Denoising time-resolved microscopy image sequences with singular value thresholding.

Time-resolved imaging in microscopy is important for the direct observation of a range of dynamic processes in both the physical and life sciences. However, the image sequences are often corrupted by noise, either as a result of high frame rates or a need to limit the radiation dose received by the sample. Here we exploit both spatial and temporal correlations using low-rank matrix recovery methods to denoise microscopy image sequences. We also make use of an unbiased risk estimator to address the issue of how much thresholding to apply in a robust and automated manner. The performance of the technique is demonstrated using simulated image sequences, as well as experimental scanning transmission electron microscopy data, where surface adatom motion and nanoparticle structural dynamics are recovered at rates of up to 32 frames per second.Junior Research Fellowship from Clare CollegeThis is the final version of the article. It first appeared from Elsevier via http://dx.doi.org/10.1016/j.ultramic.2016.05.00

A CURE for noisy magnetic resonance images: Chi-square unbiased risk estimation

In this article we derive an unbiased expression for the expected mean-squared error associated with continuously differentiable estimators of the noncentrality parameter of a chi-square random variable. We then consider the task of denoising squared-magnitude magnetic resonance image data, which are well modeled as independent noncentral chi-square random variables on two degrees of freedom. We consider two broad classes of linearly parameterized shrinkage estimators that can be optimized using our risk estimate, one in the general context of undecimated filterbank transforms, and another in the specific case of the unnormalized Haar wavelet transform. The resultant algorithms are computationally tractable and improve upon state-of-the-art methods for both simulated and actual magnetic resonance image data.Comment: 30 double-spaced pages, 11 figures; submitted for publicatio

A proximal iteration for deconvolving Poisson noisy images using sparse representations

We propose an image deconvolution algorithm when the data is contaminated by Poisson noise. The image to restore is assumed to be sparsely represented in a dictionary of waveforms such as the wavelet or curvelet transforms. Our key contributions are: First, we handle the Poisson noise properly by using the Anscombe variance stabilizing transform leading to a {\it non-linear} degradation equation with additive Gaussian noise. Second, the deconvolution problem is formulated as the minimization of a convex functional with a data-fidelity term reflecting the noise properties, and a non-smooth sparsity-promoting penalties over the image representation coefficients (e.g. $\ell_1$-norm). Third, a fast iterative backward-forward splitting algorithm is proposed to solve the minimization problem. We derive existence and uniqueness conditions of the solution, and establish convergence of the iterative algorithm. Finally, a GCV-based model selection procedure is proposed to objectively select the regularization parameter. Experimental results are carried out to show the striking benefits gained from taking into account the Poisson statistics of the noise. These results also suggest that using sparse-domain regularization may be tractable in many deconvolution applications with Poisson noise such as astronomy and microscopy

Image Denoising in Mixed Poisson-Gaussian Noise

We propose a general methodology (PURE-LET) to design and optimize a wide class of transform-domain thresholding algorithms for denoising images corrupted by mixed Poisson-Gaussian noise. We express the denoising process as a linear expansion of thresholds (LET) that we optimize by relying on a purely data-adaptive unbiased estimate of the mean-squared error (MSE), derived in a non-Bayesian framework (PURE: Poisson-Gaussian unbiased risk estimate). We provide a practical approximation of this theoretical MSE estimate for the tractable optimization of arbitrary transform-domain thresholding. We then propose a pointwise estimator for undecimated filterbank transforms, which consists of subband-adaptive thresholding functions with signal-dependent thresholds that are globally optimized in the image domain. We finally demonstrate the potential of the proposed approach through extensive comparisons with state-of-the-art techniques that are specifically tailored to the estimation of Poisson intensities. We also present denoising results obtained on real images of low-count fluorescence microscopy

Single atom imaging with time-resolved electron microscopy

Developments in scanning transmission electron microscopy (STEM) have opened up new possibilities for time-resolved imaging at the atomic scale. However, rapid imaging of single atom dynamics brings with it a new set of challenges, particularly regarding noise and the interaction between the electron beam and the specimen. This thesis develops a set of analytical tools for capturing atomic motion and analyzing the dynamic behaviour of materials at the atomic scale. Machine learning is increasingly playing an important role in the analysis of electron microscopy data. In this light, new unsupervised learning tools are developed here for noise removal under low-dose imaging conditions and for identifying the motion of surface atoms. The scope for real-time processing and analysis is also explored, which is of rising importance as electron microscopy datasets grow in size and complexity. These advances in image processing and analysis are combined with computational modelling to uncover new chemical and physical insights into the motion of atoms adsorbed onto surfaces. Of particular interest are systems for heterogeneous catalysis, where the catalytic activity can depend intimately on the atomic environment. The study of Cu atoms on a graphene oxide support reveals that the atoms undergo anomalous diffusion as a result of spatial and energetic disorder present in the substrate. The investigation is extended to examine the structure and stability of small Cu clusters on graphene oxide, with atomistic modelling used to understand the significant role played by the substrate. Finally, the analytical methods are used to study the surface reconstruction of silicon alongside the electron beam-induced motion of adatoms on the surface. Taken together, these studies demonstrate the materials insights that can be obtained with time-resolved STEM imaging, and highlight the importance of combining state-ofthe- art imaging with computational analysis and atomistic modelling to quantitatively characterize the behaviour of materials with atomic resolution.The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007–2013)/ERC grant agreement 291522–3DIMAGE, as well as from the European Union Seventh Framework Programme under Grant Agreement 312483-ESTEEM2 (Integrated Infrastructure Initiative -I3)

Image denoising based on nonlocal Bayesian singular value thresholding and Stein's unbiased risk estimator

© 1992-2012 IEEE. Singular value thresholding (SVT)- or nuclear norm minimization (NNM)-based nonlocal image denoising methods often rely on the precise estimation of the noise variance. However, most existing methods either assume that the noise variance is known or require an extra step to estimate it. Under the iterative regularization framework, the error in the noise variance estimate propagates and accumulates with each iteration, ultimately degrading the overall denoising performance. In addition, the essence of these methods is still least squares estimation, which can cause a very high mean-squared error (MSE) and is inadequate for handling missing data or outliers. In order to address these deficiencies, we present a hybrid denoising model based on variational Bayesian inference and Stein's unbiased risk estimator (SURE), which consists of two complementary steps. In the first step, the variational Bayesian SVT performs a low-rank approximation of the nonlocal image patch matrix to simultaneously remove the noise and estimate the noise variance. In the second step, we modify the conventional SURE full-rank SVT and its divergence formulas for rank-reduced eigen-triplets to remove the residual artifacts. The proposed hybrid BSSVT method achieves better performance in recovering the true image compared with state-of-the-art methods

Unsupervised training of denoisers for low-dose CT reconstruction without full-dose ground truth

Department of Electrical EngineeringRecently, deep neural network (DNN) based methods for low-dose CT have been investigated to achieve excellent performance in both image quality and compu- tational speed. However, almost all methods using DNNs for low-dose CT require clean ground truth data with full radiation dose to train the DNNs. In this work, we attempt to train DNNs for low-dose CT reconstructions with reduced tube current by investigating unsupervised training of DNNs for denoising sensor measurements or sinograms without full-dose ground truth images. In other words, our proposed methods allow training of DNNs with only noisy low-dose CT measurements. First, the Poisson Unbiased Risk Estimator (PURE) is investigated to train a DNN for denoising CT measurements, and a method is proposed for reconstructing the CT image using filtered back-projection (FBP) and the DNN trained with PURE. Then, the CT forward model-based Weighted Stein???s Unbiased Risk Estimator (WSURE) is proposed to train a DNN for denoising CT sinograms and to subsequently re- construct the CT image using FBP. Our proposed methods achieve excellent per- formance in both fast computation and reconstructed image quality, which is more comparable to the results of the DNNs trained with full-dose ground truth data than other state-of-the-art denoising methods such as the BM3D, Deep Image Prior, and Deep Decoder.clos

Computational Methods for Matrix/Tensor Factorization and Deep Learning Image Denoising

Feature learning is a technique to automatically extract features from raw data. It is widely used in areas such as computer vision, image processing, data mining and natural language processing. In this thesis, we are interested in the computational aspects of feature learning. We focus on rank matrix and tensor factorization and deep neural network models for image denoising. With respect to matrix and tensor factorization, we first present a technique to speed up alternating least squares (ALS) and gradient descent (GD) − two commonly used strategies for tensor factorization. We introduce an efficient, scalable and distributed algorithm that addresses the data explosion problem. Instead of a computationally challenging sub-step of ALS and GD, we implement the algorithm on parallel machines by using only two sparse matrix-vector products. Not only is the algorithm scalable but it is also on average 4 to 10 times faster than competing algorithms on various data sets. Next, we discuss our results of non-negative matrix factorization for hyperspectral image data in the presence of noise. We introduce a spectral total variation regularization and derive four variants of the alternating direction method of multiplier algorithm. While all four methods belong to the same family of algorithms, some perform better than others. Thus, we compare the algorithms using stimulated Raman spectroscopic image will be demonstrated. For deep neural network models, we focus on its application to image denoising. We first demonstrate how an optimal procedure leveraging deep neural networks and convex optimization can combine a given set of denoisers to produce an overall better result. The proposed framework estimates the mean squared error (MSE) of individual denoised outputs using a deep neural network; optimally combines the denoised outputs via convex optimization; and recovers lost details of the combined images using another deep neural network. The framework consistently improves denoising performance for both deterministic denoisers and neural network denoisers. Next, we apply the deep neural network to solve the image reconstruction issues of the Quanta Image Sensor (QIS), which is a single-photon image sensor that oversamples the light field to generate binary measures