GENFIRE: A generalized Fourier iterative reconstruction algorithm for high-resolution 3D imaging

Tomography has made a radical impact on diverse fields ranging from the study of 3D atomic arrangements in matter to the study of human health in medicine. Despite its very diverse applications, the core of tomography remains the same, that is, a mathematical method must be implemented to reconstruct the 3D structure of an object from a number of 2D projections. In many scientific applications, however, the number of projections that can be measured is limited due to geometric constraints, tolerable radiation dose and/or acquisition speed. Thus it becomes an important problem to obtain the best-possible reconstruction from a limited number of projections. Here, we present the mathematical implementation of a tomographic algorithm, termed GENeralized Fourier Iterative REconstruction (GENFIRE). By iterating between real and reciprocal space, GENFIRE searches for a global solution that is concurrently consistent with the measured data and general physical constraints. The algorithm requires minimal human intervention and also incorporates angular refinement to reduce the tilt angle error. We demonstrate that GENFIRE can produce superior results relative to several other popular tomographic reconstruction techniques by numerical simulations, and by experimentally by reconstructing the 3D structure of a porous material and a frozen-hydrated marine cyanobacterium. Equipped with a graphical user interface, GENFIRE is freely available from our website and is expected to find broad applications across different disciplines.Comment: 18 pages, 6 figure

Overviews of Optimization Techniques for Geometric Estimation

We summarize techniques for optimal geometric estimation from noisy observations for computer vision applications. We first discuss the interpretation of optimality and point out that geometric estimation is different from the standard statistical estimation. We also describe our noise modeling and a theoretical accuracy limit called the KCR lower bound. Then, we formulate estimation techniques based on minimization of a given cost function: least squares (LS), maximum likelihood (ML), which includes reprojection error minimization as a special case, and Sampson error minimization. We describe bundle adjustment and the FNS scheme for numerically solving them and the hyperaccurate correction that improves the accuracy of ML. Next, we formulate estimation techniques not based on minimization of any cost function: iterative reweight, renormalization, and hyper-renormalization. Finally, we show numerical examples to demonstrate that hyper-renormalization has higher accuracy than ML, which has widely been regarded as the most accurate method of all. We conclude that hyper-renormalization is robust to noise and currently is the best method

Sparse MRI and CT Reconstruction

Sparse signal reconstruction is of the utmost importance for efficient medical imaging, conducting accurate screening for security and inspection, and for non-destructive testing. The sparsity of the signal is dictated by either feasibility, or the cost and the screening time constraints of the system. In this work, two major sparse signal reconstruction systems such as compressed sensing magnetic resonance imaging (MRI) and sparse-view computed tomography (CT) are investigated. For medical CT, a limited number of views (sparse-view) is an option for whether reducing the amount of ionizing radiation or the screening time and the cost of the procedure. In applications such as non-destructive testing or inspection of large objects, like a cargo container, one angular view can take up to a few minutes for only one slice. On the other hand, some views can be unavailable due to the configuration of the system. A problem of data sufficiency and on how to estimate a tomographic image when the projection data are not ideally sufficient for precise reconstruction is one of two major objectives of this work. Three CT reconstruction methods are proposed: algebraic iterative reconstruction-reprojection (AIRR), sparse-view CT reconstruction based on curvelet and total variation regularization (CTV), and sparse-view CT reconstruction based on nonconvex L1-L2 regularization. The experimental results confirm a high performance based on subjective and objective quality metrics. Additionally, sparse-view neutron-photon tomography is studied based on Monte-Carlo modelling to demonstrate shape reconstruction, material discrimination and visualization based on the proposed 3D object reconstruction method and material discrimination signatures. One of the methods for efficient acquisition of multidimensional signals is the compressed sensing (CS). A significantly low number of measurements can be obtained in different ways, and one is undersampling, that is sampling below the Shannon-Nyquist limit. Magnetic resonance imaging (MRI) suffers inherently from its slow data acquisition. The compressed sensing MRI (CSMRI) offers significant scan time reduction with advantages for patients and health care economics. In this work, three frameworks are proposed and evaluated, i.e., CSMRI based on curvelet transform and total generalized variation (CT-TGV), CSMRI using curvelet sparsity and nonlocal total variation: CS-NLTV, CSMRI that explores shearlet sparsity and nonlocal total variation: SS-NLTV. The proposed methods are evaluated experimentally and compared to the previously reported state-of-the-art methods. Results demonstrate a significant improvement of image reconstruction quality on different medical MRI datasets

Wavelet transforms and their applications to MHD and plasma turbulence: a review

Wavelet analysis and compression tools are reviewed and different applications to study MHD and plasma turbulence are presented. We introduce the continuous and the orthogonal wavelet transform and detail several statistical diagnostics based on the wavelet coefficients. We then show how to extract coherent structures out of fully developed turbulent flows using wavelet-based denoising. Finally some multiscale numerical simulation schemes using wavelets are described. Several examples for analyzing, compressing and computing one, two and three dimensional turbulent MHD or plasma flows are presented.Comment: Journal of Plasma Physics, 201

A comparative study of limitedâ angle coneâ beam reconstruction methods for breast tomosynthesis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134781/1/mp7543.pd

Doctor of Philosophy

dissertationX-ray computed tomography (CT) is a widely popular medical imaging technique that allows for viewing of in vivo anatomy and physiology. In order to produce high-quality images and provide reliable treatment, CT imaging requires the precise knowledge of t