Revealing biomolecular structure and motion with neural ab initio cryo-EM reconstruction.

Proteins and other biomolecules form dynamic macromolecular machines that are tightly orchestrated to move, bind, and perform chemistry. Cryo-electron microscopy (cryo-EM) can access the intrinsic heterogeneity of these complexes and is therefore a key tool for understanding mechanism and function. However, 3D reconstruction of the resulting imaging data presents a challenging computational problem, especially without any starting information, a setting termed ab initio reconstruction.

Full-colour 3D holographic augmented-reality displays with metasurface waveguides.

Emerging spatial computing systems seamlessly superimpose digital information on the physical environment observed by a user, enabling transformative experiences across various domains, such as entertainment, education, communication and training. However, the widespread adoption of augmented-reality (AR) displays has been limited due to the bulky projection optics of their light engines and their inability to accurately portray three-dimensional (3D) depth cues for virtual content, among other factors. Here we introduce a holographic AR system that overcomes these challenges using a unique combination of inverse-designed full-colour metasurface gratings, a compact dispersion-compensating waveguide geometry and artificial-intelligence-driven holography algorithms.

Scalable 3D Reconstruction From Single Particle X-Ray Diffraction Images Based on Online Machine Learning.

X-ray free-electron lasers (XFELs) offer unique capabilities for measuring the structure and dynamics of biomolecules, helping us understand the basic building blocks of life. Notably, high-repetition-rate XFELs enable single particle imaging (X-ray SPI) where individual, weakly scattering biomolecules are imaged under near-physiological conditions with the opportunity to access fleeting states that cannot be captured in cryogenic or crystallized conditions. Existing X-ray SPI reconstruction algorithms, which estimate the unknown orientation of a particle in each captured image as well as its shared 3D structure, are inadequate in handling the massive datasets generated by these emerging XFELs.

Gradient Descent Provably Solves Nonlinear Tomographic Reconstruction.

In computed tomography (CT), the forward model consists of a linear Radon transform followed by an exponential nonlinearity based on the attenuation of light according to the Beer-Lambert Law. Conventional reconstruction often involves inverting this nonlinearity as a preprocessing step and then solving a convex inverse problem. However, this nonlinear measurement preprocessing required to use the Radon transform is poorly conditioned in the vicinity of high-density materials, such as metal.

Amortized Inference for Heterogeneous Reconstruction in Cryo-EM.

Cryo-electron microscopy (cryo-EM) is an imaging modality that provides unique insights into the dynamics of proteins and other building blocks of life. The algorithmic challenge of jointly estimating the poses, 3D structure, and conformational heterogeneity of a biomolecule from millions of noisy and randomly oriented 2D projections in a computationally efficient manner, however, remains unsolved. Our method, cryoFIRE, performs heterogeneous reconstruction with unknown poses in an amortized framework, thereby avoiding the computationally expensive step of pose search while enabling the analysis of conformational heterogeneity.

High-brightness holographic projection.

We propose a holographic projection system that achieves high image quality, brightness, and light efficiency. Using a novel, to the best of our knowledge, light-efficiency loss function, we are able to concentrate more light on the projection region and improve display brightness compared with conventional projectors. Leveraging emerging artificial intelligence-driven computer-generated holography and camera-in-the-loop calibration techniques, we learn a holographic wave propagation model using experimentally captured holographic images and demonstrate state-of-the-art light reallocation performance with high image quality.

Off-Axis Layered Displays: Hybrid Direct-View/Near-Eye Mixed Reality with Focus Cues.

This work introduces off-axis layered displays, the first approach to stereoscopic direct-view displays with support for focus cues. Off-axis layered displays combine a head-mounted display with a traditional direct-view display for encoding a focal stack and thus, for providing focus cues. To explore the novel display architecture, we present a complete processing pipeline for the real-time computation and post-render warping of off-axis display patterns.

CryoAI: Amortized Inference of Poses for Ab Initio Reconstruction of 3D Molecular Volumes from Real Cryo-EM Images.

Cryo-electron microscopy (cryo-EM) has become a tool of fundamental importance in structural biology, helping us understand the basic building blocks of life. The algorithmic challenge of cryo-EM is to jointly estimate the unknown 3D poses and the 3D electron scattering potential of a biomolecule from millions of extremely noisy 2D images. Existing reconstruction algorithms, however, cannot easily keep pace with the rapidly growing size of cryo-EM datasets due to their high computational and memory cost.

Modeling linear accelerator (Linac) beam data by implicit neural representation learning for commissioning and quality assurance applications.

Background: Linear accelerator (Linac) beam data commissioning and quality assurance (QA) play a vital role in accurate radiation treatment delivery and entail a large number of measurements using a variety of field sizes. How to optimize the effort in data acquisition while maintaining high quality of medical physics practice has been sought after.

Purpose: We propose to model Linac beam data through implicit neural representation (NeRP) learning.

Computational optical sensing and imaging 2021: feature issue introduction.

This Feature Issue includes 2 reviews and 34 research articles that highlight recent works in the field of Computational Optical Sensing and Imaging. Many of the works were presented at the 2021 OSA Topical Meeting on Computational Optical Sensing and Imaging, held virtually from July 19 to July 23, 2021. Articles in the feature issue cover a broad scope of computational imaging topics, such as microscopy, 3D imaging, phase retrieval, non-line-of-sight imaging, imaging through scattering media, ghost imaging, compressed sensing, and applications with new types of sensors.

Computational Optical Sensing and Imaging 2021: introduction to the feature issue.

This feature issue includes two reviews and 34 research papers that highlight recent works in the field of computational optical sensing and imaging. Many of the works were presented at the 2021 Optica (formerly OSA) Topical Meeting on Computational Optical Sensing and Imaging, held virtually from 19 July to 23 July 2021. Papers in the feature issue cover a broad scope of computational imaging topics, such as microscopy, 3D imaging, phase retrieval, non-line-of-sight imaging, imaging through scattering media, ghost imaging, compressed sensing, and applications with new types of sensors.

Larger visual changes compress time: The inverted effect of asemantic visual features on interval time perception.

Time perception is fluid and affected by manipulations to visual inputs. Previous literature shows that changes to low-level visual properties alter time judgments at the millisecond-level. At longer intervals, in the span of seconds and minutes, high-level cognitive effects (e.

Focus issue introduction: 3D image acquisition and display: technology, perception and applications.

This Feature Issue of Optics Express is organized in conjunction with the 2021 Optica (OSA) conference on 3D Image Acquisition and Display: Technology, Perception and Applications which was held virtually from 19 to 23, July 2021 as part of the Imaging and Sensing Congress 2021. This Feature Issue presents 29 articles which cover the topics and scope of the 2021 3D conference. This Introduction provides a summary of these articles.

Video See-Through Mixed Reality with Focus Cues.

This work introduces the first approach to video see-through mixed reality with full support for focus cues. By combining the flexibility to adjust the focus distance found in varifocal designs with the robustness to eye-tracking error found in multifocal designs, our novel display architecture reliably delivers focus cues over a large workspace. In particular, we introduce gaze-contingent layered displays and mixed reality focal stacks, an efficient representation of mixed reality content that lends itself to fast processing for driving layered displays in real time.

ScanGAN360: A Generative Model of Realistic Scanpaths for 360° Images.

Understanding and modeling the dynamics of human gaze behavior in 360° environments is crucial for creating, improving, and developing emerging virtual reality applications. However, recruiting human observers and acquiring enough data to analyze their behavior when exploring virtual environments requires complex hardware and software setups, and can be time-consuming. Being able to generate virtual observers can help overcome this limitation, and thus stands as an open problem in this medium.

Deep learning multi-shot 3D localization microscopy using hybrid optical-electronic computing.

Current 3D localization microscopy approaches are fundamentally limited in their ability to image thick, densely labeled specimens. Here, we introduce a hybrid optical-electronic computing approach that jointly optimizes an optical encoder (a set of multiple, simultaneously imaged 3D point spread functions) and an electronic decoder (a neural-network-based localization algorithm) to optimize 3D localization performance under these conditions. With extensive simulations and biological experiments, we demonstrate that our deep-learning-based microscope achieves significantly higher 3D localization accuracy than existing approaches, especially in challenging scenarios with high molecular density over large depth ranges.

Unfiltered holography: optimizing high diffraction orders without optical filtering for compact holographic displays.

Computer-generated holography suffers from high diffraction orders (HDOs) created from pixelated spatial light modulators, which must be optically filtered using bulky optics. Here, we develop an algorithmic framework for optimizing HDOs without optical filtering to enable compact holographic displays. We devise a wave propagation model of HDOs and use it to optimize phase patterns, which allows HDOs to contribute to forming the image instead of creating artifacts.

Holographic pancake optics for thin and lightweight optical see-through augmented reality.

Holographic pancake optics have been designed and fabricated in eyewear display optics literature dating back to 1985, however, a see-through pancake optic solution has not been demonstrated to date. The key contribution here is the first full-color volume holographic pancake optic in an optical see-through configuration for applications in mobile augmented reality. Specifically, the full-color volume holographic pancake is combined with a flat lightguide in order to achieve the optical see-through property.

Roadmap on digital holography [Invited].

This Roadmap article on digital holography provides an overview of a vast array of research activities in the field of digital holography. The paper consists of a series of 25 sections from the prominent experts in digital holography presenting various aspects of the field on sensing, 3D imaging and displays, virtual and augmented reality, microscopy, cell identification, tomography, label-free live cell imaging, and other applications. Each section represents the vision of its author to describe the significant progress, potential impact, important developments, and challenging issues in the field of digital holography.

Speckle-free holography with partially coherent light sources and camera-in-the-loop calibration.

Computer-generated holography (CGH) holds transformative potential for a wide range of applications, including direct-view, virtual and augmented reality, and automotive display systems. While research on holographic displays has recently made impressive progress, image quality and eye safety of holographic displays are fundamentally limited by the speckle introduced by coherent light sources. Here, we develop an approach to CGH using partially coherent sources.

Toward the next-generation VR/AR optics: a review of holographic near-eye displays from a human-centric perspective.

Wearable near-eye displays for virtual and augmented reality (VR/AR) have seen enormous growth in recent years. While researchers are exploiting a plethora of techniques to create life-like three-dimensional (3D) objects, there is a lack of awareness of the role of human perception in guiding the hardware development. An ultimate VR/AR headset must integrate the display, sensors, and processors in a compact enclosure that people can comfortably wear for a long time while allowing a superior immersion experience and user-friendly human-computer interaction.

Event-Based Near-Eye Gaze Tracking Beyond 10,000 Hz.

The cameras in modern gaze-tracking systems suffer from fundamental bandwidth and power limitations, constraining data acquisition speed to 300 Hz realistically. This obstructs the use of mobile eye trackers to perform, e.g.

Inference in artificial intelligence with deep optics and photonics.

Artificial intelligence tasks across numerous applications require accelerators for fast and low-power execution. Optical computing systems may be able to meet these domain-specific needs but, despite half a century of research, general-purpose optical computing systems have yet to mature into a practical technology. Artificial intelligence inference, however, especially for visual computing applications, may offer opportunities for inference based on optical and photonic systems.

Roadmap on 3D integral imaging: sensing, processing, and display.

This Roadmap article on three-dimensional integral imaging provides an overview of some of the research activities in the field of integral imaging. The article discusses various aspects of the field including sensing of 3D scenes, processing of captured information, and 3D display and visualization of information. The paper consists of a series of 15 sections from the experts presenting various aspects of the field on sensing, processing, displays, augmented reality, microscopy, object recognition, and other applications.

Three-dimensional imaging through scattering media based on confocal diffuse tomography.

Optical imaging techniques, such as light detection and ranging (LiDAR), are essential tools in remote sensing, robotic vision, and autonomous driving. However, the presence of scattering places fundamental limits on our ability to image through fog, rain, dust, or the atmosphere. Conventional approaches for imaging through scattering media operate at microscopic scales or require a priori knowledge of the target location for 3D imaging.