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.

Weakly-Supervised Semantic Segmentation of Ships Using Thermal Imagery

The United States coastline spans 95,471 miles; a distance that cannot be effectively patrolled or secured by manual human effort alone. Unmanned Aerial Vehicles (UAVs) equipped with infrared cameras and deep-learning based algorithms represent a more efficient alternative for identifying and segmenting objects of interest - namely, ships. However, standard approaches to training these algorithms require large-scale datasets of densely labeled infrared maritime images. Such datasets are not publicly available and manually annotating every pixel in a large-scale dataset would have an extreme labor cost. In this work we demonstrate that, in the context of segmenting ships in infrared imagery, weakly-supervising an algorithm with sparsely labeled data can drastically reduce data labeling costs with minimal impact on system performance. We apply weakly-supervised learning to an unlabeled dataset of 7055 infrared images sourced from the Naval Air Warfare Center Aircraft Division (NAWCAD). We find that by sparsely labeling only 32 points per image, weakly-supervised segmentation models can still effectively detect and segment ships, with a Jaccard score of up to 0.756.

MetaDIP: Accelerating Deep Image Prior with Meta Learning

Deep image prior (DIP) is a recently proposed technique for solving imaging inverse problems by fitting the reconstructed images to the output of an untrained convolutional neural network. Unlike pretrained feedforward neural networks, the same DIP can generalize to arbitrary inverse problems, from denoising to phase retrieval, while offering competitive performance at each task. The central disadvantage of DIP is that, while feedforward neural networks can reconstruct an image in a single pass, DIP must gradually update its weights over hundreds to thousands of iterations, at a significant computational cost. In this work we use meta-learning to massively accelerate DIP-based reconstructions. By learning a proper initialization for the DIP weights, we demonstrate a 10x improvement in runtimes across a range of inverse imaging tasks. Moreover, we demonstrate that a network trained to quickly reconstruct faces also generalizes to reconstructing natural image patches.

Denoising Generalized Expectation-Consistent Approximation for MRI Image Recovery

To solve inverse problems, plug-and-play (PnP) methods have been developed that 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 have been successful, 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 a large random matrix. 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 imaging (MRI) image recovery and demonstrate its advantages over existing PnP and AMP methods.

TurbuGAN: An Adversarial Learning Approach to Spatially-Varying Multiframe Blind Deconvolution with Applications to Imaging Through Turbulence

We present a self-supervised and self-calibrating multi-shot approach to imaging through atmospheric turbulence, called TurbuGAN. Our approach requires no paired training data, adapts itself to the distribution of the turbulence, leverages domain-specific data priors, outperforms existing approaches, and can generalize from tens to tens of thousands of measurements. We achieve such functionality through an adversarial sensing framework adapted from CryoGAN, which uses a discriminator network to match the distributions of captured and simulated measurements. Our framework builds on CryoGAN by (1) generalizing the forward measurement model to incorporate physically accurate and computationally efficient models for light propagation through anisoplanatic turbulence, (2) enabling adaptation to slightly misspecified forward models, and (3) leveraging domain-specific prior knowledge using pretrained generative networks, when available. We validate TurbuGAN in simulation using realistic models for atmospheric turbulence-induced distortion.

SUREMap: Predicting Uncertainty in CNN-based Image Reconstruction Using Stein's Unbiased Risk Estimate

Convolutional neural networks (CNN) have emerged as a powerful tool for solving computational imaging reconstruction problems. However, CNNs are generally difficult-to-understand black-boxes. Accordingly, it is challenging to know when they will work and, more importantly, when they will fail. This limitation is a major barrier to their use in safety-critical applications like medical imaging: Is that blob in the reconstruction an artifact or a tumor? In this work we use Stein's unbiased risk estimate (SURE) to develop per-pixel confidence intervals, in the form of heatmaps, for compressive sensing reconstruction using the approximate message passing (AMP) framework with CNN-based denoisers. These heatmaps tell end-users how much to trust an image formed by a CNN, which could greatly improve the utility of CNNs in various computational imaging applications.

Deep Learning Techniques for Inverse Problems in Imaging

Recent work in machine learning shows that deep neural networks can be used to solve a wide variety of inverse problems arising in computational imaging. We explore the central prevailing themes of this emerging area and present a taxonomy that can be used to categorize different problems and reconstruction methods. Our taxonomy is organized along two central axes: (1) whether or not a forward model is known and to what extent it is used in training and testing, and (2) whether or not the learning is supervised or unsupervised, i.e., whether or not the training relies on access to matched ground truth image and measurement pairs. We also discuss the trade-offs associated with these different reconstruction approaches, caveats and common failure modes, plus open problems and avenues for future work.

Deep S$^3$PR: Simultaneous Source Separation and Phase Retrieval Using Deep Generative Models

This paper introduces and solves the simultaneous source separation and phase retrieval (S$^3$PR) problem. S$^3$PR shows up in a number application domains, most notably computational optics, where one has multiple independent coherent sources whose phase is difficult to measure. In general, S$^3$PR is highly under-determined, non-convex, and difficult to solve. In this work, we demonstrate that by restricting the solutions to lie in the range of a deep generative model, we can constrain the search space sufficiently to solve S$^3$PR.

Keyhole Imaging: Non-Line-of-Sight Imaging and Tracking of Moving Objects Along a Single Optical Path at Long Standoff Distances

Non-line-of-sight (NLOS) imaging and tracking is an emerging paradigm that allows the shape or position of objects around corners or behind diffusers to be recovered from transient measurements. However, existing NLOS approaches require the imaging system to scan a large area on a visible surface, where the indirect light paths of hidden objects are sampled. In many applications, such as robotic vision or autonomous driving, optical access to a large scanning area may not be available, which severely limits the practicality of existing NLOS techniques. Here, we propose a new approach, dubbed keyhole imaging, that captures a sequence of transient measurements along a single optical path at long standoff distances, for example through a keyhole. Assuming that the hidden object of interest moves during the acquisition time, we capture a series of time-resolved projections of the object's shape from unknown viewpoints. We derive inverse methods based on Expectation-Maximization to recover the object's shape and location using these measurements, and we demonstrate successful experimental results with a prototype keyhole imaging system.

Deep Optics for Single-shot High-dynamic-range Imaging

High-dynamic-range (HDR) imaging is crucial for many computer graphics and vision applications. Yet, acquiring HDR images with a single shot remains a challenging problem. Whereas modern deep learning approaches are successful at hallucinating plausible HDR content from a single low-dynamic-range (LDR) image, saturated scene details often cannot be faithfully recovered. Inspired by recent deep optical imaging approaches, we interpret this problem as jointly training an optical encoder and electronic decoder where the encoder is parameterized by the point spread function (PSF) of the lens, the bottleneck is the sensor with a limited dynamic range, and the decoder is a convolutional neural network (CNN). The lens surface is then jointly optimized with the CNN in a training phase; we fabricate this optimized optical element and attach it as a hardware add-on to a conventional camera during inference. In extensive simulations and with a physical prototype, we demonstrate that this end-to-end deep optical imaging approach to single-shot HDR imaging outperforms both purely CNN-based approaches and other PSF engineering approaches.