Hierarchical Bayesian sparse image reconstruction with application to MRFM

This paper presents a hierarchical Bayesian model to reconstruct sparse images when the observations are obtained from linear transformations and corrupted by an additive white Gaussian noise. Our hierarchical Bayes model is well suited to such naturally sparse image applications as it seamlessly accounts for properties such as sparsity and positivity of the image via appropriate Bayes priors. We propose a prior that is based on a weighted mixture of a positive exponential distribution and a mass at zero. The prior has hyperparameters that are tuned automatically by marginalization over the hierarchical Bayesian model. To overcome the complexity of the posterior distribution, a Gibbs sampling strategy is proposed. The Gibbs samples can be used to estimate the image to be recovered, e.g. by maximizing the estimated posterior distribution. In our fully Bayesian approach the posteriors of all the parameters are available. Thus our algorithm provides more information than other previously proposed sparse reconstruction methods that only give a point estimate. The performance of our hierarchical Bayesian sparse reconstruction method is illustrated on synthetic and real data collected from a tobacco virus sample using a prototype MRFM instrument.Comment: v2: final version; IEEE Trans. Image Processing, 200

Semi-blind Sparse Image Reconstruction with Application to MRFM

We propose a solution to the image deconvolution problem where the convolution kernel or point spread function (PSF) is assumed to be only partially known. Small perturbations generated from the model are exploited to produce a few principal components explaining the PSF uncertainty in a high dimensional space. Unlike recent developments on blind deconvolution of natural images, we assume the image is sparse in the pixel basis, a natural sparsity arising in magnetic resonance force microscopy (MRFM). Our approach adopts a Bayesian Metropolis-within-Gibbs sampling framework. The performance of our Bayesian semi-blind algorithm for sparse images is superior to previously proposed semi-blind algorithms such as the alternating minimization (AM) algorithm and blind algorithms developed for natural images. We illustrate our myopic algorithm on real MRFM tobacco virus data.Comment: This work has been submitted to the IEEE Trans. Image Processing for possible publicatio

Sampling and Recovery of Pulse Streams

Compressive Sensing (CS) is a new technique for the efficient acquisition of signals, images, and other data that have a sparse representation in some basis, frame, or dictionary. By sparse we mean that the N-dimensional basis representation has just K<<N significant coefficients; in this case, the CS theory maintains that just M = K log N random linear signal measurements will both preserve all of the signal information and enable robust signal reconstruction in polynomial time. In this paper, we extend the CS theory to pulse stream data, which correspond to S-sparse signals/images that are convolved with an unknown F-sparse pulse shape. Ignoring their convolutional structure, a pulse stream signal is K=SF sparse. Such signals figure prominently in a number of applications, from neuroscience to astronomy. Our specific contributions are threefold. First, we propose a pulse stream signal model and show that it is equivalent to an infinite union of subspaces. Second, we derive a lower bound on the number of measurements M required to preserve the essential information present in pulse streams. The bound is linear in the total number of degrees of freedom S + F, which is significantly smaller than the naive bound based on the total signal sparsity K=SF. Third, we develop an efficient signal recovery algorithm that infers both the shape of the impulse response as well as the locations and amplitudes of the pulses. The algorithm alternatively estimates the pulse locations and the pulse shape in a manner reminiscent of classical deconvolution algorithms. Numerical experiments on synthetic and real data demonstrate the advantages of our approach over standard CS

Sampling and recovery of pulse streams

Compressive Sensing (CS) is a new technique for the efficient acquisition of signals, images, and other data that have a sparse representation in some basis, frame, or dictionary. By sparse we mean that the N -dimensional basis representation has just K &lt;&lt; N significant coefficients; in this case, the CS theory maintains that just M = O (K log N) random linear signal measurements will both preserve all of the signal information and enable robust signal reconstruction in polynomial time. In this paper, we extend the CS theory to pulse stream data, which correspond to S-sparse signals/images that are convolved with an unknown F-sparse pulse shape. Ignoring their convolutional structure, a pulse stream signal is K = SF sparse. Such signals figure prominently in a number of applications, from neuroscience to astronomy. Our specific contributions are threefold. First, we propose a pulse stream signal model and show that it is equivalent to an infinite union of subspaces. Second, we derive a lower bound on the number of measurements M required to preserve the essential information present in pulse streams. The bound is linear in the total number of degrees of freedom S + F, which is significantly smaller than the naive bound based on the total signal sparsity K = SF. Third, we develop an efficient signal recovery algorithm that infers both the shape of the impulse response as well as the locations and amplitudes of the pulses. The algorithm alternatively estimates the pulse locations and the pulse shape in a manner reminiscent of classical deconvolution algorithms. Numerical experiments on synthetic and real data demonstrate the advantages of our approach over standard CS

Reconstruction, Classification, and Segmentation for Computational Microscopy

This thesis treats two fundamental problems in computational microscopy: image reconstruction for magnetic resonance force microscopy (MRFM) and image classification for electron backscatter diffraction (EBSD). In MRFM, as in many inverse problems, the true point spread function (PSF) that blurs the image may be only partially known. The image quality may suffer from this possible mismatch when standard image reconstruction techniques are applied. To deal with the mismatch, we develop novel Bayesian sparse reconstruction methods that account for possible errors in the PSF of the microscope and for the inherent sparsity of MRFM images. Two methods are proposed: a stochastic method and a variational method. They both jointly estimate the unknown PSF and unknown image. Our proposed framework for reconstruction has the flexibility to incorporate sparsity inducing priors, thus addressing ill-posedness of this non-convex problem, Markov-Random field priors, and can be extended to other image models. To obtain scalable and tractable solutions, a dimensionality reduction technique is applied to the highly nonlinear PSF space. The experiments clearly demonstrate that the proposed methods have superior performance compared to previous methods. In EBSD we develop novel and robust dictionary-based methods for segmentation and classification of grain and sub-grain structures in polycrystalline materials. Our work is the first in EBSD analysis to use a physics-based forward model, called the dictionary, to use full diffraction patterns, and that efficiently classifies patterns into grains, boundaries, and anomalies. In particular, unlike previous methods, our method incorporates anomaly detection directly into the segmentation process. The proposed approach also permits super-resolution of grain mantle and grain boundary locations. Finally, the proposed dictionary-based segmentation method performs uncertainty quantification, i.e. p-values, for the classified grain interiors and grain boundaries. We demonstrate that the dictionary-based approach is robust to instrument drift and material differences that produce small amounts of dictionary mismatch.PhDElectrical Engineering: SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/102296/1/seunpark_1.pd