Bispectrum Inversion with Application to Multireference Alignment

We consider the problem of estimating a signal from noisy circularly-translated versions of itself, called multireference alignment (MRA). One natural approach to MRA could be to estimate the shifts of the observations first, and infer the signal by aligning and averaging the data. In contrast, we consider a method based on estimating the signal directly, using features of the signal that are invariant under translations. Specifically, we estimate the power spectrum and the bispectrum of the signal from the observations. Under mild assumptions, these invariant features contain enough information to infer the signal. In particular, the bispectrum can be used to estimate the Fourier phases. To this end, we propose and analyze a few algorithms. Our main methods consist of non-convex optimization over the smooth manifold of phases. Empirically, in the absence of noise, these non-convex algorithms appear to converge to the target signal with random initialization. The algorithms are also robust to noise. We then suggest three additional methods. These methods are based on frequency marching, semidefinite relaxation and integer programming. The first two methods provably recover the phases exactly in the absence of noise. In the high noise level regime, the invariant features approach for MRA results in stable estimation if the number of measurements scales like the cube of the noise variance, which is the information-theoretic rate. Additionally, it requires only one pass over the data which is important at low signal-to-noise ratio when the number of observations must be large

Four-dimensional cardiac imaging in living embryos via postacquisition synchronization of nongated slice sequences

Being able to acquire, visualize, and analyze 3D time series (4D data) from living embryos makes it possible to understand complex dynamic movements at early stages of embryonic development. Despite recent technological breakthroughs in 2D dynamic imaging, confocal microscopes remain quite slow at capturing optical sections at successive depths. However, when the studied motion is periodic— such as for a beating heart—a way to circumvent this problem is to acquire, successively, sets of 2D+time slice sequences at increasing depths over at least one time period and later rearrange them to recover a 3D+time sequence. In other imaging modalities at macroscopic scales, external gating signals, e.g., an electro-cardiogram, have been used to achieve proper synchronization. Since gating signals are either unavailable or cumbersome to acquire in microscopic organisms, we have developed a procedure to reconstruct volumes based solely on the information contained in the image sequences. The central part of the algorithm is a least-squares minimization of an objective criterion that depends on the similarity between the data from neighboring depths. Owing to a wavelet-based multiresolution approach, our method is robust to common confocal microscopy artifacts. We validate the procedure on both simulated data and in vivo measurements from living zebrafish embryos

Fast Super-Resolution Using an Adaptive Wiener Filter with Robustness to Local Motion

We present a new adaptive Wiener filter (AWF) super-resolution (SR) algorithm that employs a global background motion model but is also robust to limited local motion. The AWF relies on registration to populate a common high resolution (HR) grid with samples from several frames. A weighted sum of local samples is then used to perform nonuniform interpolation and image restoration simultaneously. To achieve accurate subpixel registration, we employ a global background motion model with relatively few parameters that can be estimated accurately. However, local motion may be present that includes moving objects, motion parallax, or other deviations from the background motion model. In our proposed robust approach, pixels from frames other than the reference that are inconsistent with the background motion model are detected and excluded from populating the HR grid. Here we propose and compare several local motion detection algorithms. We also propose a modified multiscale background registration method that incorporates pixel selection at each scale to minimize the impact of local motion. We demonstrate the efficacy of the new robust SR methods using several datasets, including airborne infrared data with moving vehicles and a ground resolution pattern for objective resolution analysis

Multiframe Shift Estimation

The purpose of this research was to develop a fundamental framework for a new approach to multiframe translational shift estimation in image processing. This thesis sought to create a new multiframe shift estimator, to theoretically prove and experimentally test key properties of it, and to quantify its performance according to several metrics. The new estimator was modeled successfully and was proven to be an unbiased estimator under certain common image noise conditions. Furthermore its performance was shown to be superior to the cross correlation shift estimator, a robust estimator widely used in similar image processing cases, according to several criteria. This research effort led to the derivation of a lower bound of estimation performance for the multiframe case. This valuable data analysis tool extends current boundary derivations to include prior information about the random shifting, thereby providing a more precise performance boundary

Bayesian Cram\'er-Rao Bound Estimation with Score-Based Models

The Bayesian Cram\'er-Rao bound (CRB) provides a lower bound on the error of any Bayesian estimator under mild regularity conditions. It can be used to benchmark the performance of estimators, and provides a principled design metric for guiding system design and optimization. However, the Bayesian CRB depends on the prior distribution, which is often unknown for many problems of interest. This work develops a new data-driven estimator for the Bayesian CRB using score matching, a statistical estimation technique, to model the prior distribution. The performance of the estimator is analyzed in both the classical parametric modeling regime and the neural network modeling regime. In both settings, we develop novel non-asymptotic bounds on the score matching error and our Bayesian CRB estimator. Our proofs build on results from empirical process theory, including classical bounds and recently introduced techniques for characterizing neural networks, to address the challenges of bounding the score matching error. The performance of the estimator is illustrated empirically on a denoising problem example with a Gaussian mixture prior