Double Your Views - Exploiting Symmetry in Transmission Imaging

For a plane symmetric object we can find two views - mirrored at the plane of symmetry - that will yield the exact same image of that object. In consequence, having one image of a plane symmetric object and a calibrated camera, we can automatically have a second, virtual image of that object if the 3-D location of the symmetry plane is known. In this work, we show for the first time that the above concept naturally extends to transmission imaging and present an algorithm to estimate the 3-D symmetry plane from a set of projection domain images based on Grangeat's theorem. We then exploit symmetry to generate a virtual trajectory by mirroring views at the plane of symmetry. If the plane is not perpendicular to the acquired trajectory plane, the virtual and real trajectory will be oblique. The resulting X-shaped trajectory will be data-complete, allowing for the compensation of in-plane motion using epipolar consistency. We evaluate the proposed method on a synthetic symmetric phantom and, in a proof-of-concept study, apply it to a real scan of an anthropomorphic human head phantom.Comment: Accepted for MICCAI 2018 (8 Pages

Development and Performance of a Sparsity-Exploiting Algorithm for Few-View Single Photon Emission Computed Tomogrpahy (SPECT) Reconstruction

Single Photon Emission Computed Tomography (SPECT) provides noninvasive images of the distribution of radiotracer molecules. Dynamic Single Photon Emission Computed Tomography provides information about tracer uptake and washout from a series of time-sequence images. Stationary ring-like multi-camera systems are being developed to provide rapid dynamic acquisitions with high temporal sampling. Reducing the number of cameras reduces the cost of such systems but also reduces the number of views acquired, limiting the angular sampling of the system. Novel few-view image reconstruction methods may be beneficial and are being investigated for the application of dynamic SPECT. A sparsity-exploiting algorithm intended for few-view Single Photon Emission Computed Tomography (SPECT) reconstruction is proposed and characterized. The reconstruction algorithm phenomenologically models the object as piecewise constant subject to a blurring operation. To validate that the reconstruction algorithm closely approximates the true object when the object model is known and the system is modeled exactly, projection data were generated from an object assuming this model and using the system matrix. Monte Carlo simulations were performed to provide more realistic data of a phantom with varying smoothness across the field of view. For all simulations, reconstructions were performed across a sweep of the two primary design parameters: the blurring parameter and the weighting of the total variation (TV) minimization term. A range of noise and angular sampling conditions were also investigated. Maximum-Likelihood Expectation Maximization (MLEM) reconstructions were performed to provide a reference image. Spatial resolution, accuracy, and signal-to-noise ratio were calculated and compared for all reconstructions. The results demonstrate that the reconstruction algorithm very closely approximates the true object under ideal conditions. While this reconstruction technique assumes a specific blurring model, the results suggest that the algorithm may provide high reconstruction accuracy even when the true blurring parameter is unknown. In general, increased values of the blurring parameter and TV weighting parameters reduced noise and streaking artifacts, while decreasing spatial resolution. The reconstructed images demonstrate that the reconstruction algorithm introduces low-frequency artifacts in the presence of noise, but eliminates streak artifacts due to angular undersampling. Further, as the number of views was decreased from 60 to 9 the accuracy of images reconstructed using the proposed algorithm varied by less than 3%. Overall, the results demonstrate preliminary feasibility of a sparsity-exploiting reconstruction algorithm which may be beneficial for few-view SPECT

Structural biology: a century-long journey into an unseen world

© Institute of Materials, Minerals and Mining 2015.When the first atomic structures of salt crystals were determined by the Braggs in 1912–1913, the analytical power of X-ray crystallography was immediately evident. Within a few decades the technique was being applied to the more complex molecules of chemistry and biology and is rightly regarded as the foundation stone of structural biology, a field that emerged in the 1950s when X-ray diffraction analysis revealed the atomic architecture of DNA and protein molecules. Since then the toolbox of structural biology has been augmented by other physical techniques, including nuclear magnetic resonance spectroscopy, electron microscopy, and solution scattering of X-rays and neutrons. Together these have transformed our understanding of the molecular basis of life. Here I review the major and most recent developments in structural biology that have brought us to the threshold of a landscape of astonishing molecular complexity

Fabrication and Dynamic Tuning of Periodic Structures From Holographic Lithography

In this dissertation, I fabricated one-dimensional (1D), two-dimensional (2D) and three-dimensional (3D) periodic structures through holographic lithography (HL) and backfilling conversion with different materials. Along the line, I investigated their intrinsic structure-property relationship, harness and utilize the mechanical instability, and explored novel applications as tunable periodic structures. In order to mimic butterfly wings which show both structural color and superhydrophobicity, 3D diamond photonic crystals with controllable nano-roughness (≤ 120 nm) were fabricated from epoxy-functionalized cyclohexyl polyhedral oligomeric silsesquioxanes (epoxy-POSS). The nano-roughness was generated due to microphase separation of the polymer chain segments in nonsolvents during rinsing, which could be tuned by crosslinking density of the polymer and choice of solvents. Such structure offers opportunities to realize superhydrophobicity, enhanced dye adsorption in addition to the photon management in the 3D photonic crystal. Most of current studies on tunable periodic structures show limited tunable optical property ranges, which is attractive to be expanded. 2D shape memory polymer (SMP) membranes consisting of a hexagonal array of micron-sized holes were fabricated by converting from epoxy-POSS template. Reversible color switching from transparency to colorful state was achieved through thermal-mechanical deformation, utilizing shape memory effect and mechanical instability induced pattern transformation. Continuum mechanical analyses corroborated well with experimental observations. Potential applications as displays were demonstrated via two different approaches. It is challenging to directly fabricate high aspect-ratio (AR) 1D nano-scale structures, due to depth-of-focus (DOF) limitation, pattern collapse from capillary force and distortion during solvent swelling. With HL and supercritical drying, high AR 1D nano-scale structures were fabricated with epoxy-POSS and SU-8, which avoid DOF limitation and pattern collapse. Due to enhanced thermal and mechanical stability of epoxy-POSS, 1D nanogratings (AR up to 10) with controllable periodicity, filling fraction and surface roughness, were achieved, which could be directly converted to silica-like through calcination. By exploiting swelling-induced buckling of 1D SU-8 nanowalls with nanofibers formed in-between, long-range ordered 2D nanowaves with weaker reflecting color were achieved, where degree of lateral undulation could be controlled by tuning AR and exposure dosage. Using double-exposure through photomasks, patterns with both nanowaves and nanowalls for optical display were created

Workflow automation for image analysis of 2D crystals of membrane proteins

Membrane proteins carry out various functions essential to the survival of organ- isms. They transfer signals between the cell’s internal and external environments, move molecules and ions across the membrane, act as enzymes, and allow cell adhesion. This is why membrane proteins represent more than half of all drug targets. A deeper insight into the functional mechanisms of a protein can be gained from structural information. And so far only a fraction of membrane protein structures has been determined. The topic of this thesis is structure determination of membrane proteins through electron crystallography focusing on the image processing of 2D crystals. The thesis combines both method development and structure studies. In the Methods part, state of the art processing of 2D crystal images is presented. The workflow em- bedding all the processing steps from the initial micrographs of 2D crystals to the resulting 3D electron density map of the reconstituted membrane protein is de- scribed. The possibility of autonomous high-throughput processing is discussed as the ultimate goal of automation of this workflow. An additional processing step of the workflow that captures the variation of tilt geometry in the 2D crystal is introduced. This is implemented as an iterative refinement of the local tilt geometry using a Single Particle processing approach. A great benefit of electron crystallography is the fact that through reconstitution the purified protein is embedded in a natural environment, a membrane. Biochemical manipulations of this environment can lead to structural changes, which yields insight into the functional states of the protein. An new method of analyzing these structural changes in 2D projection maps is presented here. The method identifies significant changes in the protein by distinguishing them from noise derived artifacts. The second part of this thesis covers applications of these methods in structural studies of unknown membrane proteins. In the study of the Secondary Citrate/Sodium Symporter CitS, the substrate binding domain was identified with help of the significant difference map method. The improvements of the image processing routines were directly applied in the analysis of the 2D crystals. The structural studies of nucleotide-modulated potassium channel MloK1 also benefited from the automated image processing workflow and the significant difference map, while identifying structural changes through ligand binding. To gain a more detailed electron density map of MloK1, the local tilt geometry of the crystals were refined with the single particle 3D reconstruction for 2D crystal images method

Second order nonlinear frequency generation at the nanoscale in dielectric platforms

Nonlinear frequency generation at the nanoscale is a hot research topic which is gaining increasing attention in nanophotonics. The generation of harmonics in subwavelength volumes is historically associated with the enhancement of electric fields in the interface of plasmonic structures. Recently, new platforms based on high-index dielectric nanoparticles have emerged as promising alternatives to plasmonic structures for many applications. By exploiting optically induced electric and magnetic response via multipolar Mie resonances, dielectric nanoelements may lead to innovative opportunities in nanoscale nonlinear optics. Dielectric optical nanoantennas enlarge the volume of light–matter interaction with respect to their plasmonic counterpart, since the electromagnetic field can penetrate such materials, and therefore producing a high throughput of the generated harmonics. In this review, we first recap recent developments obtained in high refractive index structures, which mainly concern nonlinear second order effects. Moreover, we discuss configurations of dielectric nano-devices where reconfigurable nonlinear behavior is achieved. The main focus of this work concerns efficient Sum Frequency Generation in dielectric nano-platforms. The reported results may serve as a reference for the development of new nonlinear devices for nanophotonic applications