Four-dimensional tomographic reconstruction by time domain decomposition

Since the beginnings of tomography, the requirement that the sample does not change during the acquisition of one tomographic rotation is unchanged. We derived and successfully implemented a tomographic reconstruction method which relaxes this decades-old requirement of static samples. In the presented method, dynamic tomographic data sets are decomposed in the temporal domain using basis functions and deploying an L1 regularization technique where the penalty factor is taken for spatial and temporal derivatives. We implemented the iterative algorithm for solving the regularization problem on modern GPU systems to demonstrate its practical use

3D particle tracking velocimetry using dynamic discrete tomography

Particle tracking velocimetry in 3D is becoming an increasingly important imaging tool in the study of fluid dynamics, combustion as well as plasmas. We introduce a dynamic discrete tomography algorithm for reconstructing particle trajectories from projections. The algorithm is efficient for data from two projection directions and exact in the sense that it finds a solution consistent with the experimental data. Non-uniqueness of solutions can be detected and solutions can be tracked individually

Non-convex image reconstruction via Expectation Propagation

Tomographic image reconstruction can be mapped to a problem of finding solutions to a large system of linear equations which maximize a function that includes \textit{a priori} knowledge regarding features of typical images such as smoothness or sharpness. This maximization can be performed with standard local optimization tools when the function is concave, but it is generally intractable for realistic priors, which are non-concave. We introduce a new method to reconstruct images obtained from Radon projections by using Expectation Propagation, which allows us to reframe the problem from an Bayesian inference perspective. We show, by means of extensive simulations, that, compared to state-of-the-art algorithms for this task, Expectation Propagation paired with very simple but non log-concave priors, is often able to reconstruct images up to a smaller error while using a lower amount of information per pixel. We provide estimates for the critical rate of information per pixel above which recovery is error-free by means of simulations on ensembles of phantom and real images.Comment: 12 pages, 6 figure

Geometric reconstruction methods for electron tomography

Electron tomography is becoming an increasingly important tool in materials science for studying the three-dimensional morphologies and chemical compositions of nanostructures. The image quality obtained by many current algorithms is seriously affected by the problems of missing wedge artefacts and nonlinear projection intensities due to diffraction effects. The former refers to the fact that data cannot be acquired over the full $180^\circ$ tilt range; the latter implies that for some orientations, crystalline structures can show strong contrast changes. To overcome these problems we introduce and discuss several algorithms from the mathematical fields of geometric and discrete tomography. The algorithms incorporate geometric prior knowledge (mainly convexity and homogeneity), which also in principle considerably reduces the number of tilt angles required. Results are discussed for the reconstruction of an InAs nanowire

Compressed Sensing Based Reconstruction Algorithm for X-ray Dose Reduction in Synchrotron Source Micro Computed Tomography

Synchrotron computed tomography requires a large number of angular projections to reconstruct tomographic images with high resolution for detailed and accurate diagnosis. However, this exposes the specimen to a large amount of x-ray radiation. Furthermore, this increases scan time and, consequently, the likelihood of involuntary specimen movements. One approach for decreasing the total scan time and radiation dose is to reduce the number of projection views needed to reconstruct the images. However, the aliasing artifacts appearing in the image due to the reduced number of projection data, visibly degrade the image quality. According to the compressed sensing theory, a signal can be accurately reconstructed from highly undersampled data by solving an optimization problem, provided that the signal can be sparsely represented in a predefined transform domain. Therefore, this thesis is mainly concerned with designing compressed sensing-based reconstruction algorithms to suppress aliasing artifacts while preserving spatial resolution in the resulting reconstructed image. First, the reduced-view synchrotron computed tomography reconstruction is formulated as a total variation regularized compressed sensing problem. The Douglas-Rachford Splitting and the randomized Kaczmarz methods are utilized to solve the optimization problem of the compressed sensing formulation. In contrast with the first part, where consistent simulated projection data are generated for image reconstruction, the reduced-view inconsistent real ex-vivo synchrotron absorption contrast micro computed tomography bone data are used in the second part. A gradient regularized compressed sensing problem is formulated, and the Douglas-Rachford Splitting and the preconditioned conjugate gradient methods are utilized to solve the optimization problem of the compressed sensing formulation. The wavelet image denoising algorithm is used as the post-processing algorithm to attenuate the unwanted staircase artifact generated by the reconstruction algorithm. Finally, a noisy and highly reduced-view inconsistent real in-vivo synchrotron phase-contrast computed tomography bone data are used for image reconstruction. A combination of prior image constrained compressed sensing framework, and the wavelet regularization is formulated, and the Douglas-Rachford Splitting and the preconditioned conjugate gradient methods are utilized to solve the optimization problem of the compressed sensing formulation. The prior image constrained compressed sensing framework takes advantage of the prior image to promote the sparsity of the target image. It may lead to an unwanted staircase artifact when applied to noisy and texture images, so the wavelet regularization is used to attenuate the unwanted staircase artifact generated by the prior image constrained compressed sensing reconstruction algorithm. The visual and quantitative performance assessments with the reduced-view simulated and real computed tomography data from canine prostate tissue, rat forelimb, and femoral cortical bone samples, show that the proposed algorithms have fewer artifacts and reconstruction errors than other conventional reconstruction algorithms at the same x-ray dose

Real-time volumetric image reconstruction and 3D tumor localization based on a single x-ray projection image for lung cancer radiotherapy

Purpose: To develop an algorithm for real-time volumetric image reconstruction and 3D tumor localization based on a single x-ray projection image for lung cancer radiotherapy. Methods: Given a set of volumetric images of a patient at N breathing phases as the training data, we perform deformable image registration between a reference phase and the other N-1 phases, resulting in N-1 deformation vector fields (DVFs). These DVFs can be represented efficiently by a few eigenvectors and coefficients obtained from principal component analysis (PCA). By varying the PCA coefficients, we can generate new DVFs, which, when applied on the reference image, lead to new volumetric images. We then can reconstruct a volumetric image from a single projection image by optimizing the PCA coefficients such that its computed projection matches the measured one. The 3D location of the tumor can be derived by applying the inverted DVF on its position in the reference image. Our algorithm was implemented on graphics processing units (GPUs) to achieve real-time efficiency. We generated the training data using a realistic and dynamic mathematical phantom with 10 breathing phases. The testing data were 360 cone beam projections corresponding to one gantry rotation, simulated using the same phantom with a 50% increase in breathing amplitude. Results: The average relative image intensity error of the reconstructed volumetric images is 6.9% +/- 2.4%. The average 3D tumor localization error is 0.8 mm +/- 0.5 mm. On an NVIDIA Tesla C1060 GPU card, the average computation time for reconstructing a volumetric image from each projection is 0.24 seconds (range: 0.17 and 0.35 seconds). Conclusions: We have shown the feasibility of reconstructing volumetric images and localizing tumor positions in 3D in near real-time from a single x-ray image.Comment: 8 pages, 3 figures, submitted to Medical Physics Lette

Joint Image Reconstruction and Segmentation Using the Potts Model

We propose a new algorithmic approach to the non-smooth and non-convex Potts problem (also called piecewise-constant Mumford-Shah problem) for inverse imaging problems. We derive a suitable splitting into specific subproblems that can all be solved efficiently. Our method does not require a priori knowledge on the gray levels nor on the number of segments of the reconstruction. Further, it avoids anisotropic artifacts such as geometric staircasing. We demonstrate the suitability of our method for joint image reconstruction and segmentation. We focus on Radon data, where we in particular consider limited data situations. For instance, our method is able to recover all segments of the Shepp-Logan phantom from $7$ angular views only. We illustrate the practical applicability on a real PET dataset. As further applications, we consider spherical Radon data as well as blurred data

Iterative CT reconstruction from few projections for the nondestructive post irradiation examination of nuclear fuel assemblies

The core components (e.g. fuel assemblies, spacer grids, control rods) of the nuclear reactors encounter harsh environment due to high temperature, physical stress, and a tremendous level of radiation. The integrity of these elements is crucial for safe operation of the nuclear power plants. The Post Irradiation Examination (PIE) can reveal information about the integrity of the elements during normal operations and off‐normal events. Computed tomography (CT) is a tool for evaluating the structural integrity of elements non-destructively. CT requires many projections to be acquired from different view angles after which a mathematical algorithm is adopted for reconstruction. Obtaining many projections is laborious and expensive in nuclear industries. Reconstructions from a small number of projections are explored to achieve faster and cost-efficient PIE. Classical reconstruction algorithms (e.g. filtered back projection) cannot offer stable reconstructions from few projections and create severe streaking artifacts. In this thesis, conventional algorithms are reviewed, and new algorithms are developed for reconstructions of the nuclear fuel assemblies using few projections. CT reconstruction from few projections falls into two categories: the sparse-view CT and the limited-angle CT or tomosynthesis. Iterative reconstruction algorithms are developed for both cases in the field of compressed sensing (CS). The performance of the algorithms is assessed using simulated projections and validated through real projections. The thesis also describes the systematic strategy towards establishing the conditions of reconstructions and finds the optimal imaging parameters for reconstructions of the fuel assemblies from few projections. --Abstract, page iii

Numerical methods for coupled reconstruction and registration in digital breast tomosynthesis.

Digital Breast Tomosynthesis (DBT) provides an insight into the fine details of normal fibroglandular tissues and abnormal lesions by reconstructing a pseudo-3D image of the breast. In this respect, DBT overcomes a major limitation of conventional X-ray mam- mography by reducing the confounding effects caused by the superposition of breast tissue. In a breast cancer screening or diagnostic context, a radiologist is interested in detecting change, which might be indicative of malignant disease. To help automate this task image registration is required to establish spatial correspondence between time points. Typically, images, such as MRI or CT, are first reconstructed and then registered. This approach can be effective if reconstructing using a complete set of data. However, for ill-posed, limited-angle problems such as DBT, estimating the deformation is com- plicated by the significant artefacts associated with the reconstruction, leading to severe inaccuracies in the registration. This paper presents a mathematical framework, which couples the two tasks and jointly estimates both image intensities and the parameters of a transformation. Under this framework, we compare an iterative method and a simultaneous method, both of which tackle the problem of comparing DBT data by combining reconstruction of a pair of temporal volumes with their registration. We evaluate our methods using various computational digital phantoms, uncom- pressed breast MR images, and in-vivo DBT simulations. Firstly, we compare both iter- ative and simultaneous methods to the conventional, sequential method using an affine transformation model. We show that jointly estimating image intensities and parametric transformations gives superior results with respect to reconstruction fidelity and regis- tration accuracy. Also, we incorporate a non-rigid B-spline transformation model into our simultaneous method. The results demonstrate a visually plausible recovery of the deformation with preservation of the reconstruction fidelity