High-resolution X-ray ptychography for magnetic imaging

The resolution in standard X-ray microscopes is limited by the focusing element, e.g. Fresnel Zone Plates (FZP), and stays in the range of 20 nm for highly efficient plates. Diffraction imaging techniques with the use of coherent X-ray radiation potentially can achieve wavelength limited resolution solving so-called “phase problem”. Ptychography is the combination of diffraction imaging and scanning transmission microscopy that provides images of extended sample areas utilizing iterative reconstruction algorithm. The main focus of this thesis is the realization of ptychographic imaging on the samples with different scattering power, as well as the investigation and improvement of the microscopic potential of this method in detailed comparison with conventional STXM imaging. The technique is applied to sub-100 nm sized magnetic structures of the current scientific interest, i.e. domain walls, vortices and skyrmions

Structured High-Harmonic Light Sources for Enhanced Extreme Ultraviolet Microscopy

Lensless imaging techniques such as ptychography have revolutionized short-wavelength metrology by enabling photon-efficient, diffraction limited, robust phase-contrast imaging of nanostructured samples. At the same time, light sources based on the extreme nonlinear optical process of high harmonic generation have enabled these and other short-wavelength metrology techniques to be carried out on a tabletop. However, due to the lack of refractive optics for manipulating extreme ultraviolet and X-ray light, short-wavelength imaging currently lacks the vast flexibility of visible light microscopy, which in part is made possible by the many optical elements available for tailoring the illumination. This thesis aims to fill this gap by integrating amplitude, phase, and polarization structured light into the high harmonic generation process to produce a great deal of flexibility in the light source at its generation, and giving initial demonstrations of how using such tailored light sources can expand the capabilities of tabletop EUV microscopy techniques.</p

py4DSTEM: a software package for multimodal analysis of four-dimensional scanning transmission electron microscopy datasets

Scanning transmission electron microscopy (STEM) allows for imaging, diffraction, and spectroscopy of materials on length scales ranging from microns to atoms. By using a high-speed, direct electron detector, it is now possible to record a full 2D image of the diffracted electron beam at each probe position, typically a 2D grid of probe positions. These 4D-STEM datasets are rich in information, including signatures of the local structure, orientation, deformation, electromagnetic fields and other sample-dependent properties. However, extracting this information requires complex analysis pipelines, from data wrangling to calibration to analysis to visualization, all while maintaining robustness against imaging distortions and artifacts. In this paper, we present py4DSTEM, an analysis toolkit for measuring material properties from 4D-STEM datasets, written in the Python language and released with an open source license. We describe the algorithmic steps for dataset calibration and various 4D-STEM property measurements in detail, and present results from several experimental datasets. We have also implemented a simple and universal file format appropriate for electron microscopy data in py4DSTEM, which uses the open source HDF5 standard. We hope this tool will benefit the research community, helps to move the developing standards for data and computational methods in electron microscopy, and invite the community to contribute to this ongoing, fully open-source project

Next generation Fourier ptychographic microscopy: computational and experimental techniques

Fourier ptychography is a recently developed computational imaging technique, which enables gigapixel image reconstruction from multiple low-resolution measurements. The technique can be implemented on simple, low-quality microscopes to achieve unprecedented image quality by exchanging optical design complexity with computational complexity. While developments have been made, demonstrations typically use well-calibrated, highperformance microscopes. Therefore, the real world performance and true benefits of(lowcost) Fourier ptychography still need to be demonstrated in out-of-lab environments where unforeseen problems are not unlikely. In this thesis, I will demonstrate how to utilise Fourier ptychography in a fast, robust and cheap manner. Two experimental prototypes will be introduced, one of them being an ultra-low-cost 3D printed microscope capable of wide-field sub-micron resolution imaging. Another prototype was built to demonstrate high-speed gigapixel imaging, capable of 100-megapixel, 1µm resolution image capture in under 3 seconds. Novel image formation models and their refinements were developed to correct the incomplete conventional model. These include partial coherence of the illumination, deviation from the plane-wave assumption, and spatially varying aberrations. Lastly, Experimental work was also heavily supplemented by novel calibration and reconstruction algorithms. Theoretical work outlined in this thesis enables the use of tilted, off-axis optical components, alleviating typically assumed parallel plane optical geometry. Optical precision requirements can also be relaxed due to novel robust calibration algorithms. As a result, low-cost 3D printed microscopes can be used

Direct 3D imaging through spatial coherence of light

Wide-field imaging is widely adopted due to its fast acquisition, cost-effectiveness and ease of use. Its extension to direct volumetric applications, however, is burdened by the trade-off between resolution and depth of field (DOF), dictated by the numerical aperture of the system. We demonstrate that such trade-off is not intrinsic to wide-field imaging, but stems from the spatial incoherence of light: images obtained through spatially coherent illumination are shown to have resolution and DOF independent of the numerical aperture. This fundamental discovery enabled us to demonstrate an optimal combination of coherent resolution-DOF enhancement and incoherent tomographic sectioning for scanning-free, wide-field 3D microscopy on a multicolor histological section.Comment: 17 pages, 6 figures. Supplemental document available upon request to the authors. Submitted to Lasers and Photonics Review

Ultrafast Dynamics of Magnetic Multilayer Films: Magneto-Optical Spectroscopy and Resonant Scattering in the Extreme Ultraviolet and Soft X-Ray Spectral Regions

This thesis focuses on studying ferromagnetic thin films with high temporal and spatial resolution using tabletop extreme ultraviolet (EUV) light sources based on high harmonic generation (HHG) and ultrafast soft X-rays from a free-electron laser. In Chapter 4, a new magneto-optical technique is developed. It allows a direct measurement of the full resonant complex EUV magneto-optical permittivity on a tabletop and thus, through a comparison with first principles calculations, is capable of capturing the microscopic mechanisms of ultrafast laser-induced demagnetization. It is found that, in Co, the demagnetization response is dominated by magnon excitations with possible smaller contributions from other mechanisms. Chapter 5 discusses the development of an efficient approach for resonant magnetic scattering (RMS) with a tabletop HHG source. This approach is used to study magnetic textures with spatial resolution. In an external magnetic field, a transition from a disordered network of stripe domains to an ordered lattice of magnetic vortices is observed in an Fe-Gd thin film. Chapter 6 presents the results of a dynamic soft X-ray RMS experiment on a disordered domain network performed at the Linear Coherent Light Source (LCLS). By directly applying the experimental data to a carefully simulated domain pattern, laser-induced transient changes in the domains are captured in real space, and strong non-uniformities in the demagnetization across the sample are observed. These non-uniformities are attributed to a combined effect of ultrafast spin-polarized currents and a gradient in the pump absorption throughout the thickness of the sample. Chapter 7 provides an outlook towards time-resolved lensless magnetic spectro-microscopy with HHG sources

Roadmap on wavefront shaping and deep imaging in complex media

The last decade has seen the development of a wide set of tools, such as wavefront shaping, computational or fundamental methods, that allow us to understand and control light propagation in a complex medium, such as biological tissues or multimode fibers. A vibrant and diverse community is now working in this field, which has revolutionized the prospect of diffraction-limited imaging at depth in tissues. This roadmap highlights several key aspects of this fast developing field, and some of the challenges and opportunities ahead. &nbsp;</p

Dynamics and force generation of flagellum and pili in Caulobacter crescentus

Surface attachment of bacteria is the first step of biofilm formation and biofilms are associated with infections and bacterial resistance. Surface attachment of bacteria is often mediated by extracellular appendages, for example flagellum and pili. The flagellum is a cork-screw like structure used for swimming and surface sensing. Pili are filamentous structures and have a wide variety of functions, among them attachment on surfaces. Because of the small diameter of flagellum and pili, direct observations of flagellum and pili are challenging under physiological conditions. C. crescentus, a model organism for biofilm formation, has an asymmetric life cycle. The sessile and stalked mother cell produces a motile daughter cell that is equipped with a flagellum and pili at the free pole. In this work we investigated the dynamics and force generation of the flagellum and pili of C. crescentus under physiological conditions employing a label-free method