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Experimental data reveals that attenuation is an important phenomenon in medical ultrasound. Attenuation is particularly important for medical applications based on nonlinear acoustics, since higher harmonics experience higher attenuation than the fundamental. Here, a method is presented to accurately solve the wave equation for nonlinear acoustic media with spatially inhomogeneous attenuation. Losses are modeled by a spatially dependent compliance relaxation function, which is included in the Westervelt equation. Introduction of absorption in the form of a causal relaxation function automatically results in the appearance of dispersion. The appearance of inhomogeneities implies the presence of a spatially inhomogeneous contrast source in the presented full-wave method leading to inclusion of forward and backward scattering. The contrast source problem is solved iteratively using a Neumann scheme, similar to the iterative nonlinear contrast source (INCS) method. The presented method is directionally independent and capable of dealing with weakly to moderately nonlinear, large scale, three-dimensional wave fields occurring in diagnostic ultrasound. Convergence of the method has been investigated and results for homogeneous, lossy, linear media show full agreement with the exact results. Moreover, the performance of the method is demonstrated through simulations involving steered and unsteered beams in nonlinear media with spatially homogeneous and inhomogeneous attenuation.

We investigate general properties of the interferograms from a frequency comb laser in a non-linear dispersive medium. The focus is on interferograms at large delay distances and in particular on their broadening, the fringe formation and shape. It is observed that at large delay distances the interferograms spread linearly and that its shape is determined by the source spectral profile. It is also shown that each intensity point of the interferogram is formed by the contribution of one dominant stationary frequency. This stationary frequency is seen to vary as a function of the path length difference even within the interferogram. We also show that the contributing stationary frequency remains constant if the evolution of a particular fringe is followed in the successive interferograms found periodically at different path length differences. This can be used to measure very large distances in dispersive media.

Providing a femtosecond optical pulse with a proper transverse spatial profile represents a fast and relatively simple method to force a quantum system to follow a prescribed temporal evolution. In the present work, we show that the quantum system presents a surprisingly high sensitivity with respect to the spatial shape of the pulse. We discuss an explicit example where differences on the order of a few nanometers in the initial pulse’s spot size induce completely different responses in the system under study.

We study focused fields which, for a given total power and a given numerical aperture, have maximum electric field amplitude in some direction in the focal point and are linearly polarized along this direction. It is shown that the optimum field is identical to the image of an electric dipole with unit magnification. In particular, the field which is the image of an electric dipole whose dipole vector is parallel to the optical axis, is identical to the field whose longitudinal component is maximum at the image point.

Emission of pulses of electromagnetic radiation in the terahertz range is observed when ultrathin gold films on glass are illuminated with femtosecond near-IR laser pulses. A distinct maximum is observed in the emitted terahertz amplitude from films of average thickness just above the percolation threshold. Our measurements suggest that the emission is through a second-order nonlinear optical rectification process, enhanced by the excitation of localized surface plasmon hot spots on the percolated metal film.

In recent years, novel ion sources have been designed and developed that have enabled focused ion beam machines to go beyond their use as nano-fabrication tools. Secondary electrons are usually taken to form images, for their yield is high and strongly dependent on the surface characteristics, in terms of chemical composition and topography. In particular, the secondary electron yield varies characteristically with the angle formed by the beam and the direction normal to the sample surface in the point of impact. Knowledge of this dependence, for different ion/atom pairs, is thus the first step toward a complete understanding of the contrast mechanism in scanning ion microscopy. In this article, experimentally obtained ion-induced secondary electron yields as a function of the incidence angle of the beam on flat surfaces of Al and Cr are reported, for usual conditions in Ga+ and He+ microscopes. The curves have been compared with models and simulations, showing a good agreement for most of the angle range; deviations from the expected behavior are addressed and explanations are suggested. It appears that the maximum value of the ion-induced secondary electron yield is very similar in all the studied cases; the yield range, however, is consistently larger for helium than for gallium, which partially explains the enhanced topographical contrast of helium microscopes over the gallium focused ion beams.

Today, the resolution in phase-contrast cryo-electron tomography is for a significant part limited by the contrast transfer function (CTF) of the microscope. The CTF is a function of defocus and thus varies spatially as a result of the tilting of the specimen and the finite specimen thickness. Models that include spatial dependencies have not been adopted in daily practice because of their high computational complexity. Here we present an algorithm which reduces the processing time for computing the ‘tilted’ CTF by more than a factor 100. Our implementation of the full 3D CTF has a processing time on the order of a Radon transform of a full tilt-series. We derive and validate an expression for the damping envelope function describing the loss of resolution due to specimen thickness. Using simulations we quantify the effects of specimen thickness on the accuracy of various forward models. We study the influence of spatially varying CTF correction and subsequent tomographic reconstruction by simulation and present a new approach for space-variant phase-flipping. We show that our CTF correction strategies are successful in increasing the resolution after tomographic reconstruction.

We demonstrate the coupling of bright and dark surface lattice resonances (SLRs), which are collective Fano resonances in 2D plasmonic crystals. As a result of this coupling, a frequency stop gap in the dispersion relation of SLRs is observed. The different field symmetries of the low- and high-frequency SLR bands lead to pronounced differences in their coupling to free-space radiation. Standing waves of very narrow spectral width compared to localized surface-plasmon resonances are formed at the high-frequency band edge, while subradiant damping onsets at the low-frequency band edge, leading the resonance into darkness. We introduce a coupled-oscillator analog to the plasmonic crystal, which serves to elucidate the physics of the coupled plasmonic resonances and which is used to estimate very high quality factors for SLRs.

Supported by the European Commission and EURAMET, a consortium of 10 participants from national metrology institutes, universities and companies has started a joint research project with the aim of overcoming current challenges in optical scatterometry for traceable linewidth metrology. Both experimental and modelling methods will be enhanced and different methods will be compared with each other and with specially adapted atomic force microscopy (AFM) and scanning electron microscopy (SEM) measurement systems in measurement comparisons. Additionally novel methods for sophisticated data analysis will be developed and investigated to reach significant reductions of the measurement uncertainties in critical dimension (CD) metrology. One final goal will be the realisation of a wafer based reference standard material for calibration of scatterometers.

We investigate the possibility of light beams that are both narrow and long range with respect to the wavelength. On the basis of spectral electromagnetic field representations, we have studied the decay of the evanescent waves, and we have obtained some bounds for the width and range of a light beam in the near-field region. The range determines the spatial bound of the near field in the direction of propagation. For a number of representative examples we found that narrow beams have a short range. Our analysis is based on the uncertainty relations between spatial position and spatial frequency.

We have constructed a mathematical model to analyze the photon efficiency of frequency-domain fluorescence lifetime imaging microscopy (FLIM). The power of the light source needed for illumination in a FLIM system and the signal-to-noise ratio of the detector have led us to a photon “budget.” These measures are relevant to many fluorescence microscope users and the results are not restricted to FLIM but applicable to widefield fluorescence microscopy in general. Limitations in photon numbers, however, are more of an issue with FLIM compared to other less quantitative types of imaging. By modeling a typical experimental configuration, examples are given for fluorophores whose absorption peaks span the visible spectrum from Fura-2 to Cy5. We have performed experiments to validate the assumptions and parameters used in our mathematical model. The influence of fluorophore concentration on the intensity of the fluorescence emission light and the Poisson distribution assumption of the detected fluorescence emission light have been validated. The experimental results agree well with the mathematical model. This photon budget is important in order to characterize the constraints involved in current fluorescent microscope systems that are used for lifetime as well as intensity measurements and to design and fabricate new systems.

The structure of the thesis is the following. The first chapter is an introduction to scanning microscopy, where the path that led to the Focused Ion Beam (FIB) is described and the main differences between electrons and ion beams are highlighted. Chapter 2 is what is normally referred to (which I do not really like) as ‘the theory chapter’. The theory of ion/matter interaction is presented in the first part of the chapter. The treatment is the standard one that can be found in the literature, but of course mine is the choice of the topics and the way in which they are presented. The second part of the chapter is a short introduction toMonte Carlo codes, and in particular to the two pieces of software that I have used for my basic simulations, SRIM/TRIM from J. Ziegler, and IONiSE from D. Joy. The third chapter is almost entirely made up of an article published in Microscopy & Microanalysis in 2011, on the subject of ion-induced Secondary Electron Emission; the paper is introduced by two small sections, the first being an introduction to ion beam imaging, the second presenting a standard theory of noise in scanning microscopy. Chapter 4 introduces the main topic of this thesis work, the one that is more dear to me: resolution in scanning ion microscopy. The chapter is a hybrid, for the theory of resolution that is presented is quite standard, but interlaced with a lot of rethinking and personal points of view, and finally adapted to the specific field of scanning ion microscopy. Chapters 5 and 6 are the first two articles published during my PhD, in Journal of Vacuum Science & Technology B. They both tackle the problem of resolution evaluation in scanning ion microscopy, the first for the Ga-FIB, the second for the He-FIB. The two papers have been published in 2008 and 2009, respectively, a time when the uniformity of the formalism was not yet mature, reason for which symbolic inconsistencies can be found in relation to the rest of the thesis, and to the list of symbols in appendix B. Choice was made to leave the papers in their published version, but this should not represent a problem, because each quantity is clearly defined. The last journal paper published within my project makes chapter 7. The scope of the paper is broad, for it proposes a method to simulate ion imaging that does not employ any Monte Carlo calculation. It can be regarded as a kind of summary of all the studies performed in the course of the project, and is followed by an appendix that explains the details of the noise analysis whose results are presented in the article. Conclusions and recommendations find their place in chapter 8. With referiment to the original main motivation, i.e. exploring the possibility of achieving atomic resolution with a Scanning IonMicroscope, it is shown that this is not possible, at least in the general case, because the sputtering of the sample limits the ultimate obtainable resolution to the nanometer range, even using very light ions. Also, it is pointed out that, in imaging systems causing strong sample modification, the concept of resolution itself can not be thought of as static; it must be regarded as dynamic instead. On the subject of Ion-Induced Secondary Electron Emission, a procedure to obtain curves of Secondary Electron yield versus incident angle of the beam is presented; the behaviour of those curves contributes to explain the much sharper contrast achievable with a He-FIB, as opposite to the more traditional Ga-FIB. Finally, it is shown that simulation of ion imaging based on the ‘yield vs. incidence angle’ curves is feasible, overcoming the computational problems that affect any Monte Carlo based approach.

This work presents the development of a non-destructive imaging technique for the investigation of the microstructure of cementite grains embedded in a ferrite matrix of medium-carbon steel. The measurements were carried out at the material science beamline of the European Synchrotron Radiation Facility (ESRF) ID11. It was shown that in-line X-ray phase-contrast tomography (PCT) can be used for the detection of cementite grains of several microns in size. X-ray PCT of the cementite structure can be achieved by either a ‘single distance’ or a ‘multiple distance’ acquisition protocol. The latter permits quantitative phase retrieval. A second imaging technique, X-ray diffraction-contrast tomography (DCT), was employed to obtain information about the shapes and crystallographic orientations of the distinct ferrite grains surrounding the cementite structures. The initial results demonstrate the feasibility of determining the geometry of the cementite grains after the austenite-ferrite phase-transformation in a non-destructive manner. The results obtained with PCT and DCT are verified with ex-situ optical microscopy studies of the same specimen.

We demonstrate the feasibility of intravascular ultrasound (IVUS) chirp imaging as well as chirp reversal ultrasound contrast imaging at intravascular ultrasound frequency. Chirp excitations were emitted with a 34 MHz single crystal intravascular transducer and compared to conventional Gaussian-shaped pulses of equal acoustic pressure. The signal to noise ratio of the chirp images was increased by up to 9 dB relative to the conventional images. Imaging of contrast microbubbles was implemented by chirp reversal, achieving a contrast to tissue ratio of 12 dB. The method shows potential for intravascular imaging of structures in and beyond coronary atherosclerotic plaques including vasa vasorum

An inspection apparatus is provided comprising in combination at least an optical microscope and an ion- or electron microscope equipped with a source for emitting a primary beam of radiation to a sample in a sample holder. The apparatus may comprise a detector for detection of secondary radiation backscattered from the sample and induced by the primary beam. The optical microscope is equipped with an light collecting device to receive in use luminescence light emitted by the sample and to focus it on a photon-detector.

Emission of terahertz radiation is observed when surface plasmons are excited on a thin film of gold, in the Kretschmann geometry. When a hemicyanine-terminated alkanethiol self-assembled monolayer of thickness 1.2 nm is deposited on the gold film, stronger terahertz emission is observed. Our experimental results confirm that enhanced terahertz emission is possible from planar gold surfaces when surface plasmons are excited.

For the optimization and development of medical ultrasound transducers and imaging modalities, the Iterative Nonlinear Contrast Source (INCS) method has been developed. This numerical method predicts the nonlinear acoustic pressure field, generated by a pulsed, plane source with an arbitrary aperture, and propagating in a three-dimensional tissue-like medium that extends over a very large domain of interest. The INCS method obtains the acoustic pressure from the nonlinear acoustic wave equation by treating the nonlinear term as a contrast source. The full nonlinear wave field is then found by iteratively solving the linearized wave problem using a Green's function method. By employing the Filtered Convolution method discussed in a companion paper, accurate field predictions are obtained at a discretization approaching two points per wavelength or period of the highest frequency of interest. In this paper, very large-scale, nonlinear field profiles are presented for transducers with cylindrical as well as phased array geometries, excited with a pulsed waveform having a center frequency of 1-2 MHz. Comparison with results obtained from models of reduced complexity shows that in all cases the INCS method accurately predicts the nonlinear field.

The refraction and scattering of nonlinear acoustic waves play an important role in the realistic application of medical ultrasound. One cause of these effects is the tissue dependence of the nonlinear medium behavior. A method that is able to model those effects is essential for the design of transducers for novel ultrasound modalities. Starting from the Westervelt equation, nonlinear pressure wave fields can be modeled via a contrast source formulation, as has been done with the INCS method. An extension of this method will be presented that can handle inhomogeneities in the coefficient of nonlinearity. The contrast source formulation results in an integral equation, which is solved iteratively using a Neumann scheme. The convergence of this scheme has been investigatedfor relevant media (e.g., blood, brain, and liver). Further, as an example, the method has been applied to compute the 1D nonlinear acoustic wave field in an inhomogeneous medium insonified by a 1 MHz Gaussian pulse propagatingup to 100 mm. The results show that the method is able to predict the propagation and the scattering effects of nonlinear acoustic waves in media with inhomogeneities in the coefficient of nonlinearity. This motivates a similar extension ofthe 3D INCS method.

Superharmonic imaging (SHI) targets a combination of the 3rd to 5th harmonics. It was proven to have certain advantages in comparison with the established imaging standards in medical utrasound. SHI enhances the spatial resolution and improves the quality of echographic images, mainly by eliminating reverberation artifacts at the chest wall. However, SHI suffers from ripple artifacts, originating from the spectral gaps in between harmonics, and degrading the temporal resolution. To solve this a chirp-based SHI protocol was employed and its characteristics investigated, i.e. point spread function (PSF). The protocol was implemented for an interleaved phased array probe (44+44 elements tuned at 1.0+3.7MHz), connected to a fully programmable ultrasound system. A linear chirp (center frequency 1MHz; bandwidth 40%) was used for excitation. To obtain the PSF, the RF traces were recorded at focus along the lateral axis and convolved with the decoding signal. This was computed using KZK simulations. A PSF comparison between a superharmonic chirp and the 3rd-harmonic of a 2.5-cycle Gaussian apodized sinus burst at 1MHz showed a decrease in axial pulse length of 46% at -6dB and 32% at the -20dB level in favor of SHI. Chirp based SHI is virtually free of ripple artifacts and therefore feasible.

We apply a phase retrieval algorithm to the intensity pattern of a Hartmann wavefront sensor to measure with enhanced accuracy the phase structure of a Hartmann hole array. It is shown that the rms wavefront error achieved by phase reconstruction is one order of magnitude smaller than the one obtained from a typical centroid algorithm. Experimental results are consistent with a phase measurement performed independently using a Shack-Hartmann wavefront sensor.