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This is my dissertation for my PhD in Applied Mathematics at the University of Arizona. My thesis is about deblurring images in the Bayesian framework with spatially varying hyperparameters and mixed regularization types.
Dissertation defense presentation dealing with deblurring Cygnus images.
Many scientific experiments such as those found in astronomy, geology, microbiology, and X-ray radiography require the use of high-energy instruments to capture images. Since blur and noise are inevitably present in any imaging system, the images must be \deblurred" to extract the full information content. Mathematically, image deblurring is an ill-posed inverse problem that requires regularization. The regularization, in turn, has a large effect on the deblurred image: different regularization strengths, and types, lead to drastically different reconstructions. Moreover, many images contain a mixture of smooth and sharp features which suggests the use of multi-regularization, i.e., varying the type of regularization (e.g. Tikhonov or total variation) across the image. We address these issues by formulating the image deblurring problem within a hierarchical Bayesian framework in which we spatially adapt the strength of the regularization and also vary the regularization type across the image. In this way, the image itself, along with corresponding regularization strength at each pixel, are described jointly by a posterior distribution which we can sample by Markov chain Monte Carlo (MCMC) methods. We illustrate our techniques on simplified test problems and apply them to high-energy X-ray images taken at the Nevada National Security Site. Numerical tests show that our new method is robustly applicable and increases the quality of the image reconstruction when compared to other (Bayesian) methods.
This is my dissertation.
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Presentation to be presented during the MSTS Science and Technology Work-in-Progress Seminar (Webex) scheduled for November 16, 2021.
Abstract We propose a regularization-based deblurring method that works efficiently for galaxy images. The spatial resolution of a ground-based telescope is generally limited by seeing conditions and is much worse than space-based telescopes. This circumstance has generated considerable research interest in the restoration of spatial resolution. Since image deblurring is a typical inverse problem and often ill-posed, solutions tend to be unstable. To obtain a stable solution, much research has adopted regularization-based methods for image deblurring, but the regularization term is not necessarily appropriate for galaxy images. Although galaxies have an exponential or Sérsic profile, the conventional regularization assumes the image profiles to behave linearly in space. The significant deviation between the assumption and real situations leads to blurring of the images and smoothing out the detailed structures. Clearly, regularization on logarithmic domain, i.e., magnitude domain, should provide a more appropriate assumption, which we explore in this study. We formulate a problem of deblurring galaxy images by an objective function with a Tikhonov regularization term on a magnitude domain. We introduce an iterative algorithm minimizing the objective function with a primal–dual splitting method. We investigate the feasibility of the proposed method using simulation and observation images. In the simulation, we blur galaxy images with a realistic point spread function and add both Gaussian and Poisson noise. For the evaluation with the observed images, we use galaxy images taken by the Subaru HSC-SSP. Both of these evaluations show that our method successfully recovers the spatial resolution of the deblurred images and significantly outperforms the conventional methods. The code is publicly available from the GitHub 〈https://github.com/kzmurata-astro/PSFdeconv_amag〉.
Deblurring is one of the most common linear inverse problems in imaging, and most methods for deblurring an image assume that the convolution kernel, the so-called point spread function (PSF), is known or attempt to reconstruct the PSF simultaneously with the image. For many experimental imaging systems, like high energy X-ray radiography systems, the PSF must be computed from calibration imagery. The associated inverse problem is large-scale, so, in order to compute meaningful uncertainties with the reconstruction, it is common to use hierarchical Bayesian models and Markov chain Monte Carlo methods for sampling from the posterior. Classical Gibbs samplers can suffer from long autocorrelation lengths in the Markov chain when the reconstructed quantity in the inverse problem is finely discretized, resulting in poor computational efficiency of the Markov chain. In this work we present partially collapsed Gibbs samplers for linear inverse problems that greatly decrease correlations in the Markov chain, thus increasing the computational efficiency of the algorithms, and we present the results of the enhanced samplers on the problem of reconstructing the point spread function for an X-ray imaging system at the U.S. Department of Energy's Nevada National Security Site.
Purpose: Deconvolution is a widely used tool in the field of image reconstruction algorithm when the linear imaging system has been blurred by the imperfect system transfer function. However, due to the nature of Gaussian-liked distribution for point spread function (PSF), the components with coherent high frequency in the image are hard to restored in most of the previous scanning imaging system, even the relatively accurate PSF is acquired. We propose a novel method for deconvolution of images which are obtained by using shape-modulated PSF. Methods: We use two different types of PSF - Gaussian shape and donut shape - to convolute the original image in order to simulate the process of scanning imaging. By employing deconvolution of the two images with corresponding given priors, the image quality of the deblurred images are compared. Then we find the critical size of the donut shape compared with the Gaussian shape which has similar deconvolution results. Through calculation of tightened focusing process using radially polarized beam, such size of donut is achievable under same conditions. Results: The effects of different relative size of donut and Gaussian shapes are investigated. When the full width at half maximum (FWHM) ratio of donut and Gaussian shape is set about 1.83, similar resolution results are obtained through our deconvolution method. Decreasing the size of donut will favor the deconvolution method. A mask with both amplitude and phase modulation is used to create a donut-shaped PSF compared with the non-modulated Gaussian PSF. Donut with size smaller than our critical value is obtained. Conclusion: The utility of donutshaped PSF are proved useful and achievable in the imaging and deconvolution processing, which is expected to have potential practical applications in high resolution imaging for biological samples.
We present a new multigrid preconditioner for the linear systems arising in the semismooth Newton method solution of certain control-constrained, quadratic distributed optimal control problems. Using a piecewise constant discretization of the control space, each semismooth Newton iteration essentially requires inverting a principal submatrix of the matrix entering the normal equations of the associated unconstrained optimal control problem, the rows (and columns) of the submatrix representing the constraints deemed inactive at the current iteration. Previously developed multigrid preconditioners for the aforementioned submatrices were based on constructing a sequence of conforming coarser spaces and proved to be of suboptimal quality for the class of problems considered. Instead, the multigrid preconditioner introduced in this work uses nonconforming coarse spaces, and it is shown that, under reasonable geometric assumptions on the constraints that are deemed inactive, the preconditioner approximates the inverse of the desired submatrix to optimal order. The preconditioner is tested numerically on a classical elliptic-constrained optimal control problem and further on a constrained image-deblurring problem.
We report N\non-blind deblurring (NBD) is a modeling method of the image deblurring problem in computer vision, where the blurring kernel is known or can be externally estimated. In this paper, we attempt to solve a parametric NBD problem, inspired by the simultaneous acquisition of ptychography and fluorescent imaging (FI). Ptychography is an imaging method that favors larger probes, i.e. convolutional kernels, while FI relies on a small probe for high resolution. Also, the kernel can be solved during ptychographic reconstruction. With Ptycho-FI using the same larger kernel, we can perform NBD on the blurred fluorescent images to achieve high-resolution FI, and thus speed up the experiments. To this end, we design a deep latent space deformation network that is directly parameterized by the kernel. The network consists of three components: encoder, deformer, and decoder, where the deformer is specifically meant to rectify the latent space representations of blurred images to a standard latent space, regardless of the kernel. The deformation network is trained with a two-stage training scheme. We conduct extensive experiments to confirm that our parametric model can adapt to drastically different blurring kernels and perform robust deblurring.
Blind image deconvolution involves two key objectives: 1) latent image and 2) blur estimation. For latent image estimation, we propose a fast deconvolution algorithm, which uses an image prior of nondimensional Gaussianity measure to enforce sparsity and an undetermined boundary condition methodology to reduce boundary artifacts. For blur estimation, a linear inverse problem with normalization and nonnegative constraints must be solved. However, the normalization constraint is ignored in many blind image deblurring methods, mainly because it makes the problem less tractable. In this paper, we show that the normalization constraint can be very naturally incorporated into the estimation process by using a Dirichlet distribution to approximate the posterior distribution of the blur. Making use of variational Dirichlet approximation, we provide a blur posterior approximation that considers the uncertainty of the estimate and removes noise in the estimated kernel. Furthermore, experiments with synthetic and real data demonstrate that the proposed method is very competitive to the state-of-the-art blind image restoration methods.
This is a presentation for SIAM's (Society for Industrial and Applied Mathematics) conference on computational science and engineering. This presentation describes research on novel techniques to deblur images under a Bayesian framework. The title of the conference is SIAM Conference on Computational Science and Engineering (CSE21). This is a VIRTUAL conference; it was originally scheduled in Fort Worth, TX. The conference dates are March 1-5, 2021. The link to the conference's website is https://www.siam.org/conferences/cm/conference/cse21
Nonnegative Least Squares (NNLS) is a fundamental constrained optimization problem encountered in many applications such as image deblurring, signal processing, nonnegative matrix factorization, magnetic microscopy, and hyperspectral imaging. Active-set based methods are a common class of algorithms for solving NNLS which identify the optimal variable set of the NNLS solution. They do so by iteratively solving a series of unconstrained least squares problems, identifying which variables violate the nonnegativity constraints, and then swapping variables in/out of consideration until the optimal set of variables is found. Several variations improving upon this method exist in the literature. In this work, we propose an active-set swap heuristic which further improves upon existing active-set based methods for NNLS. Our optimizations are based upon adding multiple variables to the passive set within a threshold of the smallest gradient value and removing variables within a similar threshold of the closest boundary constraint. We leverage these optimizations to yield a Fast Active-Set Thresholding NNLS (FAST-NNLS) algorithm which significantly outperforms the existing state-of-the-art NNLS algorithms for a wide range of problems. Rigorous convergence guarantees are proven for the proposed method. We demonstrate the effectiveness of our proposed method on multiple synthetic datasets and two realworld text analysis applications. In doing so, we present the most comprehensive NNLS solver comparison in the literature to date.
Purpose: Proton imaging that uses a modulated proton beam and an intensity detector allows a relatively fast image acquisition compared to the imaging approach based on a trajectory tracking detector. In addition, it requires a relatively simple implementation in a conventional proton therapy equipment. The model of geometric straight ray assumed in conventional computed tomography (CT) image reconstruction is however challenged by multiple-Coulomb scattering and energy straggling in the proton imaging. Radiation dose to the patient is another important issue that has to be taken care of for practical applications. In this work, the authors have investigated iterative image reconstructions after a deconvolution of the sparsely view-sampled data to address these issues in proton CT. Methods: Proton projection images were acquired using the modulated proton beams and the EBT2 film as an intensity detector. Four electron-density cylinders representing normal soft tissues and bone were used as imaged object and scanned at 40 views that are equally separated over 360°. Digitized film images were converted to water-equivalent thickness by use of an empirically derived conversion curve. For improving the image quality, a deconvolution-based image deblurring with an empirically acquired point spread function was employed. They have implemented iterative image reconstruction algorithms such as adaptive steepest descent-projection onto convex sets (ASD-POCS), superiorization method–projection onto convex sets (SM-POCS), superiorization method–expectation maximization (SM-EM), and expectation maximization-total variation minimization (EM-TV). Performance of the four image reconstruction algorithms was analyzed and compared quantitatively via contrast-to-noise ratio (CNR) and root-mean-square-error (RMSE). Results: Objects of higher electron density have been reconstructed more accurately than those of lower density objects. The bone, for example, has been reconstructed within 1% error. EM-based algorithms produced an increased image noise and RMSE as the iteration reaches about 20, while the POCS-based algorithms showed a monotonic convergence with iterations. The ASD-POCS algorithm outperformed the others in terms of CNR, RMSE, and the accuracy of the reconstructed relative stopping power in the region of lung and soft tissues. Conclusions: The four iterative algorithms, i.e., ASD-POCS, SM-POCS, SM-EM, and EM-TV, have been developed and applied for proton CT image reconstruction. Although it still seems that the images need to be improved for practical applications to the treatment planning, proton CT imaging by use of the modulated beams in sparse-view sampling has demonstrated its feasibility.
Atmospheric aerosols, such as fog and smoke, degrade optical signals via the scattering and absorption of light, making it difficult to recover information from the surrounding environment. Here, we present a technique that measures the angular distribution of light in scattering environments to help recover these degraded optical signals. This is done by passing a collimated beam through the aerosol environment and collecting the scattered and unscattered light with an f-theta scan lens. The lens transforms the angular distribution of the scattered light into the linear domain, mapping the collected light onto a detector. The measured angular scattering distribution is then used to estimate the point spread function of the environment at an arbitrary stand-off distance. This point spread function can be used to deconvolve images blurred by the aerosol environment in which the angular scattering distribution was initially measured. With this approach, we demonstrate improvements in the effective resolution of deblurred images up to 26% over a 120-cm stand-off distance. Experimentation was performed in the Sandia National Laboratories tabletop fog chamber, a platform that generates aerosol environments analogous to real-world fogs. We intend to leverage this technique in future work to develop a low-SWaP system for the in situ characterization of aerosol environments.
Image deblurring is modeled as an ill-posed, linear inverse problem and can be written in terms of an optimization problem. By adding bound and equality constraints and/or penalty terms to the objective function, the problem is regularized and a viable solution exists; however, there are few methods available for solving such constrained problems. Here we formulate two regularized solutions into constrained optimization problems and adapt an iterative augmented Lagrangian solver. Results are shown on synthetic data in one- and two-dimensions, as well as on a radiograph used to calibrate the transmission curve of a pulsed power X-ray source at a U.S. Department of Energy radiography facility.
In this study, we provide a review of the recent literature on Bayesian Blind Image Deconvolution (BID) methods. We believe that two events have marked the recent history of BID: the predominance of Variational Bayes (VB) inference as a tool to solve BID problems and the increasing interest of the computer vision community in solving BID problems. VB inference in combination with recent image models like the ones based on Super Gaussian (SG) and Scale Mixture of Gaussians (SMG) representations have led to the use of very general and powerful tools to provide clear images from blurry observations. In the provided review emphasis is paid on VB inference and the use of SG and SMG models with coverage of recent advances in sampling methods. We also provide examples of current state of the art BID methods and discuss problems that very likely will mark the near future of BID.