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

A Spectral CT Method to Directly Estimate Basis Material Maps From Experimental Photon-Counting Data

The proposed spectral CT method solves the constrained one-step spectral CT reconstruction (cOSSCIR) optimization problem to estimate basis material maps while modeling the nonlinear X-ray detection process and enforcing convex constraints on the basis map images. In order to apply the optimization-based reconstruction approach to experimental data, the presented method empirically estimates the effective energy-window spectra using a calibration procedure. The amplitudes of the estimated spectra were further optimized as part of the reconstruction process to reduce ring artifacts. A validation approach was developed to select constraint parameters. The proposed spectral CT method was evaluated through simulations and experiments with a photon-counting detector. Basis material map images were successfully reconstructed using the presented empirical spectral modeling and cOSSCIR optimization approach. In simulations, the cOSSCIR approach accurately reconstructed the basis map images

Iterative CT reconstruction using shearlet-based regularization

In computerized tomography, it is important to reduce the image noise without increasing the acquisition dose. Extensive research has been done into total variation minimization for image denoising and sparse-view reconstruction. However, TV minimization methods show superior denoising performance for simple images (with little texture), but result in texture information loss when applied to more complex images. Since in medical imaging, we are often confronted with textured images, it might not be beneficial to use TV. Our objective is to find a regularization term outperforming TV for sparse-view reconstruction and image denoising in general. A recent efficient solver was developed for convex problems, based on a split-Bregman approach, able to incorporate regularization terms different from TV. In this work, a proof-of-concept study demonstrates the usage of the discrete shearlet transform as a sparsifying transform within this solver for CT reconstructions. In particular, the regularization term is the 1-norm of the shearlet coefficients. We compared our newly developed shearlet approach to traditional TV on both sparse-view and on low-count simulated and measured preclinical data. Shearlet-based regularization does not outperform TV-based regularization for all datasets. Reconstructed images exhibit small aliasing artifacts in sparse-view reconstruction problems, but show no staircasing effect. This results in a slightly higher resolution than with TV-based regularization

Maximum-likelihood absorption tomography

Maximum-likelihood methods are applied to the problem of absorption tomography. The reconstruction is done with the help of an iterative algorithm. We show how the statistics of the illuminating beam can be incorporated into the reconstruction. The proposed reconstruction method can be considered as a useful alternative in the extreme cases where the standard ill-posed direct-inversion methods fail.Comment: 7 pages, 5 figure

A virtual world of paleontology

Computer-aided visualization and analysis of fossils has revolutionized the study of extinct organisms. Novel techniques allow fossils to be characterized in three dimensions and in unprecedented detail. This has enabled paleontologists to gain important insights into their anatomy, development, and preservation. New protocols allow more objective reconstructions of fossil organisms, including soft tissues, from incomplete remains. The resulting digital reconstructions can be used in functional analyses, rigorously testing long-standing hypotheses regarding the paleobiology of extinct organisms. These approaches are transforming our understanding of long-studied fossil groups, and of the narratives of organismal and ecological evolution that have been built upon them