Extending holographic LEED to ordered small unit cell superstructures

Following on the success of the recent application of holographic LEED to the determination of the 3D atomic geometry of Si adatoms on a SiC(111) p(3x3) surface, which enabled that structure to be solved, we show in this paper that a similar technique allows the direct recovery of the local geometry of adsorbates forming superstructures as small as p(2x2), even in the presence of a local substrate reconstruction.Comment: 10 pages, 5 figures postscript included, revtex, Phys. Rev. B in pres

Learning-based Single-step Quantitative Susceptibility Mapping Reconstruction Without Brain Extraction

Quantitative susceptibility mapping (QSM) estimates the underlying tissue magnetic susceptibility from MRI gradient-echo phase signal and typically requires several processing steps. These steps involve phase unwrapping, brain volume extraction, background phase removal and solving an ill-posed inverse problem. The resulting susceptibility map is known to suffer from inaccuracy near the edges of the brain tissues, in part due to imperfect brain extraction, edge erosion of the brain tissue and the lack of phase measurement outside the brain. This inaccuracy has thus hindered the application of QSM for measuring the susceptibility of tissues near the brain edges, e.g., quantifying cortical layers and generating superficial venography. To address these challenges, we propose a learning-based QSM reconstruction method that directly estimates the magnetic susceptibility from total phase images without the need for brain extraction and background phase removal, referred to as autoQSM. The neural network has a modified U-net structure and is trained using QSM maps computed by a two-step QSM method. 209 healthy subjects with ages ranging from 11 to 82 years were employed for patch-wise network training. The network was validated on data dissimilar to the training data, e.g. in vivo mouse brain data and brains with lesions, which suggests that the network has generalized and learned the underlying mathematical relationship between magnetic field perturbation and magnetic susceptibility. AutoQSM was able to recover magnetic susceptibility of anatomical structures near the edges of the brain including the veins covering the cortical surface, spinal cord and nerve tracts near the mouse brain boundaries. The advantages of high-quality maps, no need for brain volume extraction and high reconstruction speed demonstrate its potential for future applications.Comment: 26 page

Regularized Newton Methods for X-ray Phase Contrast and General Imaging Problems

Like many other advanced imaging methods, x-ray phase contrast imaging and tomography require mathematical inversion of the observed data to obtain real-space information. While an accurate forward model describing the generally nonlinear image formation from a given object to the observations is often available, explicit inversion formulas are typically not known. Moreover, the measured data might be insufficient for stable image reconstruction, in which case it has to be complemented by suitable a priori information. In this work, regularized Newton methods are presented as a general framework for the solution of such ill-posed nonlinear imaging problems. For a proof of principle, the approach is applied to x-ray phase contrast imaging in the near-field propagation regime. Simultaneous recovery of the phase- and amplitude from a single near-field diffraction pattern without homogeneity constraints is demonstrated for the first time. The presented methods further permit all-at-once phase contrast tomography, i.e. simultaneous phase retrieval and tomographic inversion. We demonstrate the potential of this approach by three-dimensional imaging of a colloidal crystal at 95 nm isotropic resolution.Comment: (C)2016 Optical Society of America. One print or electronic copy may be made for personal use only. Systematic reproduction and distribution, duplication of any material in this paper for a fee or for commercial purposes, or modifications of the content of this paper are prohibite

Optimization Methods for Inverse Problems

Optimization plays an important role in solving many inverse problems. Indeed, the task of inversion often either involves or is fully cast as a solution of an optimization problem. In this light, the mere non-linear, non-convex, and large-scale nature of many of these inversions gives rise to some very challenging optimization problems. The inverse problem community has long been developing various techniques for solving such optimization tasks. However, other, seemingly disjoint communities, such as that of machine learning, have developed, almost in parallel, interesting alternative methods which might have stayed under the radar of the inverse problem community. In this survey, we aim to change that. In doing so, we first discuss current state-of-the-art optimization methods widely used in inverse problems. We then survey recent related advances in addressing similar challenges in problems faced by the machine learning community, and discuss their potential advantages for solving inverse problems. By highlighting the similarities among the optimization challenges faced by the inverse problem and the machine learning communities, we hope that this survey can serve as a bridge in bringing together these two communities and encourage cross fertilization of ideas.Comment: 13 page