Abstract-Many material and biological samples in scientific imaging are characterized by non-local repeating structures. These are studied using scanning electron microscopy and electron tomography. Sparse sampling of individual pixels in a 2D image acquisition geometry, or sparse sampling of projection images with large tilt increments in a tomography experiment, can enable high speed data acquisition and minimize sample damage caused by the electron beam.In this paper, we present an algorithm for electron tomographic reconstruction and sparse image interpolation that exploits the non-local redundancy in images. We adapt a framework, termed plug-and-play (P&P) priors, to solve these imaging problems in a regularized inversion setting. The power of the P&P approach is that it allows a wide array of modern denoising algorithms to be used as a "prior model" for tomography and image interpolation. We also present sufficient mathematical conditions that ensure convergence of the P&P approach, and we use these insights to design a new non-local means denoising algorithm. Finally, we demonstrate that the algorithm produces higher quality reconstructions on both simulated and real electron microscope data, along with improved convergence properties compared to other methods.Index Terms-Plug-and-play, prior modeling, bright field electron tomography, sparse interpolation, non-local means, doublystochastic gradient non-local means, BM3D.

Regularized inversion methods for image reconstruction are used widely due to their tractability and their ability to combine complex physical sensor models with useful regularity criteria. Such methods motivated the recently developed Plug-and-Play prior method, which provides a framework to use advanced denoising algorithms as regularizers in inversion. However, the need to formulate regularized inversion as the solution to an optimization problem limits the expressiveness of possible regularity conditions and physical sensor models.In this paper, we introduce the idea of Consensus Equilibrium (CE), which generalizes regularized inversion to include a much wider variety of both forward (or data fidelity) components and prior (or regularity) components without the need for either to be expressed using a cost function. Consensus equilibrium is based on the solution of a set of equilibrium equations that balance data fit and regularity. In this framework, the problem of MAP estimation in regularized inversion is replaced by the problem of solving these equilibrium equations, which can be approached in multiple ways.The key contribution of CE is to provide a novel framework for fusing multiple heterogeneous models of physical sensors or models learned from data. We describe the derivation of the CE equations and prove that the solution of the CE equations generalizes the standard MAP estimate under appropriate circumstances.We also discuss algorithms for solving the CE equations, including a version of the Douglas-Rachford (DR)/ADMM algorithm with a novel form of preconditioning and Newton's method, both standard form and a Jacobian-free form using Krylov subspaces. We give several examples to illustrate the idea of consensus equilibrium and the convergence properties of these algorithms and demonstrate this method on some toy problems and on a denoising example in which we use an array of convolutional neural network denoisers, none of which is tuned to match the noise level in a noisy image but which in consensus can achieve a better result than any of them individually.

Magnetic Resonance Imaging (MRI) is a non-invasive diagnostic tool that provides excellent soft-tissue contrast without the use of ionizing radiation. Compared to other clinical imaging modalities (e.g., CT or ultrasound), however, the data acquisition process for MRI is inherently slow, which motivates undersampling and thus drives the need for accurate, efficient reconstruction methods from undersampled datasets. In this article, we describe the use of "plug-and-play" (PnP) algorithms for MRI image recovery. We first describe the linearly approximated inverse problem encountered in MRI. Then we review several PnP methods, where the unifying commonality is to iteratively call a denoising subroutine as one step of a larger optimizationinspired algorithm. Next, we describe how the result of the PnP method can be interpreted as a solution to an equilibrium equation, allowing convergence analysis from the equilibrium perspective. Finally, we present illustrative examples of PnP methods applied to MRI image recovery.

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Mathematical models of mitochondrial bioenergetics provide powerful analytical tools to help interpret experimental data and facilitate experimental design for elucidating the supporting biochemical and physical processes. As a next step towards constructing a complete physiologically faithful mitochondrial bioenergetics model, a mathematical model was developed targeting the cardiac mitochondrial bioenergetic based upon previous efforts, and corroborated using both transient and steady state data. The model consists of several modified rate functions of mitochondrial bioenergetics, integrated calcium dynamics and a detailed description of the K+-cycle and its effect on mitochondrial bioenergetics and matrix volume regulation. Model simulations were used to fit 42 adjustable parameters to four independent experimental data sets consisting of 32 data curves. During the model development, a certain network topology had to be in place and some assumptions about uncertain or unobserved experimental factors and conditions were explicitly constrained in order to faithfully reproduce all the data sets. These realizations are discussed, and their necessity helps contribute to the collective understanding of the mitochondrial bioenergetics.