arXiv subjects

Jonathan Dong

Publications and source records attributed to Jonathan Dong.

At least 37 records · Page 2Linked to original sources

arXiv2022

Phase Retrieval: From Computational Imaging to Machine Learning

Phase retrieval consists in the recovery of a complex-valued signal from intensity-only measurements. As it pervades a broad variety of applications, many researchers have striven to develop phase-retrieval algorithms. Classical approaches involve techniques as varied as generic gradient-descent routines or specialized spectral methods, to name a few. Yet, the phase-recovery problem remains a challenge to this day. Recently, however, advances in machine learning have revitalized the study of phase retrieval in two ways: significant theoretical advances have emerged from the analogy between phase retrieval and single-layer neural networks; practical breakthroughs have been obtained thanks to deep-learning regularization. In this tutorial, we review phase retrieval under a unifying framework that encompasses classical and machine-learning methods. We focus on three key elements: applications, overview of recent reconstruction algorithms, and the latest theoretical results.

physics.optics↗

arXiv2022

Mechanical Artifacts in Optical Projection Tomography: Classification and Automatic Calibration

Optical projection tomography (OPT) is a powerful tool for biomedical studies. It achieves 3D visualization of mesoscopic biological samples with high spatial resolution using conventional tomographic-reconstruction algorithms. However, various artifacts degrade the quality of the reconstructed images due to experimental imperfections in the OPT instruments. While many efforts have been made to characterize and correct for these artifacts, they focus on one specific type of artifacts, whereas a comprehensive catalog of all sorts of mechanical artifacts does not currently exist. In this work, we systematically document many mechanical artifacts. We rely on a 3D description of the imaging system that uses a set of angular and translational parameters. We provide a catalog of artifacts. It lists their cause, resulting effects, and existing correction methods. Then, we introduce an automatic calibration algorithm that is able to recover the unknown system parameters fed into the final 3D iterative reconstruction algorithm for a distortion-free volumetric image. Simulations with beads data and experimental results on a fluorescent textile fiber confirm that our algorithm successfully removes miscalibration artifacts in the reconstruction.

physics.optics↗

arXiv2022

Artifacts in optical projection tomography due to refractive index mismatch: model and correction

Optical Projection Tomography (OPT) is a powerful tool for 3D imaging of mesoscopic samples, thus of great importance to image whole organs for the study of various disease models in life sciences. OPT is able to achieve resolution at a few tens of microns over a large sample volume of several cubic centimeters. However, the reconstructed OPT images often suffer from artifacts caused by different kinds of physical miscalibration. This work focuses on the refractive index (RI) mismatch between the rotating object and the surrounding medium. We derive a 3D cone beam forward model to approximate the effect of RI mismatch and implement a fast and efficient reconstruction method to correct the induced seagull-shaped artifacts on experimental images of fluorescent beads.

physics.optics↗

arXiv2022

Asymptotic Stability in Reservoir Computing

Reservoir Computing is a class of Recurrent Neural Networks with internal weights fixed at random. Stability relates to the sensitivity of the network state to perturbations. It is an important property in Reservoir Computing as it directly impacts performance. In practice, it is desirable to stay in a stable regime, where the effect of perturbations does not explode exponentially, but also close to the chaotic frontier where reservoir dynamics are rich. Open questions remain today regarding input regularization and discontinuous activation functions. In this work, we use the recurrent kernel limit to draw new insights on stability in reservoir computing. This limit corresponds to large reservoir sizes, and it already becomes relevant for reservoirs with a few hundred neurons. We obtain a quantitative characterization of the frontier between stability and chaos, which can greatly benefit hyperparameter tuning. In a broader sense, our results contribute to understanding the complex dynamics of Recurrent Neural Networks.

cs.NE↗

arXiv2022

Physics-based neural network for non-invasive control of coherent light in scattering media

Optical imaging through complex media, such as biological tissues or fog, is challenging due to light scattering. In the multiple scattering regime, wavefront shaping provides an effective method to retrieve information; it relies on measuring how the propagation of different optical wavefronts are impacted by scattering. Based on this principle, several wavefront shaping techniques were successfully developed, but most of them are highly invasive and limited to proof-of-principle experiments. Here, we propose to use a neural network approach to non-invasively characterize and control light scattering inside the medium and also to retrieve information of hidden objects buried within it. Unlike most of the recently-proposed approaches, the architecture of our neural network with its layers, connected nodes and activation functions has a true physical meaning as it mimics the propagation of light in our optical system. It is trained with an experimentally-measured input/output dataset built from a series of incident light patterns and corresponding camera snapshots. We apply our physics-based neural network to a fluorescence microscope in epi-configuration and demonstrate its performance through numerical simulations and experiments. This flexible method can include physical priors and we show that it can be applied to other systems as, for example, non-linear or coherent contrast mechanisms.

physics.optics↗

arXiv2021

Fundamental bounds on the precision of iSCAT, COBRI and dark-field microscopy for 3D localization and mass photometry

Interferometric imaging is an emerging technique for particle tracking and mass photometry. Mass or position are estimated from weak signals, coherently scattered from nanoparticles or single molecules, and interfered with a co-propagating reference. In this work, we perform a statistical analysis and derive lower bounds on the measurement precision of the parameters of interest from shot-noise limited images. This is done by computing the classical Cramér-Rao bound for localization and mass estimation, using a precise vectorial model of interferometric imaging techniques. We then derive fundamental bounds valid for any imaging system, based on the quantum Cramér-Rao formalism. This approach enables a rigorous and quantitative comparison of common techniques such as interferometric scattering microscopy (iSCAT), Coherent Brightfield microscopy (COBRI), and dark-field microscopy. In particular, we demonstrate that the light collection geometry in iSCAT greatly increases the axial position sensitivity, and that the Quantum Cramér-Rao bound for mass estimation yields a minimum relative estimation error of $σ_m/m=1/(2\sqrt{N})$, where $N$ is the number of collected scattered photons.

physics.optics↗

arXiv2021

Fundamental bounds on the precision of classical phase microscopes

A wide variety of imaging systems have been designed to measure phase variations, with applications from physics to biology and medicine. In this work, we theoretically compare the precision of phase estimations achievable with classical phase microscopy techniques, operated at the shot-noise limit. We show how the Cramér-Rao bound is calculated for any linear optical system, including phase-contrast microscopy, phase-shifting holography, spatial light interference microscopy, and local optimization of wavefronts for phase imaging. Through these examples, we demonstrate how this general framework can be applied for the design and optimization of classical phase microscopes. Our results show that wavefront shaping is required to design phase microscopes with optimal phase precision.

physics.optics↗

arXiv2021

Accelerating ptychographic reconstructions using spectral initializations

Ptychography is a promising phase retrieval technique for label-free quantitative phase imaging. Recent advances in phase retrieval algorithms witnessed the development of spectral methods, in order to accelerate gradient descent algorithms. Using spectral initializations on experimental data, for the first time we report three times faster ptychographic reconstructions than with a standard gradient descent algorithm and improved resilience to noise. Coming at no additional computational cost compared to gradient-descent-based algorithms, spectral methods have the potential to be implemented in large-scale iterative ptychographic algorithms.

physics.optics↗

arXiv2020

Large-Scale Optical Reservoir Computing for Spatiotemporal Chaotic Systems Prediction

Reservoir computing is a relatively recent computational paradigm that originates from a recurrent neural network and is known for its wide range of implementations using different physical technologies. Large reservoirs are very hard to obtain in conventional computers, as both the computation complexity and memory usage grow quadratically. We propose an optical scheme performing reservoir computing over very large networks potentially being able to host several millions of fully connected photonic nodes thanks to its intrinsic properties of parallelism and scalability. Our experimental studies confirm that, in contrast to conventional computers, the computation time of our optical scheme is only linearly dependent on the number of photonic nodes of the network, which is due to electronic overheads, while the optical part of computation remains fully parallel and independent of the reservoir size. To demonstrate the scalability of our optical scheme, we perform for the first time predictions on large spatiotemporal chaotic datasets obtained from the Kuramoto-Sivashinsky equation using optical reservoirs with up to 50 000 optical nodes. Our results are extremely challenging for conventional von Neumann machines, and they significantly advance the state of the art of unconventional reservoir computing approaches, in general.

physics.optics↗

arXiv2020

Reservoir Computing meets Recurrent Kernels and Structured Transforms

Reservoir Computing is a class of simple yet efficient Recurrent Neural Networks where internal weights are fixed at random and only a linear output layer is trained. In the large size limit, such random neural networks have a deep connection with kernel methods. Our contributions are threefold: a) We rigorously establish the recurrent kernel limit of Reservoir Computing and prove its convergence. b) We test our models on chaotic time series prediction, a classic but challenging benchmark in Reservoir Computing, and show how the Recurrent Kernel is competitive and computationally efficient when the number of data points remains moderate. c) When the number of samples is too large, we leverage the success of structured Random Features for kernel approximation by introducing Structured Reservoir Computing. The two proposed methods, Recurrent Kernel and Structured Reservoir Computing, turn out to be much faster and more memory-efficient than conventional Reservoir Computing.

stat.ML↗

arXiv2020

Non-invasive single-shot recovery of point-spread function of a memory effect based scattering imaging system

Accessing the point-spread function (PSF) of a complex optical system is important for a variety of imaging applications. However, placing an invasive point source is often impractical, and estimating it blindly with multiple frames is slow and requires a complex non-linear optimization. Here, we introduce a simple single-shot method to non-invasively recover the accurate PSF of an isoplanatic imaging system, in the context of multiple light scattering. Our approach is based on the reconstruction of any unknown sparse hidden object using the autocorrelation imaging technique, followed by a deconvolution with a blur kernel derived from the statistics of a speckle pattern. A deconvolution on the camera image then retrieves the accurate PSF of the system, enabling further imaging applications. We demonstrate numerically and experimentally the effectiveness of this approach compared to previous deconvolution techniques.

physics.optics↗

arXiv2020

Non-invasive focusing and imaging in scattering media with a fluorescence-based transmission matrix

In biological microscopy, light scattering represents the main limitation to image at depth. Recently, a set of wavefront shaping techniques has been developed in order to manipulate coherent light in strongly disordered materials. The Transmission Matrix approach has shown its capability to inverse the effect of scattering and efficiently focus light. In practice, the matrix is usually measured using an invasive detector or low-resolution acoustic guide stars. Here, we introduce a non-invasive and all-optical strategy based on linear fluorescence to reconstruct the transmission matrices, to and from a fluorescent object placed inside a scattering medium. It consists in demixing the incoherent patterns emitted by the object using low-rank factorizations and phase retrieval algorithms. We experimentally demonstrate the efficiency of this method through robust and selective focusing. Additionally, from the same measurements, it is possible to exploit memory effect correlations to image and reconstruct extended objects. This approach opens up a new route towards imaging in scattering media with linear or non-linear contrast mechanisms.

physics.optics↗

arXiv2019

Kernel computations from large-scale random features obtained by Optical Processing Units

Approximating kernel functions with random features (RFs)has been a successful application of random projections for nonparametric estimation. However, performing random projections presents computational challenges for large-scale problems. Recently, a new optical hardware called Optical Processing Unit (OPU) has been developed for fast and energy-efficient computation of large-scale RFs in the analog domain. More specifically, the OPU performs the multiplication of input vectors by a large random matrix with complex-valued i.i.d. Gaussian entries, followed by the application of an element-wise squared absolute value operation - this last nonlinearity being intrinsic to the sensing process. In this paper, we show that this operation results in a dot-product kernel that has connections to the polynomial kernel, and we extend this computation to arbitrary powers of the feature map. Experiments demonstrate that the OPU kernel and its RF approximation achieve competitive performance in applications using kernel ridge regression and transfer learning for image classification. Crucially, thanks to the use of the OPU, these results are obtained with time and energy savings.

cs.ET↗

arXiv2019

Optical Reservoir Computing using multiple light scattering for chaotic systems prediction

Reservoir Computing is a relatively recent computational framework based on a large Recurrent Neural Network with fixed weights. Many physical implementations of Reservoir Computing have been proposed to improve speed and energy efficiency. In this study, we report new advances in Optical Reservoir Computing using multiple light scattering to accelerate the recursive computation of the reservoir states. Two different spatial light modulation technologies, namely, phase or binary amplitude modulations, are compared. Phase modulation is a promising direction already employed in other photonic implementations of Reservoir Computing. Additionally, we report a Digital-Micromirror-based Reservoir Computing at up to 640 Hz, more than double the previously reported frequency using a remotely controlled optical device developed by LightOn, and present new binarization strategies to improve the performance of binarized Reservoir Computing.

cs.ET↗

arXiv2019

Non-invasive light focusing in scattering media using speckle variance optimization

Optical imaging deep inside scattering media remains a fundamental problem in bio-imaging. While wavefront shaping has been shown to allow focusing of coherent light at depth, achieving it non-invasively remains a challenge. Various feedback mechanisms, in particular acoustic or non-linear fluorescence-based, have been put forward for this purpose. Non-invasive focusing at depth on fluorescent objects with linear excitation is, however, still unresolved. Here we report a simple method for focusing inside a scattering medium in an epi-detection geometry with a linear signal: optimizing the spatial variance of low contrast speckle patterns emitted by a set of fluorescent sources. Experimentally, we demonstrate robust and efficient focusing of scattered light on a single source, and show that this variance optimization method is formally equivalent to previous optimization strategies based on two-photon fluorescence. Our technique should generalize to a large variety of incoherent contrast mechanisms and holds interesting prospects for deep bio-imaging.

physics.optics↗

arXiv2018

Fast compressive Raman bio-imaging via matrix completion

Raman microscopy is a powerful method combining non-invasiveness with no special sample preparation. Because of this remarkable simplicity, it has been widely exploited in many fields, ranging from life and materials sciences, to engineering. Notoriously, due to the required imaging speeds for bio-imaging, it has remained a challenge how to use this technique for dynamic and large-scale imaging. Recently, compressive Raman has been put forward, allowing for fast imaging, therefore solving the issue of speed. Yet, due to the need of strong a priori information of the species forming the hyperspectrum, it has remained elusive how to apply this technique for microspectroscopy of (dynamic) biological tissues. Combining an original spectral under-sampling measurement technique with matrix completion framework for reconstruction, we demonstrate fast and inexpensive label-free molecular imaging of biological specimens (brain tissues and single cells). Therefore, our results open interesting perspectives for clinical and cell biology applications using the much faster compressive Raman framework.

physics.med-ph↗

arXiv2018

Spectral Method for Multiplexed Phase Retrieval and Application in Optical Imaging in Complex Media

We introduce a generalized version of phase retrieval called multiplexed phase retrieval. We want to recover the phase of amplitude-only measurements from linear combinations of them. This corresponds to the case in which multiple incoherent sources are sampled jointly, and one would like to recover their individual contributions. We show that a recent spectral method developed for phase retrieval can be generalized to this setting, and that its performance follows a phase transition behavior. We apply this new technique to light focusing at depth in a complex medium. Experimentally, although we only have access to the sum of the intensities on multiple targets, we are able to separately focus on each ones, thus opening potential applications in deep fluorescence imaging and light delivery

eess.IV↗

arXiv2018

Scaling up Echo-State Networks with multiple light scattering

Echo-State Networks and Reservoir Computing have been studied for more than a decade. They provide a simpler yet powerful alternative to Recurrent Neural Networks, every internal weight is fixed and only the last linear layer is trained. They involve many multiplications by dense random matrices. Very large networks are difficult to obtain, as the complexity scales quadratically both in time and memory. Here, we present a novel optical implementation of Echo-State Networks using light-scattering media and a Digital Micromirror Device. As a proof of concept, binary networks have been successfully trained to predict the chaotic Mackey-Glass time series. This new method is fast, power efficient and easily scalable to very large networks.

cs.ET↗