Scholars@Duke
Roarke Horstmeyer

Roarke Horstmeyer

Assistant Professor of Biomedical Engineering
Biomedical Engineering
roarke.w.horstmeyer@duke.edu
Box 90281, Durham, NC 27708-0548
Fitzpatrick Center (CIEMAS) Room 2569, 101 Science Drive, Durham, NC 27701
Office hours

Selected Publications

Computational 3D topographic microscopy from terabytes of data per sample

Journal Article Journal of Big Data · December 1, 2024 We present a large-scale computational 3D topographic microscope that enables 6-gigapixel profilometric 3D imaging at micron-scale resolution across >110 cm2 areas over multi-millimeter axial ranges. Our computational microscope, termed STARCAM (Scanning T ... Full text Cite

A comprehensive overview of diffuse correlation spectroscopy: Theoretical framework, recent advances in hardware, analysis, and applications.

Journal Article NeuroImage · September 2024 Diffuse correlation spectroscopy (DCS) is a powerful tool for assessing microvascular hemodynamic in deep tissues. Recent advances in sensors, lasers, and deep learning have further boosted the development of new DCS methods. However, newcomers might feel ... Full text Cite

Deep focusing with broadband light

Journal Article Nature Photonics · July 1, 2024 Broadband energy can be delivered to extended targets deep inside a multiple-scattering system, paving ways for using broadband, partially incoherent light in a wide range of applications, such as deep-tissue imaging, laser therapy and optogenetics. ... Full text Cite

Anisotropic regularization for sparsely sampled and noise-robust Fourier ptychography.

Journal Article Optics express · July 2024 Fourier ptychography (FP) is a powerful computational imaging technique that provides super-resolution and quantitative phase imaging capabilities by scanning samples in Fourier space with angle-varying illuminations. However, the image reconstruction in F ... Full text Cite

Tensorial tomographic Fourier ptychography with applications to muscle tissue imaging

Journal Article Advanced Photonics · March 1, 2024 We report tensorial tomographic Fourier ptychography (T2oFu), a nonscanning label-free tomographic microscopy method for simultaneous imaging of quantitative phase and anisotropic specimen information in 3D. Built upon Fourier ptychography, a quantitative ... Full text Cite

Innovations in signal/image processing and data analysis in optical microscopy

Chapter · January 1, 2024 Modern optical imaging relies on several computational techniques to address different challenges and fundamental limitations, such as noise, limited space-bandwidth product, unwanted color variability and quantification of relevant image features. A wide ... Full text Cite

Message from the Chairs

Journal Article 2024 IEEE International Conference on Computational Photography, ICCP 2024 - Proceedings · January 1, 2024 Full text Cite

Efficient signal extraction for diffuse correlation spectroscopy with SPAD arrays at low photon regimes

Conference Microscopy Histopathology and Analytics, Microscopy 2024 in Proceedings Optica Biophotonics Congress: Biomedical Optics 2024, Translational, Microscopy, OCT, OTS, BRAIN - Part of Optica Biophotonics Congress: Biomedical Optics · January 1, 2024 SPAD arrays have shown potential for improving SNR for diffuse correlation spectroscopy in low photon regimes. Here, we will explore different methods of integrating parallelized DCS signals in such regimes for deep blood flow extraction. ... Cite

Efficient signal extraction for diffuse correlation spectroscopy with SPAD arrays at low photon regimes

Conference Optical Tomography and Spectroscopy, OT and S 2024 in Proceedings Optica Biophotonics Congress: Biomedical Optics 2024, Translational, Microscopy, OCT, OTS, BRAIN - Part of Optica Biophotonics Congress: Biomedical Optics · January 1, 2024 SPAD arrays have shown potential for improving SNR for diffuse correlation spectroscopy in low photon regimes. Here, we will explore different methods of integrating parallelized DCS signals in such regimes for deep blood flow extraction. ... Cite

Micro-camera Arrays for Ultra-widefield, Multi-site Cellular Resolution Calcium Imaging Across the Dorsal Cortex of Behaving Mice

Conference Optics and the Brain, BRAIN 2024 in Proceedings Optica Biophotonics Congress: Biomedical Optics 2024, Translational, Microscopy, OCT, OTS, BRAIN - Part of Optica Biophotonics Congress: Biomedical Optics · January 1, 2024 Here, we introduce a miniaturized multi camera microscope that can simultaneously capture cellular resolution neural activity from multiple large fields of view of the cortex in a freely moving mouse. ... Cite

Efficient signal extraction for diffuse correlation spectroscopy with SPAD arrays at low photon regimes

Conference Optics and the Brain, BRAIN 2024 in Proceedings Optica Biophotonics Congress: Biomedical Optics 2024, Translational, Microscopy, OCT, OTS, BRAIN - Part of Optica Biophotonics Congress: Biomedical Optics · January 1, 2024 SPAD arrays have shown potential for improving SNR for diffuse correlation spectroscopy in low photon regimes. Here, we will explore different methods of integrating parallelized DCS signals in such regimes for deep blood flow extraction. ... Cite

Efficient signal extraction for diffuse correlation spectroscopy with SPAD arrays at low photon regimes

Conference Optical Tomography and Spectroscopy, OT and S 2024 in Proceedings Optica Biophotonics Congress: Biomedical Optics 2024, Translational, Microscopy, OCT, OTS, BRAIN - Part of Optica Biophotonics Congress: Biomedical Optics · January 1, 2024 SPAD arrays have shown potential for improving SNR for diffuse correlation spectroscopy in low photon regimes. Here, we will explore different methods of integrating parallelized DCS signals in such regimes for deep blood flow extraction. ... Full text Cite

Micro-camera Arrays for Ultra-widefield, Multi-site Cellular Resolution Calcium Imaging Across the Dorsal Cortex of Behaving Mice

Conference Optics and the Brain, BRAIN 2024 in Proceedings Optica Biophotonics Congress: Biomedical Optics 2024, Translational, Microscopy, OCT, OTS, BRAIN - Part of Optica Biophotonics Congress: Biomedical Optics · January 1, 2024 Here, we introduce a miniaturized multi camera microscope that can simultaneously capture cellular resolution neural activity from multiple large fields of view of the cortex in a freely moving mouse. ... Full text Cite

Digital staining in optical microscopy using deep learning - a review

Journal Article PhotoniX · December 1, 2023 Until recently, conventional biochemical staining had the undisputed status as well-established benchmark for most biomedical problems related to clinical diagnostics, fundamental research and biotechnology. Despite this role as gold-standard, staining pro ... Full text Cite

SEMPAI: a Self-Enhancing Multi-Photon Artificial Intelligence for Prior-Informed Assessment of Muscle Function and Pathology.

Journal Article Advanced science (Weinheim, Baden-Wurttemberg, Germany) · October 2023 Deep learning (DL) shows notable success in biomedical studies. However, most DL algorithms work as black boxes, exclude biomedical experts, and need extensive data. This is especially problematic for fundamental research in the laboratory, where often onl ... Full text Cite

scatterBrains: an open database of human head models and companion optode locations for realistic Monte Carlo photon simulations.

Journal Article Journal of biomedical optics · October 2023 SignificanceMonte Carlo (MC) simulations are currently the gold standard in the near-infrared and diffuse correlation spectroscopy (NIRS/DCS) communities for generating light transport paths through tissue. However, realistic and diverse models th ... Full text Cite

High-resolution single-photon imaging with physics-informed deep learning.

Journal Article Nature communications · September 2023 High-resolution single-photon imaging remains a big challenge due to the complex hardware manufacturing craft and noise disturbances. Here, we introduce deep learning into SPAD, enabling super-resolution single-photon imaging with enhancement of bit depth ... Full text Cite

Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second.

Journal Article Nat Photonics · May 2023 Wide field of view microscopy that can resolve 3D information at high speed and spatial resolution is highly desirable for studying the behaviour of freely moving model organisms. However, it is challenging to design an optical instrument that optimises al ... Full text Open Access Link to item Cite

Multi-modal imaging using a cascaded microscope design.

Journal Article Optics letters · April 2023 We present a multi-modal fiber array snapshot technique (M-FAST) based on an array of 96 compact cameras placed behind a primary objective lens and a fiber bundle array. Our technique is capable of large-area, high-resolution, multi-channel video acquisiti ... Full text Cite

Imaging across multiple spatial scales with the multi-camera array microscope

Journal Article Optica · April 1, 2023 This paper experimentally examines different configurations of a multi-camera array microscope (MCAM) imaging technology. The MCAM is based upon a densely packed array of “micro-cameras” to jointly image across a large field-of-view (FOV) at high resolutio ... Full text Cite

Parallelized computational 3D video microscopy of freely moving organisms at multiple gigapixels per second.

Journal Article ArXiv · January 19, 2023 To study the behavior of freely moving model organisms such as zebrafish (Danio rerio) and fruit flies (Drosophila) across multiple spatial scales, it would be ideal to use a light microscope that can resolve 3D information over a wide field of view (FOV) ... Link to item Cite

High-throughput imaging across multiple spatial scales with the multi-camera array microscope (MCAM)

Conference Proceedings of SPIE - The International Society for Optical Engineering · January 1, 2023 “Anyone who uses a microscope has likely noticed the limitation of the trade-off between the field of view and the resolution”.1 To acquire highly resolved images at large fields of view, existing techniques typically record sequential images at different ... Full text Cite

Computational 3D surface microscopy from terabytes of data with a self-supervised reconstruction algorithm

Conference Imaging Systems and Applications in Proceedings Optica Imaging Congress, 3D, COSI, DH, FLatOptics, IS, pcAOP - Part of Imaging and Applied Optics Congress 2023 · January 1, 2023 We present a computational 3D profilometric microscope employing an array of 54 cameras and 3-axis scanning to produce multi-TB datasets per sample. Using stereo and sharpness cues, our self-supervised reconstruction algorithm generates 6-gigapixel reconst ... Full text Cite

Computational 3D surface microscopy from terabytes of data with a self-supervised reconstruction algorithm

Conference Computational Optical Sensing and Imaging in Proceedings Optica Imaging Congress, 3D, COSI, DH, FLatOptics, IS, pcAOP - Part of Imaging and Applied Optics Congress 2023 · January 1, 2023 We present a computational 3D profilometric microscope employing an array of 54 cameras and 3-axis scanning to produce multi-TB datasets per sample. Using stereo and sharpness cues, our self-supervised reconstruction algorithm generates 6-gigapixel reconst ... Full text Cite

Anisotropic intensity diffraction tomography

Conference Computational Optical Sensing and Imaging in Proceedings Optica Imaging Congress, 3D, COSI, DH, FLatOptics, IS, pcAOP - Part of Imaging and Applied Optics Congress 2023 · January 1, 2023 We present a new non-scanning technique to reconstruct tomographic permittivity metrics of anisotropy samples from polarized intensity measurements. We apply the method to image both calibration targets and 3D tissue samples. ... Full text Cite

Multi-scale speckle-plethysmography with a multi-camera array microscope

Conference Computational Optical Sensing and Imaging in Proceedings Optica Imaging Congress, 3D, COSI, DH, FLatOptics, IS, pcAOP - Part of Imaging and Applied Optics Congress 2023 · January 1, 2023 We present a high spatial resolution speckle-plethysmography (SPG) system with 0.3 gigapixels per snapshot, using a recently developed parallelized array microscope. We demonstrate an SPG video monitoring physarum cytoplasmic streaming through a thin scatt ... Full text Cite

Fourier Ptychographic Iterative Engine Based on Alternating Direction Method of Multipliers with Anisotropic Total-Variation Regularization

Conference Computational Optical Sensing and Imaging in Proceedings Optica Imaging Congress, 3D, COSI, DH, FLatOptics, IS, pcAOP - Part of Imaging and Applied Optics Congress 2023 · January 1, 2023 We propose an ADMM-based phase retrieval algorithm for FP that utilizes anisotropic total variation regularization for the object function and L2 regularization for pupil functions. All our results in simulation and real experiments demonstrate that our al ... Full text Cite

Fourier Light Field Camera Array Microscope for Mesoscale 3D Imaging

Conference 3D Image Acquisition and Display: Technology, Perception and Applications in Proceedings Optica Imaging Congress, 3D, COSI, DH, FLatOptics, IS, pcAOP 2023 · January 1, 2023 We present the Fourier Light field Camera Array Microscope (FL-CAM) for high-throughput, single-snapshot 3D imaging. The FL-CAM substitutes a synchronized array of 48 independent imaging systems for micro-lens array of typical light field systems. ... Full text Cite

Gigapixel imaging with a novel multi-camera array microscope.

Journal Article Elife · December 14, 2022 The dynamics of living organisms are organized across many spatial scales. However, current cost-effective imaging systems can measure only a subset of these scales at once. We have created a scalable multi-camera array microscope (MCAM) that enables compr ... Full text Open Access Link to item Cite

Applications and Extensions of Fourier Ptychography

Journal Article Microscopy Today · November 1, 2022 Abstract:This is the third article within a three-part series on Fourier ptychography, which is a computational microscopy technique for high-resolution, large field-of-view imaging. While the previous artic ... Full text Cite

Roadmap on wavefront shaping and deep imaging in complex media

Journal Article JPhys Photonics · October 1, 2022 The last decade has seen the development of a wide set of tools, such as wavefront shaping, computational or fundamental methods, that allow us to understand and control light propagation in a complex medium, such as biological tissues or multimode fibers. ... Full text Cite

Fourier Ptychography Part II: Phase Retrieval and High-Resolution Image Formation

Journal Article Microscopy Today · September 1, 2022 Abstract:This article is the second within a three-part series on Fourier ptychography, which is a computational microscopy technique for high-resolution, large field-of-view imaging. While the first article ... Full text Cite

Imaging Dynamics Beneath Turbid Media via Parallelized Single-Photon Detection.

Journal Article Advanced science (Weinheim, Baden-Wurttemberg, Germany) · August 2022 Noninvasive optical imaging through dynamic scattering media has numerous important biomedical applications but still remains a challenging task. While standard diffuse imaging methods measure optical absorption or fluorescent emission, it is also well-est ... Full text Cite

A multiple instance learning approach for detecting COVID-19 in peripheral blood smears.

Journal Article PLOS Digit Health · August 2022 A wide variety of diseases are commonly diagnosed via the visual examination of cell morphology within a peripheral blood smear. For certain diseases, such as COVID-19, morphological impact across the multitude of blood cell types is still poorly understoo ... Full text Open Access Link to item Cite

Optical imaging and spectroscopy for the study of the human brain: status report.

Journal Article Neurophotonics · August 2022 This report is the second part of a comprehensive two-part series aimed at reviewing an extensive and diverse toolkit of novel methods to explore brain health and function. While the first report focused on neurophotonic tools mostly applicable to animal s ... Full text Cite

Introduction to Fourier Ptychography: Part I

Journal Article Microscopy Today · May 2022 Abstract:Fourier ptychography is an emerging computational microscopy technique that can generate gigapixel-scale images of biological samples. With only the addition of a low-cost LED array to a standard digital microscope ... Full text Cite

Quantitative Jones matrix imaging using vectorial Fourier ptychography.

Journal Article Biomed Opt Express · March 1, 2022 This paper presents a microscopic imaging technique that uses variable-angle illumination to recover the complex polarimetric properties of a specimen at high resolution and over a large field-of-view. The approach extends Fourier ptychography, which is a ... Full text Link to item Cite

The Role of Machine Learning in Cardiovascular Pathology.

Journal Article Can J Cardiol · February 2022 Machine learning has seen slow but steady uptake in diagnostic pathology over the past decade to assess digital whole-slide images. Machine learning tools have incredible potential to standardise, and likely even improve, histopathologic diagnoses, but the ... Full text Link to item Cite

Increasing a microscope's effective field of view via overlapped imaging and machine learning.

Journal Article Optics express · January 2022 This work demonstrates a multi-lens microscopic imaging system that overlaps multiple independent fields of view on a single sensor for high-efficiency automated specimen analysis. Automatic detection, classification and counting of various morphological f ... Full text Cite

Evaluation of U-Net Based Architectures for Automatic Aortic Dissection Segmentation

Journal Article ACM Transactions on Computing for Healthcare · January 1, 2022 Segmentation and reconstruction of arteries is important for a variety of medical and engineering fields, such as surgical planning and physiological modeling. However, manual methods can be laborious and subject to a high degree of human variability. In t ... Full text Cite

Transient Motion Classification Through Turbid Volumes via Parallelized Single-Photon Detection and Deep Contrastive Embedding.

Journal Article Frontiers in neuroscience · January 2022 Fast noninvasive probing of spatially varying decorrelating events, such as cerebral blood flow beneath the human skull, is an essential task in various scientific and clinical settings. One of the primary optical techniques used is diffuse correlation spe ... Full text Cite

Speckle contrast diffuse correlation spectroscopy with parallelized single photon detection

Conference Optics InfoBase Conference Papers · January 1, 2022 We present a 32 × 32 SPAD array-based speckle contrast diffuse correlation analysis method, which allows monitoring fast decorrelating deep tissue dynamics using a long source-detector separation. ... Cite

Parallelized 16-gigapixel microscopy for rapid imaging of multiple whole slides

Conference Optics InfoBase Conference Papers · January 1, 2022 We present a new multi-camera array microscope (MCAM) that can capture images at single micrometer resolution over 54 cm2 fields of view, which contain up to 16 gigapixels, and associated software for seamless viewing and analysis. ... Cite

Gigapixel-per-second, wide-field 3D topographic imaging with physics-supervised learning

Conference Optics InfoBase Conference Papers · January 1, 2022 We present a new interleaved multi-camera microscope architecture and a physics-supervised multi-ocular stereo neural network that enable simultaneous photometric and 3D topographic imaging of freely-moving organisms over 135 cm2 at throughputs exceeding 5 ... Cite

Tensorial tomographic differential phase-contrast microscopy

Conference IEEE International Conference on Computational Photography, ICCP 2022 · January 1, 2022 We report Tensorial Tomographic Differential Phase-Contrast microscopy (T2DPC), a quantitative label-free tomographic imaging method for simultaneous measurement of phase and anisotropy. T2DPC extends differential phase-contrast microscopy, a quantitative ... Full text Cite

Quantized Fourier ptychography with binary images from SPAD cameras

Journal Article Photonics Research · October 1, 2021 Recently developed single-photon avalanche diode (SPAD) array cameras provide single-photon sensitivity and picosecond-scale time gating for time-of-flight measurements, with applications in LIDAR and fluorescence lifetime imaging. As compared to standard ... Full text Cite

Quantitative Jones matrix imaging using vectorial Fourier ptychography

Journal Article · September 30, 2021 This paper presents a microscopic imaging technique that uses variable-angle illumination to recover the complex polarimetric properties of a specimen at high resolution and over a large field-of-view. The approach extends Fourier ptychography, which is a ... Open Access Link to item Cite

Imaging dynamics beneath turbid media via parallelized single-photon detection

Journal Article · July 3, 2021 Noninvasive optical imaging through dynamic scattering media has numerous important biomedical applications but still remains a challenging task. While standard diffuse imaging methods measure optical absorption or fluorescent emission, it is also well-est ... Open Access Link to item Cite

Deep image prior for undersampling high-speed photoacoustic microscopy.

Journal Article Photoacoustics · June 2021 Photoacoustic microscopy (PAM) is an emerging imaging method combining light and sound. However, limited by the laser's repetition rate, state-of-the-art high-speed PAM technology often sacrifices spatial sampling density (i.e., undersampling) for i ... Full text Open Access Cite

Deep image prior for undersampling high-speed photoacoustic microscopy

Journal Article Photoacoustics · June 1, 2021 Photoacoustic microscopy (PAM) is an emerging imaging method combining light and sound. However, limited by the laser's repetition rate, state-of-the-art high-speed PAM technology often sacrifices spatial sampling density (i.e., undersampling) for increase ... Full text Cite

Ultrasensitive point-of-care immunoassay for secreted glycoprotein detects Ebola infection earlier than PCR.

Journal Article Sci Transl Med · April 7, 2021 Ebola virus (EBOV) hemorrhagic fever outbreaks have been challenging to deter due to the lack of health care infrastructure in disease-endemic countries and a corresponding inability to diagnose and contain the disease at an early stage. EBOV vaccines and ... Full text Link to item Cite

Reconstructing Undersampled Photoacoustic Microscopy Images Using Deep Learning.

Journal Article IEEE transactions on medical imaging · February 2021 One primary technical challenge in photoacoustic microscopy (PAM) is the necessary compromise between spatial resolution and imaging speed. In this study, we propose a novel application of deep learning principles to reconstruct undersampled PAM images and ... Full text Cite

Fast and sensitive diffuse correlation spectroscopy with highly parallelized single photon detection

Journal Article APL Photonics · February 1, 2021 Diffuse correlation spectroscopy (DCS) is a well-established method that measures rapid changes in scattered coherent light to identify blood flow and functional dynamics within a tissue. While its sensitivity to minute scatterer displacements leads to a n ... Full text Cite

Increasing a microscope’s effective field of view via overlapped imaging and machine learning

Journal Article Optics InfoBase Conference Papers · January 1, 2021 We demonstrate a multi-lenses microscopic imaging system that records overlapping fields-of-view for high-efficiency automated specimen analysis. We show both in simulation and experiment how our system can achieve accurate target object detection on overl ... Cite

High throughput acquisition and analysis of bacterial colony features using gigapixel microscopy

Conference Optics InfoBase Conference Papers · January 1, 2021 We utilize Gigapixel microscopy to quantify morphological features in bacterial colonies across multi-well plates. This system augments high-throughput assays by synchronously capturing valuable phenotypic information and is demonstrated here in an acquisi ... Cite

Rapid imaging of deep-tissue motion with parallelized diffuse correlation spectroscopy

Conference Optics InfoBase Conference Papers · January 1, 2021 We present a highly parallelized approach to diffuse correlation spectroscopy (DCS) using a 32 × 32 single-photon avalanche diode (SPAD) array, which allows imaging dynamic scattering events buried deep within tissue phantom at a 2.5Hz frame rate without r ... Cite

Mesoscopic photogrammetry with an unstabilized phone camera

Conference Proceedings of the IEEE Computer Society Conference on Computer Vision and Pattern Recognition · January 1, 2021 We present a feature-free photogrammetric technique that enables quantitative 3D mesoscopic (mm-scale height variation) imaging with tens-of-micron accuracy from sequences of images acquired by a smartphone at close range (several cm) under freehand motion ... Full text Cite

Physics-Enhanced Machine Learning for Virtual Fluorescence Microscopy

Conference Proceedings of the IEEE International Conference on Computer Vision · January 1, 2021 This paper introduces a new method of data-driven microscope design for virtual fluorescence microscopy. We use a deep neural network (DNN) to effectively design optical patterns for specimen illumination that substantially improve upon the ability to infe ... Full text Cite

Mesoscopic photogrammetry with an unstabilized phone camera

Journal Article CVPR 2021 · December 10, 2020 We present a feature-free photogrammetric technique that enables quantitative 3D mesoscopic (mm-scale height variation) imaging with tens-of-micron accuracy from sequences of images acquired by a smartphone at close range (several cm) under freehand motion ... Open Access Link to item Cite

Multi-element microscope optimization by a learned sensing network with composite physical layers.

Journal Article Optics letters · October 2020 Standard microscopes offer a variety of settings to help improve the visibility of different specimens to the end microscope user. Increasingly, however, digital microscopes are used to capture images for automated interpretation by computer algorithms (e. ... Full text Cite

Towards an intelligent microscope: Adaptively learned illumination for optimal sample classification

Journal Article ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings · May 1, 2020 Recent machine learning techniques have dramatically changed how we process digital images. However, the way in which we capture images is still largely driven by human intuition and experience. This restriction is in part due to the many available degrees ... Full text Open Access Cite

Physics-enhanced machine learning for virtual fluorescence microscopy

Journal Article · April 8, 2020 This paper introduces a new method of data-driven microscope design for virtual fluorescence microscopy. Our results show that by including a model of illumination within the first layers of a deep convolutional neural network, it is possible to learn task ... Open Access Link to item Cite

Diffraction tomography with a deep image prior.

Journal Article Optics express · April 2020 We present a tomographic imaging technique, termed Deep Prior Diffraction Tomography (DP-DT), to reconstruct the 3D refractive index (RI) of thick biological samples at high resolution from a sequence of low-resolution images collected under angularly vary ... Full text Open Access Cite

Fourier ptychography: current applications and future promises.

Journal Article Optics express · March 2020 Traditional imaging systems exhibit a well-known trade-off between the resolution and the field of view of their captured images. Typical cameras and microscopes can either "zoom in" and image at high-resolution, or they can "zoom out" to see a larger area ... Full text Cite

Learned Integrated Sensing Pipeline: Reconfigurable Metasurface Transceivers as Trainable Physical Layer in an Artificial Neural Network.

Journal Article Advanced science (Weinheim, Baden-Wurttemberg, Germany) · February 2020 The rapid proliferation of intelligent systems (e.g., fully autonomous vehicles) in today's society relies on sensors with low latency and computational effort. Yet current sensing systems ignore most available a priori knowledge, notably in the design of ... Full text Cite

Generation and characterization of focused helical x-ray beams.

Journal Article Science advances · February 2020 The phenomenon of orbital angular momentum (OAM) affects a variety of important applications in visible optics, including optical tweezers, free-space communication, and 3D localization for fluorescence imaging. The lack of suitable wavefront shaping optic ... Full text Cite

Fast sensitive diffuse correlation spectroscopy with a SPAD array

Conference Optics InfoBase Conference Papers · January 1, 2020 We develop a highly parallelized DCS system using a 32 × 32 single-photon avalanche diode array, and demonstrate its sensitivity improvement in a DMD-based phantom study and an in vivo forehead blood flow experiment. ... Full text Cite

Classifying decorrelation events hidden beneath scattering media via SPAD array detection

Conference Optics InfoBase Conference Papers · January 1, 2020 We present a technique to detect and classify different spatiotemporal dynamic events within thick (5mm) and rapidly decorrelating (10-4s) scattering media using a SPAD array and an unsupervised deep embedding algorithm. ... Cite

Towards a vectorial treatment of Fourier ptychographic microscopy

Conference Optics InfoBase Conference Papers · January 1, 2020 We present a new imaging technique that captures and reconstructs the complex-valued polarization-dependent properties of a sample in a Jones matrix formalism at an extended resolution through the acquisition of multiple intensity-only measurements. ... Cite

Learned sensing: jointly optimized microscope hardware for accurate image classification.

Journal Article Biomedical optics express · December 2019 Since its invention, the microscope has been optimized for interpretation by a human observer. With the recent development of deep learning algorithms for automated image analysis, there is now a clear need to re-design the microscope's hardware for specif ... Full text Open Access Cite

Imaging the behavior and neural activity of freely moving organisms with a gigapixel microscope

Conference Optics InfoBase Conference Papers · January 1, 2019 We present a micro-camera array microscope that images at cellular-level detail across hundreds of square centimeters. We demonstrate how this microscope can image the behavior and fluorescent neural activity of freely swimming zebrafish ... Full text Cite

Depth tracking using a multi-aperture microscope

Conference Optics InfoBase Conference Papers · January 1, 2019 We present a multi-aperture gigapixel microscope that is capable of imaging a 600cm2 area at 10 micrometer resolution and can simultaneously track the depth of objects within the scene. We demonstrate this capability by tracking freely swimming zebrafish l ... Full text Cite

Scattering correlations of time-gated light

Journal Article Optica · April 20, 2018 Manipulating the propagation of light through scattering media remains a major challenge for many applications, including astronomy, biomedical imaging, and colloidal optics. Light can be focused through inhomogeneous media into any desired point with wave ... Full text Open Access Cite

Convolutional neural networks that teach microscopes how to image

Journal Article · September 21, 2017 Deep learning algorithms offer a powerful means to automatically analyze the content of medical images. However, many biological samples of interest are primarily transparent to visible light and contain features that are difficult to resolve with a standa ... Link to item Cite

Generalized optical memory effect

Journal Article Optica · August 20, 2017 The optical memory effect is a well-known type of tilt/tilt wave correlation that is observed in coherent fields, allowing control over scattered light through thin and diffusive materials. Here we show that the optical memory effect is a special case of a ... Full text Open Access Cite

Subsampled phase retrieval for temporal resolution enhancement in lensless on-chip holographic video.

Journal Article Biomedical optics express · March 2017 On-chip holographic video is a convenient way to monitor biological samples simultaneously at high spatial resolution and over a wide field-of-view. However, due to the limited readout rate of digital detector arrays, one often faces a tradeoff between the ... Full text Cite

Dictionary-based phase retrieval for space-time super resolution using lens-free on-chip holographic video

Conference Optics InfoBase Conference Papers · January 1, 2017 We propose a dictionary-based phase retrieval approach for monitoring in vivo biological samples based on lens-free on-chip holographic video. Our results present a temporal increase of 9× with 4×4 sub-sampling. ... Full text Cite

High-speed holographic imaging using compressed sensing and phase retrieval

Conference Proceedings of SPIE - The International Society for Optical Engineering · January 1, 2017 Digital in-line holography serves as a useful encoder for spatial information. This allows three-dimensional reconstruction from a two-dimensional image. This is applicable to the tasks of fast motion capture, particle tracking etc. Sampling high resolutio ... Full text Cite

Subsampled Phase Retrieval for On-chip Lensless Holographic Video

Journal Article · December 7, 2016 On-chip holographic video is a convenient way to monitor biological samples simultaneously at high spatial resolution and over a wide field-of-view. However, due to the limited readout rate of digital detector arrays, one often faces a tradeoff between the ... Link to item Cite

Toward Long-Distance Subdiffraction Imaging Using Coherent Camera Arrays

Journal Article IEEE Transactions on Computational Imaging · September 1, 2016 In this work, we propose using camera arrays coupled with coherent illumination as an effective method of improving spatial resolution in long distance images by a factor of ten and beyond. Recent advances in ptychography have demonstrated that one can ima ... Full text Cite

Diffraction tomography with Fourier ptychography.

Journal Article Optica · August 2016 This paper presents a technique to image the complex index of refraction of a sample across three dimensions. The only required hardware is a standard microscope and an array of LEDs. The method, termed Fourier ptychographic tomography (FPT), first capture ... Full text Cite

Aperture scanning Fourier ptychographic microscopy.

Journal Article Biomedical optics express · August 2016 Fourier ptychographic microscopy (FPM) is implemented through aperture scanning by an LCOS spatial light modulator at the back focal plane of the objective lens. This FPM configuration enables the capturing of the complex scattered field for a 3D sample bo ... Full text Cite

Standardizing the resolution claims for coherent microscopy

Journal Article Nature Photonics · February 1, 2016 Full text Cite

Wide field-of-view fluorescence image deconvolution with aberration-estimation from Fourier ptychography.

Journal Article Biomedical optics express · February 2016 This paper presents a method to simultaneously acquire an aberration-corrected, wide field-of-view fluorescence image and a high-resolution coherent bright-field image using a computational microscopy method. First, the procedure applies Fourier ptychograp ... Full text Cite

Volumetric phase imaging using Fourier ptychography

Conference Optics InfoBase Conference Papers · January 1, 2016 Fourier ptychography uses angularly varying illumination and post-processing algorithms to create gigapixel images. Here, we extend this work to measure the 3D refractive index profile of thick specimens at high resolution. ... Full text Cite

Translation correlations in anisotropically scattering media

Journal Article Nature Physics · July 31, 2015 Controlling light propagation across scattering media by wavefront shaping holds great promise for a wide range of communications and imaging applications. But, finding the right shape for the wavefront is a challenge when the mapping between input and out ... Full text Cite

Physically secure and fully reconfigurable data storage using optical scattering

Conference Proceedings of the 2015 IEEE International Symposium on Hardware-Oriented Security and Trust, HOST 2015 · June 29, 2015 This paper presents an optical method of storing random cryptographic keys within a reconfigurable volume of polymer-dispersed liquid crystal (PDLC). We suggest a PDLC-based device that functions as an integrated optical physical unclonable function (PUF). ... Full text Cite

Digital pathology with Fourier ptychography.

Journal Article Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society · June 2015 Fourier ptychographic microscopy (FPM) is a recently introduced method of acquiring high-resolution, wide field of view (FOV) giga-pixel histology images. The FPM procedure first acquires a sequence of low-resolution images of a sample under variable-angle ... Full text Cite

Solving ptychography with a convex relaxation.

Journal Article New journal of physics · May 2015 Ptychography is a powerful computational imaging technique that transforms a collection of low-resolution images into a high-resolution sample reconstruction. Unfortunately, algorithms that currently solve this reconstruction problem lack stability, robust ... Full text Cite

High numerical aperture Fourier ptychography: principle, implementation and characterization.

Journal Article Optics express · February 2015 Fourier ptychography (FP) utilizes illumination control and computational post-processing to increase the resolution of bright-field microscopes. In effect, FP extends the fixed numerical aperture (NA) of an objective lens to form a larger synthetic system ... Full text Cite

Guidestar-assisted wavefront-shaping methods for focusing light into biological tissue.

Journal Article Nature photonics · January 2015 In the field of biomedical optics, optical scattering has traditionally limited the range of imaging within tissue to a depth of one millimetre. A recently developed class of wavefront-shaping techniques now aims to overcome this limit and achieve diffract ... Full text Cite

Overlapped Fourier coding for optical aberration removal.

Journal Article Optics express · October 2014 We present an imaging procedure that simultaneously optimizes a camera's resolution and retrieves a sample's phase over a sequence of snapshots. The technique, termed overlapped Fourier coding (OFC), first digitally pans a small aperture across a camera's ... Full text Cite

Modeling extensions of fourier ptychographic microscopy

Conference Microscopy and Microanalysis · August 1, 2014 Full text Cite

Aperture-scanning Fourier ptychography for 3D refocusing and super-resolution macroscopic imaging.

Journal Article Optics express · June 2014 We report an imaging scheme, termed aperture-scanning Fourier ptychography, for 3D refocusing and super-resolution macroscopic imaging. The reported scheme scans an aperture at the Fourier plane of an optical system and acquires the corresponding intensity ... Full text Cite

A model for ultrasound modulated light in a turbid medium

Conference Progress in Biomedical Optics and Imaging - Proceedings of SPIE · March 12, 2014 The ability to focus light in most tissue degrades quickly with depth due to high optical scattering. Researchers have investigated using both ultrasound (US) and light synergistically to overcome this difficulty. Ultrasound has been utilized to modulated ... Full text Cite

Reconfigurable random bit storage using polymer-dispersed liquid crystal

Journal Article · March 10, 2014 We present an optical method of storing random cryptographic keys, at high densities, within an electronically reconfigurable volume of polymer-dispersed liquid crystal (PDLC) film. We demonstrate how temporary application of a voltage above PDLC's saturat ... Link to item Cite

Diffusion model for ultrasound-modulated light.

Journal Article Journal of biomedical optics · March 2014 Researchers use ultrasound (US) to modulate diffusive light in a highly scattering medium like tissue. This paper analyzes the US-optical interaction in the scattering medium and derives an expression for the US-modulated optical radiance. The diffusion ap ... Full text Cite

Fourier pt ychographic microscopy

Journal Article Optics and Photonics News · January 1, 2014 Full text Cite

A phase space model of Fourier ptychographic microscopy.

Journal Article Optics express · January 2014 A new computational imaging technique, termed Fourier ptychographic microscopy (FPM), uses a sequence of low-resolution images captured under varied illumination to iteratively converge upon a high-resolution complex sample estimate. Here, we propose a mat ... Full text Cite

Physical key-protected one-time pad.

Journal Article Scientific reports · December 2013 We describe an encrypted communication principle that forms a secure link between two parties without electronically saving either of their keys. Instead, random cryptographic bits are kept safe within the unique mesoscopic randomness of two volumetric sca ... Full text Cite

Secure storage of cryptographic keys within random volumetric materials

Conference CLEO: Applications and Technology, CLEO_AT 2013 · November 19, 2013 We present a device to optically access gigabits of random keys stored within an object's microscopic randomness. We demonstrate how this device may allow two parties to securely communicate without digitally saving any sensitive information. © OSA 2013. ... Cite

Quantitative phase imaging via Fourier ptychographic microscopy.

Journal Article Optics letters · November 2013 Fourier ptychographic microscopy (FPM) is a recently developed imaging modality that uses angularly varying illumination to extend a system's performance beyond the limit defined by its optical components. The FPM technique applies a novel phase-retrieval ... Full text Cite

Wide-field, high-resolution Fourier ptychographic microscopy.

Journal Article Nature photonics · September 2013 In this article, we report an imaging method, termed Fourier ptychographic microscopy (FPM), which iteratively stitches together a number of variably illuminated, low-resolution intensity images in Fourier space to produce a wide-field, high-resolution com ... Full text Cite

Characterization of spatially varying aberrations for wide field-of-view microscopy.

Journal Article Optics express · July 2013 We describe a simple and robust approach for characterizing the spatially varying pupil aberrations of microscopy systems. In our demonstration with a standard microscope, we derive the location-dependent pupil transfer functions by first capturing multipl ... Full text Cite

Speckle-scale focusing in the diffusive regime with time-reversal of variance-encoded light (TROVE).

Journal Article Nature photonics · April 2013 Focusing of light in the diffusive regime inside scattering media has long been considered impossible. Recently, this limitation has been overcome with time reversal of ultrasound-encoded light (TRUE), but the resolution of this approach is fundamentally l ... Full text Cite

Analysis and modeling of an ultrasound-modulated guide star to increase the depth of focusing in a turbid medium.

Journal Article Journal of biomedical optics · February 2013 The effects of strong scattering in tissue limit the depth to which light may be focused. However, it has been shown that scattering may be reduced utilizing adaptive optics with a focused ultrasound (US) beam guidestar. The optical signal traveling throug ... Full text Cite

Fourier ptychographic microscopy: A method for pushing standard microscope beyond its physical limitations

Conference Asia Communications and Photonics Conference, ACP · January 1, 2013 I will report a method termed Fourier Ptychographic Microscopy (FPM), that effectively transforms a 2X standard microscope into a general microscope with 20X resolution and a field-of-view of ∼120 mm2. © OSA 2013. ... Cite

Secure storage of cryptographic keys within random volumetric materials

Conference 2013 Conference on Lasers and Electro-Optics, CLEO 2013 · January 1, 2013 We present a device to optically access gigabits of random keys stored within an object's microscopic randomness. We demonstrate how this device may allow two parties to securely communicate without digitally saving any sensitive information. © 2013 The Op ... Full text Cite

Fourier ptychographic microscopy: A method for pushing standard microscope beyond its physical limitations

Conference Asia Communications and Photonics Conference, ACP · January 1, 2013 I will report a method termed Fourier Ptychographic Microscopy (FPM), that effectively transforms a 2X standard microscope into a general microscope with 20X resolution and a field-of-view of ∼120 mm2. © OSA 2013. ... Full text Cite

Markov speckle for efficient random bit generation.

Conference Optics express · November 2012 Optical speckle is commonly observed in measurements using coherent radiation. While lacking experimental validation, previous work has often assumed that speckle's random spatial pattern follows a Markov process. Here, we present a derivation and experime ... Full text Cite

Partially coherent ambiguity functions for depth-variant point spread function design

Conference Progress in Electromagnetics Research Symposium · December 26, 2011 The ambiguity function (AF) provides a convenient way to model how a camera with a modified aperture responds to defocus. We use the AF to design an optimal aperture distribution, which creates a depth-variant point spread function (PSF) from a sparse set ... Cite

Re-designing the camera for computational photography

Journal Article SPIE Newsroom · June 6, 2011 Full text Cite

Validity of Wigner distribution function for ray-based imaging

Conference 2011 IEEE International Conference on Computational Photography, ICCP 2011 · May 23, 2011 In this work we provide an introduction to the Wigner Distribution Function (WDF) using geometric optics principles. The WDF provides a useful model of wave-fields, allowing simulation of diffraction and interference effects. We attempt to explain these Fo ... Full text Cite

Highlighted depth-of-field photography: Shining light on focus

Journal Article ACM Transactions on Graphics · January 1, 2011 We present a photographic method to enhance intensity differences between objects at varying distances from the focal plane. By combining a unique capture procedure with simple image processing techniques, the detected brightness of an object is decreased ... Full text Cite

Alternative Models of the Rotating Beam

Conference Digital Holography and Three-Dimensional Imaging · 2011 Full text Cite

Creating aperture masks in phase space

Conference Optics InfoBase Conference Papers · December 1, 2010 The Wigner distribution is used to model the PSF of an aperture mask at different defocus planes. Algorithmic methods of determining an optimal mask pattern for a desired set of impulse responses are investigated. ©2010 Optical Society of America. ... Cite

Iterative aperture mask design in phase space using a rank constraint.

Journal Article Optics express · October 2010 We present an iterative camera aperture design procedure, which determines an optimal mask pattern based on a sparse set of desired intensity distributions at different focal depths. This iterative method uses the ambiguity function as a tool to shape the ... Full text Cite

View-Dependent Displays and the Space of Light Fields

Journal Article · July 30, 2010 In this paper we explore how light propagates from thin elements into a volume for viewing. In particular, devices that are typically connected with geometric optics, like parallax barriers, differ in treatment with those that obey physical optics, like ho ... Link to item Cite

Dual-band imaging system based on a compact coaxial folded optic architecture

Conference Optics InfoBase Conference Papers · December 1, 2009 We present an unconventional coaxial architecture for simultaneous acquisition of images in two discrete spectral bands. The approach is realized by taking advantage of a novel annular folded lens design previously developed under the DARPA/MONTAGE program ... Cite

Modified light field architecture for reconfigurable multimode imaging

Conference Proceedings of SPIE - The International Society for Optical Engineering · December 1, 2009 Light field cameras can simultaneously capture the spatial location and angular direction of light rays emanating from a scene. By placing a variable bandpass filter in the aperture of a light field camera, we demonstrate the ability to multiplex the visib ... Full text Cite

Flexible multimodal camera using a light field architecture

Conference 2009 IEEE International Conference on Computational Photography, ICCP 09 · December 1, 2009 We present a modified conventional camera that is able to collect multimodal images in a single exposure. Utilizing a light field architecture in conjunction with multiple filters placed in the pupil plane of a main lens, we are able to digitally reconstru ... Full text Cite

Dual-band imaging system based on a compact coaxial folded optic architecture

Conference Optics InfoBase Conference Papers · January 1, 2009 We present an unconventional coaxial architecture for simultaneous acquisition of images in two discrete spectral bands. The approach is realized by taking advantage of a novel annular folded lens design previously developed under the DARPA/MONTAGE program ... Full text Cite

Pupil plane multiplexing for multi-domain imaging sensors

Conference Proceedings of SPIE - The International Society for Optical Engineering · September 29, 2008 We describe an approach to polarimetric imaging based on a unique folded imaging system with an annular aperture. The novelty of this approach lies in the system's collection architecture, which segments the pupil plane to measure the individual polarimetr ... Full text Cite

12C/13C ratio in planetary nebulae from the IUE archives

Journal Article Astrophysical Journal · April 20, 2004 We investigated the abundance ratio of 12C/13C in planetary nebulae by examining emission lines arising from C III 2s2p 3P2,1,00 → 2s21S0. Spectra were retrieved from the International Ultraviolet Explorer archives, and multiple spectra of the same object ... Full text Cite