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Laura Waller

Publications and source records attributed to Laura Waller.

At least 37 records · Page 2Linked to original sources

Sample Motion for Structured Illumination Fluorescence Microscopy

Structured illumination microscopy (SIM) uses a set of images captured with different illumination patterns to computationally reconstruct resolution beyond the diffraction limit. Here, we propose an alternative approach using a single speckle illumination pattern and relying on inherent sample motion to encode the super-resolved information in multiple raw images. From a set of raw fluorescence images captured as the sample moves, we jointly estimate both the sample motion and the super-resolved image. We demonstrate the feasibility of the proposed method both in simulation and in experiment.

physics.optics↗

Multi-modal deformable image registration using untrained neural networks

Image registration techniques usually assume that the images to be registered are of a certain type (e.g. single- vs. multi-modal, 2D vs. 3D, rigid vs. deformable) and there lacks a general method that can work for data under all conditions. We propose a registration method that utilizes neural networks for image representation. Our method uses untrained networks with limited representation capacity as an implicit prior to guide for a good registration. Unlike previous approaches that are specialized for specific data types, our method handles both rigid and non-rigid, as well as single- and multi-modal registration, without requiring changes to the model or objective function. We have performed a comprehensive evaluation study using a variety of datasets and demonstrated promising performance.

eess.IV↗

Estimation-theoretic analysis of lensless imaging

We analyze lensless imaging systems with estimation-theoretic techniques based on Fisher information. Our analysis evaluates multiple optical encoder designs on objects with varying sparsity, in the context of both Gaussian and Poisson noise models. Our simulations verify that lensless imaging system performance is object-dependent and highlight tradeoffs between encoder multiplexing and object sparsity, showing quantitatively that sparse objects tolerate higher levels of multiplexing than dense objects. Insights from our analysis promise to inform and improve optical encoder designs for lensless imaging.

eess.IV↗

Noise2Image: Noise-Enabled Static Scene Recovery for Event Cameras

Event cameras, also known as dynamic vision sensors, are an emerging modality for measuring fast dynamics asynchronously. Event cameras capture changes of log-intensity over time as a stream of 'events' and generally cannot measure intensity itself; hence, they are only used for imaging dynamic scenes. However, fluctuations due to random photon arrival inevitably trigger noise events, even for static scenes. While previous efforts have been focused on filtering out these undesirable noise events to improve signal quality, we find that, in the photon-noise regime, these noise events are correlated with the static scene intensity. We analyze the noise event generation and model its relationship to illuminance. Based on this understanding, we propose a method, called Noise2Image, to leverage the illuminance-dependent noise characteristics to recover the static parts of a scene, which are otherwise invisible to event cameras. We experimentally collect a dataset of noise events on static scenes to train and validate Noise2Image. Our results provide a novel approach for capturing static scenes in event cameras, solely from noise events, without additional hardware.

cs.CV↗

Unified, Verifiable Neural Simulators for Electromagnetic Wave Inverse Problems

Simulators based on neural networks offer a path to orders-of-magnitude faster electromagnetic wave simulations. Existing models, however, only address narrowly tailored classes of problems and only scale to systems of a few dozen degrees of freedom (DoFs). Here, we demonstrate a single, unified model capable of addressing scattering simulations with thousands of DoFs, of any wavelength, any illumination wavefront, and freeform materials, within broad configurable bounds. Based on an attentional multi-conditioning strategy, our method also allows non-recurrent supervision on and prediction of intermediate physical states, which provides improved generalization with no additional data-generation cost. Using this O(1)-time intermediate prediction capability, we propose and prove a rigorous, efficiently computable upper bound on prediction error, allowing accuracy guarantees at inference time for all predictions. After training solely on randomized systems, we demonstrate the unified model across a suite of challenging multi-disciplinary inverse problems, finding strong efficacy and speed improvements up to 96% for problems in optical tomography, beam shaping through volumetric random media, and freeform photonic inverse design, with no problem-specific training. Our findings demonstrate a path to universal, verifiably accurate neural surrogates for existing scattering simulators, and our conditioning and training methods are directly applicable to any PDE admitting a time-domain iterative solver.

physics.optics↗

Non-Destructive, High-Resolution, Chemically Specific, 3D Nanostructure Characterization using Phase-Sensitive EUV Imaging Reflectometry

Next-generation nano and quantum devices have increasingly complex 3D structure. As the dimensions of these devices shrink to the nanoscale, their performance is often governed by interface quality or precise chemical or dopant composition. Here we present the first phase-sensitive extreme ultraviolet imaging reflectometer. It combines the excellent phase stability of coherent high-harmonic sources, the unique chemical- and phase-sensitivity of extreme ultraviolet reflectometry, and state-of-the-art ptychography imaging algorithms. This tabletop microscope can non-destructively probe surface topography, layer thicknesses, and interface quality, as well as dopant concentrations and profiles. High-fidelity imaging was achieved by implementing variable-angle ptychographic imaging, by using total variation regularization to mitigate noise and artifacts in the reconstructed image, and by using a high-brightness, high-harmonic source with excellent intensity and wavefront stability. We validate our measurements through multiscale, multimodal imaging to show that this technique has unique advantages compared with other techniques based on electron and scanning-probe microscopies.

physics.optics↗

Wavefront Randomization Improves Deconvolution

The performance of an imaging system is limited by optical aberrations, which cause blurriness in the resulting image. Digital correction techniques, such as deconvolution, have limited ability to correct the blur, since some spatial frequencies in the scene are not measured adequately (i.e., 'zeros' of the system transfer function). We prove that the addition of a random mask to an imaging system removes its dependence on aberrations, reducing the likelihood of zeros in the transfer function and consequently decreasing the sensitivity to noise during deconvolution. In simulation, we show that this strategy improves image quality over a range of aberration types, aberration strengths, and signal-to-noise ratios.

cs.CV↗

The Berkeley Single Cell Computational Microscopy (BSCCM) Dataset

Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the performance of computational imaging systems, especially those that incorporate machine learning, is sample-dependent. Thus, standardized datasets are an essential tool for comparing the performance of different approaches. Here, we introduce the Berkeley Single Cell Computational Microscopy (BSCCM) dataset, which contains over ~12,000,000 images of 400,000 of individual white blood cells. The dataset contains images captured with multiple illumination patterns on an LED array microscope and fluorescent measurements of the abundance of surface proteins that mark different cell types. We hope this dataset will provide a valuable resource for the development and testing of new algorithms in computational microscopy and computer vision with practical biomedical applications.

cs.CV↗

BiPMAP: A Toolbox for Predictions of Perceived Motion Artifacts on Modern Displays

Presenting dynamic scenes without incurring motion artifacts visible to observers requires sustained effort from the display industry. A tool that predicts motion artifacts and simulates artifact elimination through optimizing the display configuration is highly desired to guide the design and manufacture of modern displays. Despite the popular demands, there is no such tool available in the market. In this study, we deliver an interactive toolkit, Binocular Perceived Motion Artifact Predictor (BiPMAP), as an executable file with GPU acceleration. BiPMAP accounts for an extensive collection of user-defined parameters and directly visualizes a variety of motion artifacts by presenting the perceived continuous and sampled moving stimuli side-by-side. For accurate artifact predictions, BiPMAP utilizes a novel model of the human contrast sensitivity function to effectively imitate the frequency modulation of the human visual system. In addition, BiPMAP is capable of deriving various in-plane motion artifacts for 2D displays and depth distortion in 3D stereoscopic displays.

eess.SP↗

Fast non-iterative algorithm for 3D point-cloud holography

Recently developed iterative and deep learning-based approaches to computer-generated holography (CGH) have been shown to achieve high-quality photorealistic 3D images with spatial light modulators. However, such approaches remain overly cumbersome for patterning sparse collections of target points across a photoresponsive volume in applications including biological microscopy and material processing. Specifically, in addition to requiring heavy computation that cannot accommodate real-time operation in mobile or hardware-light settings, existing sampling-dependent 3D CGH methods preclude the ability to place target points with arbitrary precision, limiting accessible depths to a handful of planes. Accordingly, we present a non-iterative point cloud holography algorithm that employs fast deterministic calculations in order to efficiently allocate patches of SLM pixels to different target points in the 3D volume and spread the patterning of all points across multiple time frames. Compared to a matched-performance implementation of the iterative Gerchberg-Saxton algorithm, our algorithm's relative computation speed advantage was found to increase with SLM pixel count, exceeding 100,000x at 512x512 array format.

cs.GR↗

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.

physics.optics↗

Dynamic Structured Illumination Microscopy with a Neural Space-time Model

Structured illumination microscopy (SIM) reconstructs a super-resolved image from multiple raw images captured with different illumination patterns; hence, acquisition speed is limited, making it unsuitable for dynamic scenes. We propose a new method, Speckle Flow SIM, that uses static patterned illumination with moving samples and models the sample motion during data capture in order to reconstruct the dynamic scene with super-resolution. Speckle Flow SIM relies on sample motion to capture a sequence of raw images. The spatio-temporal relationship of the dynamic scene is modeled using a neural space-time model with coordinate-based multi-layer perceptrons (MLPs), and the motion dynamics and the super-resolved scene are jointly recovered. We validate Speckle Flow SIM for coherent imaging in simulation and build a simple, inexpensive experimental setup with off-the-shelf components. We demonstrate that Speckle Flow SIM can reconstruct a dynamic scene with deformable motion and 1.88x the diffraction-limited resolution in experiment.

physics.optics↗

Dancing under the stars: video denoising in starlight

Imaging in low light is extremely challenging due to low photon counts. Using sensitive CMOS cameras, it is currently possible to take videos at night under moonlight (0.05-0.3 lux illumination). In this paper, we demonstrate photorealistic video under starlight (no moon present, $<$0.001 lux) for the first time. To enable this, we develop a GAN-tuned physics-based noise model to more accurately represent camera noise at the lowest light levels. Using this noise model, we train a video denoiser using a combination of simulated noisy video clips and real noisy still images. We capture a 5-10 fps video dataset with significant motion at approximately 0.6-0.7 millilux with no active illumination. Comparing against alternative methods, we achieve improved video quality at the lowest light levels, demonstrating photorealistic video denoising in starlight for the first time.

cs.CV↗

Three-dimensional bi-functional refractive index and fluorescence microscopy (BRIEF)

Fluorescence microscopy is a powerful tool for imaging biological samples with molecular specificity. In contrast, phase microscopy provides label-free measurement of the sample's refractive index (RI), which is an intrinsic optical property that quantitatively relates to cell morphology, mass, and stiffness. Conventional imaging techniques measure either the labeled fluorescence (functional) information or the label-free RI (structural) information, though it may be valuable to have both. For example, biological tissues have heterogeneous RI distributions, causing sample-induced scattering that degrades the fluorescence image quality. When both fluorescence and 3D RI are measured, one can use the RI information to digitally correct multiple-scattering effects in the fluorescence image. Here, we develop a new computational multi-modal imaging method based on epi-mode microscopy that reconstructs both 3D fluorescence and 3D RI from a single dataset. We acquire dozens of fluorescence images, each 'illuminated' by a single fluorophore, then solve an inverse problem with a multiple-scattering forward model. We experimentally demonstrate our method for epi-mode 3D RI imaging and digital correction of multiple-scattering effects in fluorescence images.

physics.optics↗

Sparse deep computer-generated holography for optical microscopy

Computer-generated holography (CGH) has broad applications such as direct-view display, virtual and augmented reality, as well as optical microscopy. CGH usually utilizes a spatial light modulator that displays a computer-generated phase mask, modulating the phase of coherent light in order to generate customized patterns. The algorithm that computes the phase mask is the core of CGH and is usually tailored to meet different applications. CGH for optical microscopy usually requires 3D accessibility (i.e., generating overlapping patterns along the $z$-axis) and micron-scale spatial precision. Here, we propose a CGH algorithm using an unsupervised generative model designed for optical microscopy to synthesize 3D selected illumination. The algorithm, named sparse deep CGH, is able to generate sparsely distributed points in a large 3D volume with higher contrast than conventional CGH algorithms.

physics.optics↗

A MEMS-based optical scanning system for precise, high-speed neural interfacing

Optical scanning is a prevalent technique for optical neural interfaces where light delivery with high spatial and temporal precision is desired. However, due to the sequential nature of point-scanning techniques, the settling time of optical modulators is a major bottleneck for throughput and limits random-access targeting capabilities. While fast lateral scanners exist, commercially available varifocal elements are constrained to >3ms settling times, limiting the speed of the overall system to hundreds of Hz. Faster focusing methods exist but cannot combine fast operation and dwelling capability with electrical and optical efficiency. Here, we present a varifocal mirror comprised of an array of piston-motion MEMS micromirrors and a custom driver ASIC, offering fast operation with dwelling capability while maintaining high diffraction efficiency. The ASIC features a reconfigurable nonlinear DAC to simultaneously compensate for the built-in nonlinearity of electrostatic actuators and the global process variations in MEMS mirrors. Experimental results demonstrate a wide continuous sweeping range that spans 22 distinctly resolvable depth planes with refresh rates greater than 12 kHz.

physics.app-ph↗

Roadmap on Wavefront Shaping and deep imaging in complex media

The last decade has seen the development of a wide set of tools, such as wavefront shaping, computational or fundamental methods, that allow to understand and control light propagation in a complex medium, such as biological tissues or multimode fibers. A vibrant and diverse community is now working on this field, that has revolutionized the prospect of diffraction-limited imaging at depth in tissues. This roadmap highlights several key aspects of this fast developing field, and some of the challenges and opportunities ahead.

physics.optics↗

Distributed Reconstruction Algorithm for Electron Tomography with Multiple-scattering Samples

Three-dimensional electron tomography is used to understand the structure and properties of samples in chemistry, materials science, geoscience, and biology. With the recent development of high-resolution detectors and algorithms that can account for multiple-scattering events, thicker samples can be examined at finer resolution, resulting in larger reconstruction volumes than previously possible. In this work, we propose a distributed computing framework that reconstructs large volumes by decomposing a projected tilt-series into smaller datasets such that sub-volumes can be simultaneously reconstructed on separate compute nodes using a cluster. We demonstrate our method by reconstructing a multiple-scattering layered clay (montmorillonite) sample at high resolution from a large field-of-view tilt-series phase contrast transmission electron microscopty dataset.

physics.comp-ph↗