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Numerous dual-energy CT (DECT) techniques have been developed in the past few decades. Dual-energy CT (DECT) statistical iterative reconstruction (SIR) has demonstrated its potential for reducing noise and increasing accuracy. Our lab proposed a joint statistical DECT algorithm for stopping power estimation and showed that it outperforms competing image-based material-decomposition methods. However, due to its slow convergence and the high computational cost of projections, the elapsed time of 3D DECT SIR is often not clinically acceptable. Therefore, to improve its convergence, we have embedded DECT SIR into a deep learning model-based unrolled network for 3D DECT reconstruction (MB-DECTNet) that can be trained in an end-to-end fashion. This deep learning-based method is trained to learn the shortcuts between the initial conditions and the stationary points of iterative algorithms while preserving the unbiased estimation property of model-based algorithms. MB-DECTNet is formed by stacking multiple update blocks, each of which consists of a data consistency layer (DC) and a spatial mixer layer, where the spatial mixer layer is the shrunken U-Net, and the DC layer is a one-step update of an arbitrary traditional iterative method. Although the proposed network can be combined with numerous iterative DECT algorithms, we demonstrate its performance with the dual-energy alternating minimization (DEAM). The qualitative result shows that MB-DECTNet with DEAM significantly reduces noise while increasing the resolution of the test image. The quantitative result shows that MB-DECTNet has the potential to estimate attenuation coefficients accurately as traditional statistical algorithms but with a much lower computational cost.

CT images have been used to generate radiation therapy treatment plans for more than two decades. Dual-energy CT (DECT) has shown high accuracy in estimating electronic density or proton stopping-power maps used in treatment planning. However, the presence of metal implants introduces severe streaking artifacts in the reconstructed images, affecting the diagnostic accuracy and treatment performance. In order to reduce the metal artifacts in DECT, we introduce a metal-artifact reduction scheme for iterative DECT algorithms. An estimate is substituted for the corrupt data in each iteration. We utilize normalized metal-artifact reduction (NMAR) composed with image-domain decomposition to initialize the algorithm and speed up the convergence. A fully 3D joint statistical DECT algorithm, dual-energy alternating minimization (DEAM), with the proposed scheme is tested on experimental and clinical helical data acquired on a Philips Brilliance Big Bore scanner. We compared DEAM with the proposed method to the original DEAM and vendor reconstructions with and without metal-artifact reduction for orthopedic implants (O-MAR). The visualization and quantitative analysis show that DEAM with the proposed method has the best performance in reducing streaking artifacts caused by metallic objects.

Dual-energy CT (DECT) has been widely investigated to generate more informative and more accurate images in the past decades. For example, Dual-Energy Alternating Minimization (DEAM) algorithm achieves sub-percentage uncertainty in estimating proton stopping-power mappings from experimental 3-mm collimated phantom data. However, elapsed time of iterative DECT algorithms is not clinically acceptable, due to their low convergence rate and the tremendous geometry of modern helical CT scanners. A CNN-based initialization method is introduced to reduce the computational time of iterative DECT algorithms. DEAM is used as an example of iterative DECT algorithms in this work. The simulation results show that our method generates denoised images with greatly improved estimation accuracy for adipose, tonsils, and muscle tissue. Also, it reduces elapsed time by approximately 5-fold for DEAM to reach the same objective function value for both simulated and real data.

The single-scatter approximation is fundamental in many tomographic imaging problems including x-ray scatter imaging and optical scatter imaging for certain media. In all cases, noisy measurements are affected by both local scatter events and nonlocal attenuation. Prior works focus on reconstructing one of two images: scatter density or total attenuation. However, both images are media specific and useful for object identification. Nonlocal effects of the attenuation image on the data are summarized by the broken ray transform (BRT). While analytic inversion formulas exist, poor conditioning of the inverse problem is only exacerbated by noisy measurements and sampling errors. This has motivated interest in the related star transforms incorporating BRT measurements from multiple source-detector pairs. However, all analytic methods operate on the log of the data. For media comprising regions with no scatter a new approach is required. We are the first to present a joint estimation algorithm based on Poisson data models for a single-scatter measurement geometry. Monotonic reduction of the log-likelihood function is guaranteed for our iterative algorithm while alternating image updates. We also present a fast algorithm for computing the discrete BRT forward operator. Our generalized approach can incorporate both transmission and scatter measurements from multiple source-detector pairs. Transmission measurements resolve low-frequency ambiguity in the joint image estimation problem, while multiple scatter measurements resolve the attenuation image. The benefits of joint estimation, over single-image estimation, vary with problem scaling. Our results quantify these benefits and should inform design of future acquisition systems., Comment: 13 pages, 5 figures

Non-smooth regularization is widely used in image reconstruction to eliminate the noise while preserving subtle image structures. In this work, we investigate the use of proximal Newton (PN) method to solve an optimization problem with a smooth data-fidelity term and total variation (TV) regularization arising from image reconstruction applications. Specifically, we consider a nonlinear Poisson-modeled single-energy X-ray computed tomography reconstruction problem with the data-fidelity term given by the I-divergence. The PN algorithm is compared to state-of-the-art first-order proximal algorithms, such as the well-established fast iterative shrinkage and thresholding algorithm (FISTA), both in terms of the number of iterations and time to solutions. We discuss the key factors that influence the performance of PN, including the strength of regularization, the stopping criterion for both sub-problem and main-problem, and the use of exact or approximated Hessian operators.

The significance of the broken ray transform (BRT) is due to its occurrence in a number of modalities spanning optical, x-ray, and nuclear imaging. When data are indexed by the scatter location, the BRT is both linear and shift invariant. Analyzing the BRT as a linear system provides a new perspective on the inverse problem. In this framework we contrast prior inversion formulas and identify numerical issues. This has practical benefits as well. We clarify the extent of data required for global reconstruction by decomposing the BRT as a linear combination of cone beam transforms. Additionally we leverage the two dimensional Fourier transform to derive new inversion formulas that are computationally efficient for arbitrary scatter angles. Results of numerical simulations are presented.

In the classic sparsity-driven problems, the fundamental L-1 penalty method has been shown to have good performance in reconstructing signals for a wide range of problems. However this performance relies on a good choice of penalty weight which is often found from empirical experiments. We propose an algorithm called the Laplacian variational automatic relevance determination (Lap-VARD) that takes this penalty weight as a parameter of a prior Laplace distribution. Optimization of this parameter using an automatic relevance determination framework results in a balance between the sparsity and accuracy of signal reconstruction. Our algorithm is implemented in a transmission tomography model with sparsity constraint in wavelet domain., Comment: 5 pages 2 figures

Image reconstruction in X-ray transmission tomography has been an important research field for decades. In light of data volume increasing faster than processor speeds, one needs accelerated iterative algorithms to solve the optimization problem in the X-ray CT application. Incremental methods, in which a subset of data is being used at each iteration to accelerate the computations, have been getting more popular lately in the machine learning and mathematical optimization fields. The most popular member of this family of algorithms in the X-ray CT field is ordered-subsets. Even though it performs well in earlier iterations, the lack of convergence in later iterations is a known phenomenon. In this paper, we propose two incremental methods that use Jensen surrogates for the X-ray CT application, one stochastic and one ordered-subsets type. Using measured data, we show that the stochastic variant we propose outperforms other algorithms, including the gradient descent counterparts.

In x-ray coherent scatter tomography, tomographic measurements of the forward scatter distribution are used to infer scatter densities within a volume. A radiopaque 2D pattern placed between the object and the detector array enables the disambiguation between different scatter events. The use of a fan beam source illumination to speed up data acquisition relative to a pencil beam presents computational challenges. To facilitate the use of iterative algorithms based on a penalized Poisson log-likelihood function, efficient computational implementation of the forward and backward models are needed. Our proposed implementation exploits physical symmetries and structural properties of the system and suggests a joint system-algorithm design, where the system design choices are influenced by computational considerations, and in turn lead to reduced reconstruction time. Computational-time speedups of approximately 146 and 32 are achieved in the computation of the forward and backward models, respectively. Results validating the forward model and reconstruction algorithm are presented on simulated analytic and Monte Carlo data., Comment: This paper has been submitted to IEEE Transactions on Computational Imaging for consideration. 18 pages, 6 figures

We consider X-ray coherent scatter imaging, where the goal is to reconstruct momentum transfer profiles (spectral distributions) at each spatial location from multiplexed measurements of scatter. Each material is characterized by a unique momentum transfer profile (MTP) which can be used to discriminate between different materials. We propose an iterative image reconstruction algorithm based on a Poisson noise model that can account for photon-limited measurements as well as various second order statistics of the data. To improve image quality, previous approaches use edge-preserving regularizers to promote piecewise constancy of the image in the spatial domain while treating each spectral bin separately. Instead, we propose spectrally grouped regularization that promotes piecewise constant images along the spatial directions but also ensures that the MTPs of neighboring spatial bins are similar, if they contain the same material. We demonstrate that this group regularization results in improvement of both spectral and spatial image quality. We pursue an optimization transfer approach where convex decompositions are used to lift the problem such that all hyper-voxels can be updated in parallel and in closed-form. The group penalty introduces a challenge since it is not directly amendable to these decompositions. We use the alternating directions method of multipliers (ADMM) to replace the original problem with an equivalent sequence of sub-problems that are amendable to convex decompositions, leading to a highly parallel algorithm. We demonstrate the performance on real data., Comment: Presented at IEEE Nuclear Science Symposium and Medical Imaging Conference (NSS/MIC) 2015. 4 pages, 2 figures

Three-dimensional x-ray CT image reconstruction in baggage scanning in security applications is an important research field. The variety of materials to be reconstructed is broader than medical x-ray imaging. Presence of high attenuating materials such as metal may cause artifacts if analytical reconstruction methods are used. Statistical modeling and the resultant iterative algorithms are known to reduce these artifacts and present good quantitative accuracy in estimates of linear attenuation coefficients. However, iterative algorithms may require computations in order to achieve quantitatively accurate results. For the case of baggage scanning, in order to provide fast accurate inspection throughput, they must be accelerated drastically. There are many approaches proposed in the literature to increase speed of convergence. This paper presents a new method that estimates the wavelet coefficients of the images in the discrete wavelet transform domain instead of the image space itself. Initially, surrogate functions are created around approximation coefficients only. As the iterations proceed, the wavelet tree on which the updates are made is expanded based on a criterion and detail coefficients at each level are updated and the tree is expanded this way. For example, in the smooth regions of the image the detail coefficients are not updated while the coefficients that represent the high-frequency component around edges are being updated, thus saving time by focusing computations where they are needed. This approach is implemented on real data from a SureScan (TM) x1000 Explosive Detection System and compared to straightforward implementation of the unregularized alternating minimization of O'Sullivan and Benac [1].

New imaging techniques are in great demand for investigating underground plant roots systems which play an important role in crop production. Compared with other non-destructive imaging modalities, PET can image plant roots in natural soil and produce dynamic 3D functional images which reveal the temporal dynamics of plant-environment interactions. In this study, we combined PET with optical projection tomography (OPT) to evaluate its potential for plant root phenotyping. We used a dedicated high resolution plant PET imager that has a 14 cm transaxial and 10 cm axial field of views, and multi-bed imaging capability. The image resolution is around 1.25 mm using ML-EM reconstruction algorithm. B73 inbred maize seeds were germinated and then grown in a sealed jar with transparent gel-based media. PET scanning started on the day when the first green leaf appeared, and was carried out once a day for 5 days. Each morning, around 10 mCi of 11CO2 was administrated into a custom built plant labeling chamber. After 10 minutes, residual activity was flushed out with fresh air before a 2-h PET scan started. For the OPT imaging, the jar was placed inside an acrylic cubic container filled with water, illuminated with a uniform surface light source, and imaged by a DSLR camera from 72 angles to acquire optical images for OPT reconstruction. The same plant was imaged 3 times a day by the OPT system. Plant roots growth is measured from the optical images. Co-registered PET and optical images indicate that most of the hot spots appeared in later time points of the PET images correspond to the most actively growing root tips. The strong linear correlation between 11C allocation at root tips measured by PET and eventual root growth measured by OPT suggests that we can use PET as a phenotyping tool to measure how a plant makes subterranean carbon allocation decisions in different environmental scenarios., Comment: 5 pages, 10 figures

We propose a globally convergent alternating minimization (AM) algorithm for image reconstruction in transmission tomography, which extends automatic relevance determination (ARD) to Poisson noise models with Beer's law. The algorithm promotes solutions that are sparse in the pixel/voxel-differences domain by introducing additional latent variables, one for each pixel/voxel, and then learning these variables from the data using a hierarchical Bayesian model. Importantly, the proposed AM algorithm is free of any tuning parameters with image quality comparable to standard penalized likelihood methods. Our algorithm exploits optimization transfer principles which reduce the problem into parallel 1D optimization tasks (one for each pixel/voxel), making the algorithm feasible for large-scale problems. This approach considerably reduces the computational bottleneck of ARD associated with the posterior variances. Positivity constraints inherent in transmission tomography problems are also enforced. We demonstrate the performance of the proposed algorithm for x-ray computed tomography using synthetic and real-world datasets. The algorithm is shown to have much better performance than prior ARD algorithms based on approximate Gaussian noise models, even for high photon flux., Comment: Changes relative to the previous version: (1) Minor changes in abstract; (2) The results for simulated data contain another comparison to a previous method; (3) Corrected Eq. (6.3); (4) Additional discussions in Secs.1,7,8

PET provides in vivo molecular and functional imaging capability that is crucial to studying the interaction of plant with changing environment at the whole-plant level. We have developed a dedicated plant PET imager that features high spatial resolution, housed in a fully controlled environment provided by a plant growth chamber (PGC). The system currently contains two types of detector modules: 84 microPET R4 block detectors with 2.2 mm crystals to provide a large detecting area; and 32 Inveon block detectors with 1.5 mm crystals to provide higher spatial resolution. Outputs of the four microPET block detectors in a modular housing are concatenated by a custom printed circuit board to match the output characteristics of an Inveon detector. All the detectors are read out by QuickSilver electronics. The detector modules are configured to full rings with a 15 cm diameter trans-axial field of view (FOV) for dynamic tomographic imaging of small plants. Potentially, the Inveon detectors can be reconfigured to quarter-rings to get a 25 cm FOV using step-and-shoot motion. The imager contains 2 linear stages to position detectors at different heights for multi-bed scanning, and 2 rotation stages to collect coincidence events from all angles. The PET system has been built and integrated into the PGC. The system has a typical energy resolution of 15% for Inveon blocks and 24% for R4 blocks; timing resolution of 1.8 ns; and sensitivity of 1.3%,1.4%,3.0% measured at center of FOV, 5 cm off to R4 half-ring and 5 cm off to Inveon half-ring, respectively(with a 350-650 KeV energy and 3.1 ns timing window). System spatial resolution is similar to that of commercial microPET sytems, with 1.25 mm rod sources in the micro-Derenzo phantom resolved using ML-EM algorithm. Preliminary imaging experiments using different plants labeled with 11C-CO2 produced high-quality dynamic PET images., Comment: 19 pages

In this paper, designs and analyses of compressive recognition systems are discussed, and also a method of establishing a dual connection between designs of good communication codes and designs of recognition systems is presented. Pattern recognition systems based on compressed patterns and compressed sensor measurements can be designed using low-density matrices. We examine truncation encoding where a subset of the patterns and measurements are stored perfectly while the rest is discarded. We also examine the use of LDPC parity check matrices for compressing measurements and patterns. We show how more general ensembles of good linear codes can be used as the basis for pattern recognition system design, yielding system design strategies for more general noise models., Comment: Submitted and accepted to ISIT 2007

Biological and machine pattern recognition systems face a common challenge: Given sensory data about an unknown object, classify the object by comparing the sensory data with a library of internal representations stored in memory. In many cases of interest, the number of patterns to be discriminated and the richness of the raw data force recognition systems to internally represent memory and sensory information in a compressed format. However, these representations must preserve enough information to accommodate the variability and complexity of the environment, or else recognition will be unreliable. Thus, there is an intrinsic tradeoff between the amount of resources devoted to data representation and the complexity of the environment in which a recognition system may reliably operate. In this paper we describe a general mathematical model for pattern recognition systems subject to resource constraints, and show how the aforementioned resource-complexity tradeoff can be characterized in terms of three rates related to number of bits available for representing memory and sensory data, and the number of patterns populating a given statistical environment. We prove single-letter information theoretic bounds governing the achievable rates, and illustrate the theory by analyzing the elementary cases where the pattern data is either binary or Gaussian.