arXiv subjects

Jonathan Dong

Publications and source records attributed to Jonathan Dong.

At least 19 recordsLinked to original sources

arXiv2026

Optical Reservoir Computing with Structural Nonlinearity for Forecasting Chaotic Time Series

Optical computing offers a promising route to high-speed, energy-efficient information processing. However, implementing nonlinear operations typically requires strong light-matter interactions. Here, we introduce structural nonlinearity into an optical reservoir computing architecture, using only linear components. A digital micromirror device acts as a reconfigurable scattering potential, while the propagation of light through a scattering medium provides the high-dimensional mode mixing. By enforcing a second interaction with the wavefront shaper, we obtain a quadratic mapping of the input within the reservoir. A single experimental apparatus simultaneously implements conventional and structurally nonlinear reservoir architectures, enabling a direct comparison on forecasting of the chaotic Mackey-Glass time series. We demonstrate that the structurally nonlinear reservoir improves short-term prediction accuracy and better preserves the long-term dynamics of the chaotic system, demonstrating the potential of structural nonlinearity for low-power optical computing.

physics.optics↗

arXiv2025

A global inverse-problem approach to quantitative photo-switching optoacoustic mesoscopy

In this paper, we propose a global framework that includes a detailed model of the photo-switching and acoustic processes for photo-switching optoacoustic mesoscopy, based on the underlying physics. We efficiently implement two forward models as matrix-free linear operators and join them as one forward operator. Then, we reconstruct the concentration maps directly from the temporal series of acoustic signals through the resolution of one combined inverse problem. For robustness against noise and clean unmixing results, we adopt a hybrid regularization technique composed of the $l_1$ and total-variation regularizers applied to two different spaces. We use a proximal-gradient algorithm to solve the minimization problem. Our numerical results show that our regularized one-step approach is the most robust in terms of noise and experimental setup. It consistently achieves higher-quality images, as compared to two-step or unregularized methods.

physics.optics↗

arXiv2025

Structured Random Models for Phase Retrieval with Optical Diffusers

Phase retrieval is a nonlinear inverse problem that arises in a wide range of imaging modalities, from electron microscopy to Fourier ptychography. In particular, the reconstruction is facilitated when the sensing matrix is i.i.d. random, enabling strong theoretical guarantees and efficient reconstruction algorithms. However, its applicability is restricted by excessive computational costs. In this paper, we propose structured random models for phase retrieval, where we emulate a dense random matrix by a cascade of structured transforms and random diagonal matrices. We reduce the complexity from quadratic to log-linear at no cost in reconstruction performance. Through a spectral method initialization followed by gradient descent, robust reconstruction is obtained at an oversampling ratio as low as 2.8. Moreover, we observe that the reconstruction performance is solely determined by the singular-value distribution of the forward matrix. This class of models can directly be implemented with basic optical elements such as lenses and diffusers, paving the way for large-scale phase imaging with robust reconstruction guarantees.

physics.optics↗

arXiv2025

When Higher Resolution Reduces Precision: Quantum Limits of Off-Axis Interferometric Scattering Microscopy

Coherent interferometric scattering microscopy (iscat) enables nanoparticle tracking on microsecond timescales and with nanometer precision, and has become a key tool in structural and cellular biophysics. The achievable localization precision in such experiments is fundamentally limited by photon shot noise. Here, we analyze three-dimensional localization precision under oblique illumination in iscat using the framework of (Quantum) Fisher Information. We show that tilting the illumination can enhance localization precision and accuracy per detected photon, while increasing robustness to defocusing. Surprisingly, rotating coherent scattering microscopy (rocs), which incoherently averages oblique illuminations, achieves higher spatial resolution but lower localization precision. Our results establish the quantum limits of off-axis interferometric imaging and reveal that resolution and precision can behave in opposite ways -- a key insight for designing next-generation coherent microscopes.

physics.optics↗

arXiv2025

Breaking the Weak Recovery Limit in Random Phase Retrieval with Learned Regularizers

We seek to recover an unknown signal from nonlinear amplitude-only measurements, a challenging inverse problem. Strong theoretical guarantees have been established for idealized random measurements, defining the sampling ratio required for signal recovery. However, these results neglect signal priors, which can fundamentally shift these limits, potentially enabling reconstruction with far fewer measurements and simpler models. We evaluate a variety of image priors in the context of severe undersampling with physically-grounded random measurement models. Our results show that these priors enable accurate recovery well below the weak recovery limit, the theoretical threshold required for recovery better than a random guess.

eess.IV↗

arXiv2025

Revisiting Deep Information Propagation: Fractal Frontier and Finite-size Effects

Information propagation characterizes how input correlations evolve across layers in deep neural networks. This framework has been well studied using mean-field theory, which assumes infinitely wide networks. However, these assumptions break down for practical, finite-size networks. In this work, we study information propagation in randomly initialized neural networks with finite width and reveal that the boundary between ordered and chaotic regimes exhibits a fractal structure. This shows the fundamental complexity of neural network dynamics, in a setting that is independent of input data and optimization. To extend this analysis beyond multilayer perceptrons, we leverage recently introduced Fourier-based structured transforms, and show that information propagation in convolutional neural networks also follow the same behavior. In practice, our investigation highlights the importance of finite network depth with respect to the tradeoff between separation and robustness.

cs.LG↗

arXiv2025

DeepInverse: A Python package for solving imaging inverse problems with deep learning

DeepInverse is an open-source PyTorch-based library for solving imaging inverse problems. The library covers all crucial steps in image reconstruction from the efficient implementation of forward operators (e.g., optics, MRI, tomography), to the definition and resolution of variational problems and the design and training of advanced neural network architectures. In this paper, we describe the main functionality of the library and discuss the main design choices.

eess.IV↗

arXiv2025

Phasebook: A Survey of Selected Open Problems in Phase Retrieval

Phase retrieval is an inverse problem that, on one hand, is crucial in many applications across imaging and physics, and, on the other hand, leads to deep research questions in theoretical signal processing and applied harmonic analysis. This survey paper is an outcome of the recent workshop Phase Retrieval in Mathematics and Applications (PRiMA) (held on August 5--9 2024 at the Lorentz Center in Leiden, The Netherlands) that brought together experts working on theoretical and practical aspects of the phase retrieval problem with the purpose to formulate and explore essential open problems in the field.

cs.IT↗

arXiv2025

Revisiting PSF models: unifying framework and high-performance implementation

Localization microscopy often relies on detailed models of point spread functions. For applications such as deconvolution or PSF engineering, accurate models for light propagation in imaging systems with high numerical aperture are required. Different models have been proposed based on 2D Fourier transforms or 1D Bessel integrals. The most precise ones combine a vectorial description of the electric field and precise aberration models. However, it may be unclear which model to choose, as there is no comprehensive comparison between the Fourier and Bessel approaches yet. Moreover, many existing libraries are written in Java (e.g. our previous PSF generator software) or MATLAB, which hinders the integration into deep learning algorithms. In this work, we start from the original Richards-Wolf integral and revisit both approaches in a systematic way. We present a unifying framework in which we prove the equivalence between the Fourier and Bessel strategies and detail a variety of correction factors applicable to both of them. Then, we provide a high-performance implementation of our theoretical framework in the form of an open-source library that is built on top of PyTorch, a popular library for deep learning. It enables us to benchmark the accuracy and computational speed of different models, thus allowing for an in-depth comparison of the existing models for the first time. We show that the Bessel strategy is optimal for axisymmetric beams while the Fourier approach can be applied to more general scenarios. Our work enables efficient PSF computation on CPU or GPU, which can then be included in simulation and optimization pipelines.

physics.optics↗

arXiv2025

Perturbative Fourier Ptychographic Microscopy for Fast Quantitative Phase Imaging

In computational phase imaging with a microscope equipped with an array of light emitting diodes as illumination unit, conventional Fourier ptychographic microscopy achieves high resolution and wide-field reconstructions but is constrained by a lengthy acquisition time. Conversely, differential phase contrast (DPC) offers fast imaging but is limited in resolution. Here, we introduce perturbative Fourier ptychographic microscopy (pFPM). pFPM is an extension of DPC that incorporates dark-field illumination to enable fast, high-resolution, wide-field quantitative phase imaging with few measurements. We interpret DPC as the initial iteration of a Gauss-Newton algorithm with quadratic regularization and generalize it to multiple iterations and more sophisticated regularizers. This broader framework is not restricted to bright-field measurements and allows us to overcome resolution limitations of DPC. We develop tailored annular dark-field illumination patterns that align with the perturbative interpretation and lead to an improvement in the quality of reconstruction with respect to other common illumination schemes. Consequently, our methodology combines an enhanced phase reconstruction algorithm with a specialized illumination strategy and offers significant advantages in both imaging speed and resolution.

physics.optics↗

arXiv2024

Point-Spread-Function Engineering in MINFLUX: Optimality of Donut and Half-Moon Excitation Patterns

Localization microscopy enables imaging with resolutions that surpass the conventional optical diffraction limit. Notably, the MINFLUX method achieves super-resolution by shaping the excitation point-spread function (PSF) to minimize the required photon flux for a given precision. Various beam shapes have recently been proposed to improve localization efficiency, yet their optimality remains an open question. In this work, we deploy a numerical and theoretical framework to determine optimal excitation patterns for MINFLUX. Such a computational approach allows us to search for new beam patterns in a fast and low-cost fashion, and to avoid time-consuming and expensive experimental explorations. We show that the conventional donut beam is a robust optimum when the excitation beams are all constrained to the same shape. Further, our PSF engineering framework yields two pairs of half-moon beams (orthogonal to each other) which can improve the theoretical localization precision by a factor of about two.

physics.optics↗

arXiv2024

Structured Random Model for Fast and Robust Phase Retrieval

Phase retrieval, a nonlinear problem prevalent in imaging applications, has been extensively studied using random models, some of which with i.i.d. sensing matrix components. While these models offer robust reconstruction guarantees, they are computationally expensive and impractical for real-world scenarios. In contrast, Fourier-based models, common in applications such as ptychography and coded diffraction imaging, are computationally more efficient but lack the theoretical guarantees of random models. Here, we introduce structured random models for phase retrieval that combine the efficiency of fast Fourier transforms with the versatility of random diagonal matrices. These models emulate i.i.d. random matrices at a fraction of the computational cost. Our approach demonstrates robust reconstructions comparable to fully random models using gradient descent and spectral methods. Furthermore, we establish that a minimum of two structured layers is necessary to achieve these structured-random properties. The proposed method is suitable for optical implementation and offers an efficient and robust alternative for phase retrieval in practical imaging applications.

physics.optics↗

arXiv2024

Detection and Positive Reconstruction of Cognitive Distortion sentences: Mandarin Dataset and Evaluation

This research introduces a Positive Reconstruction Framework based on positive psychology theory. Overcoming negative thoughts can be challenging, our objective is to address and reframe them through a positive reinterpretation. To tackle this challenge, a two-fold approach is necessary: identifying cognitive distortions and suggesting a positively reframed alternative while preserving the original thought's meaning. Recent studies have investigated the application of Natural Language Processing (NLP) models in English for each stage of this process. In this study, we emphasize the theoretical foundation for the Positive Reconstruction Framework, grounded in broaden-and-build theory. We provide a shared corpus containing 4001 instances for detecting cognitive distortions and 1900 instances for positive reconstruction in Mandarin. Leveraging recent NLP techniques, including transfer learning, fine-tuning pretrained networks, and prompt engineering, we demonstrate the effectiveness of automated tools for both tasks. In summary, our study contributes to multilingual positive reconstruction, highlighting the effectiveness of NLP in cognitive distortion detection and positive reconstruction.

cs.CL↗

arXiv2024

Model-based temporal unmixing towards quantitative photo-switching optoacoustic tomography

Optoacoustic (OA) imaging combined with reversibly photoswitchable proteins has emerged as a promising technology for the high-sensitivity and multiplexed imaging of cells in live tissues in preclinical research. Through carefully-designed illumination schedules of ON and OFF laser pulses, the resulting OA signal is a multiplex of different reporter species and the background. We propose a model-based variational framework to computationally unmix and image different species of photo-switching reporters using optoacoustic tomography. It is based on a detailed mathematical description of the photo-switching mechanism, which models how relevant physical parameters such as the kinetic constants and light fluence impact the switching signal. We introduce an algorithm that operates on images, as opposed to traditional pixelwise approaches. It takes the form of an iterative inversion combined with tailored $\ell_1$ and total-variation regularization to increase the robustness to noise and to improve the unmixing quality. We show that our method is able to disentangle multiple spatially overlapping labels and to recover continuous maps of quantities of interest on controlled phantoms and mice experiments.

physics.optics↗

arXiv2024

Comparison of Reservoir Computing topologies using the Recurrent Kernel approach

Reservoir Computing (RC) has become popular in recent years thanks to its fast and efficient computational capabilities. Standard RC has been shown to be equivalent in the asymptotic limit to Recurrent Kernels, which helps in analyzing its expressive power. However, many well-established RC paradigms, such as Leaky RC, Sparse RC, and Deep RC, are yet to be systematically analyzed in such a way. We define the Recurrent Kernel limit of all these RC topologies and conduct a convergence study for a wide range of activation functions and hyperparameters. Our findings provide new insights into various aspects of Reservoir Computing. First, we demonstrate that there is an optimal sparsity level which grows with the reservoir size. Furthermore, our analysis suggests that Deep RC should use reservoir layers of decreasing sizes. Finally, we perform a benchmark demonstrating the efficiency of Structured Reservoir Computing compared to vanilla and Sparse Reservoir Computing.

cs.LG↗

arXiv2023

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. This work has two contributions. First, we systematically document a catalog of mechanical artifacts based on a 3D description of the imaging system that uses a set of angular and translational parameters. Then, we introduce a calibration algorithm that recovers 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.

cs.CV↗

arXiv2023

Single-pixel transmission matrix recovery via 2-photon fluorescence

Imaging at depth in opaque materials has long been a challenge. Recently, wavefront shaping has enabled significant advance for deep imaging. Nevertheless, most non-invasive wavefront shaping methods require cameras, lack the sensitivity for deep imaging under weak optical signals, or can only focus on a single "guidestar". Here, we retrieve the transmission matrix (TM) non-invasively using two-photon fluorescence exploiting a general single-pixel detection framework, allowing to achieve single-target focus on multiple guidestars spread beyond the memory effect range. In addition, if we assume memory effect correlations exist in the transmission matrix, we are able to significantly reduce the number of measurements needed.

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↗