Supervision by Denoising.

Learning-based image reconstruction models, such as those based on the U-Net, require a large set of labeled images if good generalization is to be guaranteed. In some imaging domains, however, labeled data with pixel- or voxel-level label accuracy are scarce due to the cost of acquiring them. This problem is exacerbated further in domains like medical imaging, where there is no single ground truth label, resulting in large amounts of repeat variability in the labels. Therefore, training reconstruction networks to generalize better by learning from both labeled and unlabeled examples (called semi-supervised learning) is problem of practical and theoretical interest. However, traditional semi-supervised learning methods for image reconstruction often necessitate handcrafting a differentiable regularizer specific to some given imaging problem, which can be extremely time-consuming. In this work, we propose "supervision by denoising" (SUD), a framework to supervise reconstruction models using their own denoised output as labels. SUD unifies stochastic averaging and spatial denoising techniques under a spatio-temporal denoising framework and alternates denoising and model weight update steps in an optimization framework for semi-supervision. As example applications, we apply SUD to two problems from biomedical imaging-anatomical brain reconstruction (3D) and cortical parcellation (2D)-to demonstrate a significant improvement in reconstruction over supervised-only and ensembling baselines. Our code available at https://github.com/seannz/sud.

NeuWS: Neural wavefront shaping for guidestar-free imaging through static and dynamic scattering media.

Diffraction-limited optical imaging through scattering media has the potential to transform many applications such as airborne and space-based imaging (through the atmosphere), bioimaging (through skin and human tissue), and fiber-based imaging (through fiber bundles). Existing wavefront shaping methods can image through scattering media and other obscurants by optically correcting wavefront aberrations using high-resolution spatial light modulators-but these methods generally require (i) guidestars, (ii) controlled illumination, (iii) point scanning, and/or (iv) statics scenes and aberrations. We propose neural wavefront shaping (NeuWS), a scanning-free wavefront shaping technique that integrates maximum likelihood estimation, measurement modulation, and neural signal representations to reconstruct diffraction-limited images through strong static and dynamic scattering media without guidestars, sparse targets, controlled illumination, nor specialized image sensors. We experimentally demonstrate guidestar-free, wide field-of-view, high-resolution, diffraction-limited imaging of extended, nonsparse, and static/dynamic scenes captured through static/dynamic aberrations.

Roadmap on Deep Learning for Microscopy.

Through digital imaging, microscopy has evolved from primarily being a means for visual observation of life at the micro- and nano-scale, to a quantitative tool with ever-increasing resolution and throughput. Artificial intelligence, deep neural networks, and machine learning are all niche terms describing computational methods that have gained a pivotal role in microscopy-based research over the past decade. This Roadmap is written collectively by prominent researchers and encompasses selected aspects of how machine learning is applied to microscopy image data, with the aim of gaining scientific knowledge by improved image quality, automated detection, segmentation, classification and tracking of objects, and efficient merging of information from multiple imaging modalities. We aim to give the reader an overview of the key developments and an understanding of possibilities and limitations of machine learning for microscopy. It will be of interest to a wide cross-disciplinary audience in the physical sciences and life sciences.

EXPECTATION CONSISTENT PLUG-AND-PLAY FOR MRI.

For image recovery problems, plug-and-play (PnP) methods have been developed that replace the proximal step in an optimization algorithm with a call to an application-specific denoiser, often implemented using a deep neural network. Although such methods have been successful, they can be improved. For example, the denoiser is often trained using white Gaussian noise, while PnP's denoiser input error is often far from white and Gaussian, with statistics that are difficult to predict from iteration to iteration. PnP methods based on approximate message passing (AMP) are an exception, but only when the forward operator behaves like a large random matrix. In this work, we design a PnP method using the expectation consistent (EC) approximation algorithm, a generalization of AMP, that offers predictable error statistics at each iteration, from which a deep-net denoiser can be effectively trained.

Denoising Generalized Expectation-Consistent Approximation for MR Image Recovery.

To solve inverse problems, plug-and-play (PnP) methods replace the proximal step in a convex optimization algorithm with a call to an application-specific denoiser, often implemented using a deep neural network (DNN). Although such methods yield accurate solutions, they can be improved. For example, denoisers are usually designed/trained to remove white Gaussian noise, but the denoiser input error in PnP algorithms is usually far from white or Gaussian. Approximate message passing (AMP) methods provide white and Gaussian denoiser input error, but only when the forward operator is sufficiently random. In this work, for Fourier-based forward operators, we propose a PnP algorithm based on generalized expectation-consistent (GEC) approximation-a close cousin of AMP-that offers predictable error statistics at each iteration, as well as a new DNN denoiser that leverages those statistics. We apply our approach to magnetic resonance (MR) image recovery and demonstrate its advantages over existing PnP and AMP methods.