arXiv subjects

YongKeun Park

Publications and source records attributed to YongKeun Park.

At least 19 recordsLinked to original sources

arXiv2026

Imaging biofilms in three dimensions: modalities, quantitative readouts, and the path to four-dimensional measurement

Biofilms are spatially structured microbial communities whose architecture, chemistry, mechanics, and cellular states evolve over time. Bulk assays and two-dimensional projections remain useful, but cannot alone resolve how these properties vary with depth or change during growth, treatment, dispersal, and regrowth. Imaging provides complementary routes to three-dimensional measurement: fluorescence microscopy supplies molecular, taxonomic, and functional specificity; optical coherence tomography resolves mesoscale architecture and dynamics; quantitative phase imaging and holotomography report refractive index and biomass-related changes; Raman methods provide chemical and metabolic contrast; and Brillouin microscopy probes mechanical response. We compare these modalities using four independent descriptors-contrast provenance, live volumetric capability, perturbation, and demonstrated biofilm use-and connect their signals to quantitative biological readouts. No single modality simultaneously maximizes spatial coverage, resolution, acquisition speed, molecular specificity, and low perturbation. Implementations from any contrast class can serve as a longitudinal backbone when perturbation is empirically controlled at the relevant spatial and temporal scale, while molecularly specific measurements remain indispensable for identifying species, molecules, and functional states. We therefore frame four-dimensional biofilm measurement as a validated measurement architecture that integrates a low-perturbation volumetric backbone with spatially registered, molecularly specific measurements acquired continuously or at predefined validation points. Achieving this integration will require compatible cultivation formats, controlled imaging dose, shared quantitative parameters, and robust cross-modality registration.

physics.bio-ph↗

arXiv2026

Quantitative three-dimensional absorption imaging in standard brightfield microscopes

Optical absorption is a primary, label-defining contrast across biology, pathology, and materials science, yet three-dimensional quantitative absorption imaging has remained largely inaccessible to the brightfield microscopes used in everyday practice. We introduce quantitative absorption tomography (QAT), which recovers volumetric distributions of the extinction coefficient by treating brightfield image formation as a linear inverse problem in logarithmic intensity space and inverting a three-dimensional absorption optical transfer function. Under weak-scattering conditions, QAT yields spectrally resolved, three-dimensional absorption maps from through-focus image stacks acquired on standard brightfield platforms, without interferometry, coherent illumination, or sample rotation. We use QAT to track melanin dynamics in living melanoma cells without exogenous labels, image pigment organization in intact Petunia hybrida petals in vivo, and reconstruct chromogenic contrast across large H&E-stained human tissue volumes. By establishing absorption as a directly measurable volumetric quantity within standard brightfield workflows, QAT positions chromogenic contrast as a quantitative axis alongside fluorescence- and refractive-index-based imaging.

physics.optics↗

arXiv2026

Design principles for optoelectronic light-scattering reservoir computing at the edge of chaos

Physical reservoir computing offers an energy-efficient route to sequential cognitive inference by outsourcing nonlinear temporal mixing to hardware substrates with rich intrinsic dynamics, with free-space light-scattering systems particularly attractive for their parallelism and reconfigurability-yet practical design principles linking hardware control variables to computational performance have remained unestablished. Here, we establish such principles by systematically mapping three physical control axes of a reconfigurable optoelectronic light-scattering reservoir-reservoir dynamics, input-reservoir coupling, and reservoir interconnectivity-and identifying a quantitative optimum along each axis. Within this design landscape, we observe a memory-capacity peak that coincides with near-zero maximal Lyapunov exponent and is quantitatively reproduced in numerical simulation, extending edge-of-chaos confirmations previously reported in ion-gating and spin-wave reservoirs into the photonic substrate. The two remaining axes exhibit a density-magnitude trade-off in input coupling and an intermediate optimum in reservoir interconnectivity. Operating at the resulting three-axis optimum, the reservoir achieves stable Mackey-Glass chaotic time-series prediction in free-running mode and 84.5% blind classification accuracy on the 10-class Speech Commands spoken-digit benchmark; the principles, stated in substrate-specific units yet rooted in substrate-independent concepts of criticality and balanced coupling, provide a transferable framework for reconfigurable optical reservoir hardware.

physics.optics↗

arXiv2026

Programmable spatial coherence tomography: diffraction-limited three-dimensional reflection imaging under modulated monochromatic illumination

Depth sectioning in reflection microscopy has predominantly relied on temporal coherence gating. Here we show that volumetric reflection tomography at diffraction-limited resolution can be achieved under monochromatic illumination by engineering spatial, rather than temporal, coherence. In programmable spatial coherence tomography (PSCT), a sequence of pupil-coded illumination patterns with angular-spectrum diversity generates measurement redundancy enabling the system to calibrate itself, jointly retrieving aberrations, illumination profiles, and sample motion without guide stars or modal priors. We demonstrate label-free volumetric imaging of thick human tissues, organoids, frequency-resolved dynamic contrast, and high-resolution in vivo brain imaging through a cranial window. These results position PSCT as an alternative to temporal coherence based reflection imaging in complex biological systems.

physics.optics↗

arXiv2026

Holotomography in 2025: From Morphometric Imaging to AI-Driven Multimodal Phenotyping

By 2025, holotomography (HT) has matured from a niche optical modality into a versatile platform for quantitative, label-free imaging in biomedicine. By reconstructing the three-dimensional refractive-index (RI) distribution of cells and tissues, HT enables high-resolution volumetric imaging with low phototoxicity and minimal sample perturbation. This Review surveys recent advances in the field and highlights three emerging directions: (i) the incorporation of deep-learning approaches for virtual staining, phenotypic classification, and automated analysis; (ii) the extension of HT to structurally complex biological systems, including organoids and thick tissue specimens; and (iii) the integration of HT with complementary modalities, such as Raman and polarization-sensitive microscopy, to enhance molecular and biophysical specificity. We summarize current HT applications spanning subcellular phenotyping, metabolic and mechanical profiling, and early-stage clinical studies in areas such as infectious disease and pathology. Finally, we discuss remaining technical and translational challenges and outline a roadmap for the prospective integration of HT into digital pathology and high-throughput screening workflows.

physics.bio-ph↗

arXiv2026

Video-rate holographic telepresence via single-shot, reference-free wavefront measurement

We present a reference-free holographic telepresence system that directly captures and replays complex optical wavefronts from a single intensity speckle measurement. Using a pre-characterized geometric phase diffuser, the incident field self-interferes to form a speckle pattern, from which the wavefront is recovered via a speckle-correlation scattering-matrix approach and refined using smoothed amplitude flow with Nesterov acceleration. The reconstructed phase is directly projected onto a spatial light modulator for holographic replay. We demonstrate volumetric refocusing, dynamic three-dimensional reconstruction, and sustained video-rate operation at approximately 28 frames per second with modest communication bandwidth. The results highlight measurement-driven wavefront acquisition as a practical pathway toward compact and physically faithful holographic telepresence.

physics.optics↗

arXiv2025

Morphology-Preserving Holotomography: Quantitative Analysis of 3D Organoid Dynamics

Organoids are three-dimensional (3D) in vitro models for studying tissue development, disease progression, and physiological responses. Holotomography (HT) enables long-term, label-free imaging of live organoids by reconstructing volumetric refractive-index (RI) maps, but quantitative analysis is limited by the missing-cone artifact, which introduces anisotropic resolution and axial distortion. Here, we present a quantitative analysis framework that addresses the missing-cone problem at the level of image representation rather than reconstruction. We introduce morphology-preserving holotomography (MP-HT), a torus-shaped spatial filtering strategy that emphasizes high-spatial-frequency RI texture while suppressing low-frequency components most susceptible to missing-cone-induced distortion. Based on MP-HT, we develop a 3D segmentation pipeline for robust separation of epithelial and luminal structures, together with a model-based RI quantification approach that incorporates the system point spread function to enable morphology-independent estimation of dry-mass density and total dry mass. We apply the framework to long-term imaging of live hepatic organoids undergoing expansion, collapse, and fusion. The results demonstrate consistent segmentation across diverse geometries and reveal coordinated epithelial-lumen remodeling, breakdown of morphometric homeostasis during collapse, and transient biophysical fluctuations during fusion. Overall, this work establishes a physically transparent and reproducible approach for quantitative, label-free analysis of organoid dynamics in three dimensions.

physics.med-ph↗

arXiv2025

Incoherent dielectric tensor tomography for quantitative 3D measurement of biaxial anisotropy

Biaxial anisotropy, arising from distinct optical responses along three principal directions, underlies the complex structure of many crystalline, polymeric, and biological materials. However, existing techniques such as X-ray diffraction and electron microscopy require specialized facilities or destructive preparation and cannot provide full three-dimensional (3D) information. Here we introduce incoherent dielectric tensor tomography (iDTT), a non-interferometric optical imaging method that quantitatively reconstructs the 3D dielectric tensor under incoherent, polarization-diverse illumination. By combining polarization diversity and angular-spectrum modulation, iDTT achieves speckle-free and vibration-robust mapping of biaxial birefringence with submicron resolution. Simulations and experiments on uniaxial and biaxial samples validate its quantitative accuracy. Applied to mixed and polycrystalline materials, iDTT distinguishes crystal types by their birefringent properties and reveals 3D grain orientations and boundaries. This approach establishes iDTT as a practical and accessible tool for quantitative, label-free characterization of biaxial anisotropy in diverse materials.

physics.optics↗

arXiv2025

Refractive Index-Correlated Pseudocoloring for Adaptive Color Fusion in Holotomographic Cytology

Conventional bright-field (BF) cytology of thyroid fine-needle aspiration biopsy (FNAB) suffers from staining variability and limited subcellular contrast. Here, we present a refractive index-correlated pseudocoloring (RICP) framework that integrates quantitative refractive index (RI) maps obtained by holotomography (HT) with color BF images to enhance diagnostic interpretability. The imaging platform combines a digital micromirror device (DMD)-based HT system with an RGB LED illumination module, enabling simultaneous acquisition of RI tomograms and BF images from PAP-stained thyroid samples. The RICP algorithm adaptively embeds RI-derived structural information into the least-occupied hue channel, preserving color fidelity while enhancing nuclear and cytoplasmic contrast. Applied to benign and malignant thyroid clusters, RICP revealed diagnostically relevant features such as nucleoli, lipid droplets, and nuclear irregularities, and hue-saturation analysis quantitatively differentiated cytological categories. This perceptually grounded, label-free framework bridges conventional color cytology and quantitative optical imaging for improved diagnostic precision.

physics.optics↗

arXiv2025

Speckle-based X-ray microtomography via preconditioned Wirtinger flow

Quantitative phase imaging has been extensively studied in X-ray microtomography to improve the sensitivity and specificity of measurements, especially for low atomic number materials. However, obtaining quantitative phase images typically requires additional measurements or assumptions, which significantly limits the practical applicability. Here, we present preconditioned Wirtinger flow (PWF): an assumption-free, single-shot quantitative X-ray phase imaging method. Accurate phase retrieval is demonstrated using a specialized gradient-based algorithm with an accurate physical model. Partial coherence of the source is taken into account, extending the potential applications to bench-top sources. Improved accuracy and spatial resolution over conventional speckle tracking methods are experimentally demonstrated. The various samples are explored to demonstrate the robustness and versatility of PWF.

physics.optics↗

arXiv2025

Pupil Phase Series: A Fast, Accurate, and Energy-Conserving Model for Forward and Inverse Light Scattering in Thick Biological Samples

We present the pupil phase series (PPS), a fast and accurate forward scattering algorithm for simulating and inverting multiple light scattering in large biological samples. PPS achieves high-angle scattering accuracy and energy conservation simultaneously by introducing a spatially varying phase modulation in the pupil plane. By expanding the scattering term into a Taylor series, PPS achieves high precision while maintaining computational efficiency. We integrate PPS into a quasi-Newton inverse solver to reconstruct the three-dimensional refractive index of a 180 um-thick human organoid. Compared to linear reconstruction, our method recovers subcellular features-such as nuclei and vesicular structures-deep within the sample volume. PPS offers a scalable and interpretable alternative to conventional solvers, paving the way for high-throughput, label-free imaging of optically thick biological tissues.

physics.optics↗

arXiv2025

Quantitative X-ray Schlieren Nanotomography for Hyperspectral Phase and Absorption Imaging

Hyperspectral X-rays imaging holds promise for three-dimensional (3D) chemical analysis but remains limited in simultaneously capturing phase and absorption information due to complex setups and data burdens. We introduce quantitative X-ray schlieren nanotomography (XSN), a simple, fast, and high-resolution X-ray phase imaging technique that overcomes these limitations. XSN employs a partially coherent illumination and a pupil-plane cutoff filter to encode directional phase contrast, enabling single-shot acquisition. A quasi-Newton iterative algorithm reconstructs quantitative phase and absorption images from intensity data, even under strong scattering conditions. Scanning across X-ray energies further allows four-dimensional imaging (3D spatial & spectral). We validate the method's accuracy and resolution on reference samples and apply it to lithium battery cathodes, visualizing nanoscale microcracks and mapping chemical compositions. XSN provides a robust framework for hyperspectral phase nanotomography with broad applicability across materials science, biology, and energy research.

physics.optics↗

arXiv2025

Compression benchmarking of holotomography data using the OME-Zarr storage format

Holotomography (HT) is a label-free, three-dimensional imaging technique that captures refractive index distributions of biological samples at sub-micron resolution. As modern HT systems enable high-throughput and large-scale acquisition, they produce terabyte-scale datasets that require efficient data management. This study presents a systematic benchmarking of data compression strategies for HT data stored in the OME-Zarr format, a cloud-compatible, chunked data structure suitable for scalable imaging workflows. Using representative datasets-including embryo, tissue, and birefringent tissue volumes-we evaluated combinations of preprocessing filters and 25 compression configurations across multiple compression levels. Performance was assessed in terms of compression ratio, bandwidth, and decompression speed. A throughput-based evaluation metric was introduced to simulate real-world conditions under varying network constraints, supporting optimal compressor selection based on system bandwidth. The results offer practical guidance for storage and transmission of large HT datasets and serve as a reference for implementing scalable, FAIR-aligned imaging workflows in cloud and high-performance computing environments.

physics.optics↗

arXiv2025

Generalized reciprocal diffractive imaging for stand-alone, reference-free, fast-measurable quantitative phase microscopy

Optical microscopy has been employed to derive salient characteristics of an object in various fields, including cell biology, flow cytometry, biopsy, and neuroscience. In particular, measuring the phase of light scattered from an object aroused great interest by allowing retrieving quantitative parameters such as refractive index, an intrinsic property of a material. Reciprocal diffractive imaging (RDI) has succeeded in recovering the light field scattered from diffusive objects without special restrictions on illumination and sample support from a single-shot intensity in the reference-free regime. However, RDI is limited to imaging samples in the diffusive regime, making application to biological samples difficult. Here, we extend RDI to biological applications by spatially filtering the transmitted fields in the pupil plane. The proposed method is demonstrated by imaging the objects with known structures and various biological samples, showing its capability as a stand-alone optical microscope. We believe that the presented advance could be at the forefront of quantitative phase imaging due to the unique advantages the technique possesses.

physics.optics↗

arXiv2025

Advances in imaging techniques for the study of individual bacteria and their pathophysiology

Bacterial heterogeneity is pivotal for adaptation to diverse environments, posing significant challenges in microbial diagnostics and therapeutic interventions. Recent advancements in high-resolution optical microscopy have revolutionized our ability to observe and characterize individual bacteria, offering unprecedented insights into their metabolic states and behaviors at the single-cell level. This review discusses the transformative impact of various high-resolution imaging techniques, including fluorescence and label-free imaging, which have enhanced our understanding of bacterial pathophysiology. These methods provide detailed visualizations that are crucial for developing targeted treatments and improving clinical diagnostics. We highlight the integration of these imaging techniques with computational tools, which has facilitated rapid, accurate pathogen identification and real-time monitoring of bacterial responses to treatments. The ongoing development of these optical imaging technologies promises to significantly advance our understanding of microbiology and to catalyze the translation of these insights into practical healthcare solutions.

physics.bio-ph↗

arXiv2024

Digital cytometry: extraction of forward and side scattering signals from holotomography

Flow cytometry is a cornerstone technique in medical and biological research, providing crucial information about cell size and granularity through forward scatter (FSC) and side scatter (SSC) signals. Despite its widespread use, the precise relationship between these scatter signals and corresponding microscopic images remains underexplored. Here, we investigate this intrinsic relationship by utilizing scattering theory and holotomography, a three-dimensional quantitative phase imaging (QPI) technique. We demonstrate the extraction of FSC and SSC signals from individual, unlabeled cells by analyzing their three-dimensional refractive index distributions obtained through holotomography. Additionally, we introduce a method for digitally windowing SSC signals to facilitate effective segmentation and morphology-based cell type classification. Our approach bridges the gap between flow cytometry and microscopic imaging, offering a new perspective on analyzing cellular characteristics with high accuracy and without the need for labeling.

physics.optics↗

arXiv2024

Rytov Approximation of Vectorial Waves by Modifying Scattering Matrixes: Precise Reconstruction of Dielectric Tensor Tomography

Analyzing 3D anisotropic materials presents significant challenges, especially when assessing 3D orientations, material distributions, and anisotropies through scattered light, due to the inherently vectorial nature of light-matter interactions. In this study, we formulate a scattering theory based on the Rytov approximation, commonly employed in scalar wave tomography, tailored to accommodate vector waves by modifying the scattering matrix. Using this formulation, we investigate the intricate 3D structure of liquid crystals with multiple topological defects exploiting dielectric tensor tomography. By leveraging dielectric tensor tomography, we successfully visualize these topological defects in three dimensions, a task that conventional 2D imaging techniques fail to achieve.

physics.optics↗

arXiv2024

High-precision and low-noise dielectric tensor tomography using a micro-electromechanical system mirror

Dielectric tensor tomography is an imaging technique for mapping three-dimensional distributions of dielectric properties in transparent materials. This work introduces an enhanced illumination strategy employing a micro-electromechanical system mirror to achieve high precision and reduced noise in imaging. This illumination approach allows for precise manipulation of light, significantly improving the accuracy of angle control and minimizing diffraction noise compared to traditional beam steering approaches. Our experiments have successfully reconstructed the dielectric properties of liquid crystal droplets, which are known for their anisotropic structures, while demonstrating a notable reduction in background noise of the imag-es. Additionally, the technique has been applied to more complex samples, revealing its capability to achieve a high signal-to-noise ratio. This development represents a significant step forward in the field of birefringence imaging, offering a powerful tool for detailed study of materials with anisotropic properties.

physics.optics↗