flux of coherent X-ray beams from synchrotron radiation facilities,combined with the nano-focus capabilities developed in recent years, have made it possible to probe nano-crystals.The 4th generation of synchrotrons, including MAX IV in Lund, Sweden, has even higher brilliance than previoussources. Diffraction imaging techniques using synchrotron radiation can reveal small strains down to 10-4-10-5. Thefield of coherent imaging pushes the limits of resolutions below the size of the focus. With Bragg ptychography, thedisplacement field in a crystal can be probed with resolution beyond the probe focus by numerically reconstructingthe phase.This thesis includes the development of X-ray nano-diffraction methods for the characterizing of nanowires, includingGaInP/InP barcode nanowires, p-i-n InP nanowire devices and metal halide perovskite CsPbBr3 nanowires. Itincludes a theoretical background of the scattering mechanisms in Thomson scattering in nano-crystals, goesthrough the formalism for coherent diffraction imaging, crystal structure and deformation in nanoobjects and thetechnical aspects of the experimental setup and measurement. Moreover, theoretical modelling of elastic strainrelaxation in these nanowires was performed with finite element modelling.Single III-V nanowire heterostructures and III-V nanowire devices were probed with scanning XRD and Braggprojection ptychography (BPP). How the techniques compare to each other and how the results are affected by thedifferent approximations that are made in the respective technique was explored. Finite element simulationscombined with nano-diffraction revealed that the lattice mismatch of 1.5% could be relaxed elastically for thediameter of 180 nm. From the strain mapping of the nanowire device, we found how the contacting of the nanowirebends the nanowire resulting in a tilt normal to the substrate.Single perovskite metal-halide perovskite CsPb(Br(1-x)Clx)3 nanowire heterostructures were characterized withscanning nano-XRD and XRF, which showed that the lattice spacing was affected by composition and strain.Composition gradients revealed that Cl diffusion had taken place within the heterostructure. Furthermore, extractingthe lattice tilts from shifts of the Bragg peak revealed a ferroelastic domain structure with simultaneously existinglattice tilts. These findings are beneficial for the further development of MHP nanowires devices