arXiv subjects

Seokchan Yoon

Publications and source records attributed to Seokchan Yoon.

At least 19 recordsLinked to original sources

arXiv2026

Refractive-index tomography of opaque tissue from its own backscattered light

The refractive index (RI) is an intrinsic, label-free marker of a living cell's dry mass and subcellular morphology, and hence of its physiological state. Its three-dimensional (3D) reconstruction has become a powerful way to study cells and tissues in their native state, spanning cell growth, drug response and disease diagnosis. Yet this capability rests on a fundamental constraint: the RI can be recovered only from light transmitted through the specimen, which demands optical access to both sides. The cells that matter most -- those within thick tissues, intact organs and living animals -- are therefore out of reach. A tissue, however, can illuminate its own cells from behind: light backscattered by intrinsic tissue structures beneath a cell carries the same transmission information a microscope would collect from the far side. Here we develop a divide-and-conquer inverse-scattering framework that recovers this transmission from the backscattering and reconstructs a cell's 3D RI. We demonstrate label-free, quantitative imaging of cells within an engineered tissue, and a living mouse through its intact skull, where we further quantify the dry mass of individual osteocytes in vivo. By removing the need for two-sided access, this reflection-only approach extends RI tomography into living tissue, enabling non-destructive, longitudinal imaging of cells in their native environment.

physics.optics↗

arXiv2025

Decoding angular light paths for solving the inverse scattering problem

Multiple scattering in complex media scrambles the deterministic mapping between input and output fields, limiting wave control and imaging. Conventional inverse scattering strategies rely on discrete spatial layers, but this assumption breaks down in volumetric media where scattering is continuously distributed, particularly near the object plane. Here we introduce a framework that reformulates light transport in terms of scattering angles rather than spatial layers. We show that decomposing scattered waves into angular deflection components--each associated with a spatially invariant point spread function--provides a compact and depth-independent description of volumetric scattering. This representation is particularly effective in forward-scattering biological tissues, where most scattered energy is confined to a narrow angular range. Leveraging this angular sparsity, we develop a progressive inverse algorithm that retrieves dominant angular components from reflection measurements, converting multiply scattered light into usable signal by more than an order of magnitude of the ballistic signal. We demonstrate in vivo recovery of subcellular osteocyte networks through intact mouse skulls, a regime inaccessible to existing methods. These results establish the scattering-angle basis as a general physical framework for decoding information scrambled by disorder, extending the reach of deep optical imaging.

physics.optics↗

arXiv2024

Implementation of reflection matrix microscopy: An algorithm perspective

Over the past decade, reflection matrix microscopy (RMM) and advanced image reconstruction algorithms have emerged to address the fundamental imaging depth limitations of optical microscopy in thick biological tissues and complex media. In this study, we introduce significant advancements in reflection matrix processing algorithms, including logical indexing, power iterations, and low-frequency blocking. These enhance the processing speed of aperture synthesis, 3D image reconstruction, and aberration correction by orders of magnitude. Detailed algorithm implementations, along with experimental data, are provided to facilitate the widespread adoption of RMM in various deep-tissue imaging applications.

physics.optics↗

arXiv2024

Multiphoton super-resolution imaging via virtual structured illumination

Imaging in thick biological tissues is often degraded by sample-induced aberrations, which reduce image quality and resolution, particularly in super-resolution techniques. While hardware-based adaptive optics, which correct aberrations using wavefront shaping devices, provide an effective solution, their complexity and cost limit accessibility. Computational methods offer simpler alternatives but struggle with complex aberrations due to the incoherent nature of fluorescence. Here, we present a deep-tissue super-resolution imaging framework that addresses these challenges with minimal hardware modification. By replacing the photodetector in a standard laser-scanning microscope with a camera, we measure an incoherent response matrix (IRM). A dual deconvolution algorithm is developed to decompose the IRM into excitation and emission optical transfer functions and the object spectrum. The proposed method simultaneously corrects excitation and emission point-spread functions (PSFs), achieving a resolution of {\lambda}/4, comparable to structured illumination microscopy. Unlike existing computational methods that rely on vector decomposition of a single convoluted PSF, our matrix-based approach enhances image reconstruction, particularly for high spatial frequency components, enabling super-resolution even in the presence of complex aberrations. We validated this framework with two-photon super-resolution imaging, achieving a lateral resolution of 130 nanometers at a depth of 180 micrometers in thick mouse brain tissue.

physics.optics↗

arXiv2023

Synthetic aperture phase imaging of second harmonic generation field with computational adaptive optics

Second-harmonic generation (SHG) microscopy provides label-free imaging of biological tissues with unique contrast mechanisms, but its resolution is limited by the diffraction limit. Here, we present the first experimental demonstration of super-resolution quantitative phase imaging of the SHG field based on synthetic aperture Fourier holographic microscopy. We discuss the mathematical model of synthetic-aperture imaging of SHG fields, as well as the computational adaptive optics technique for correcting sample-induced aberration. We demonstrate proof-of-concept experiments where SHG targets are embedded within a thick scattering medium to validate the performance of the proposed imaging technique. It is shown to be able to overcome the conventional Abbe diffraction limit even in the complex aberrations and strong multiple scattering. We also demonstrate SHG-based super-resolution deep-tissue phase imaging of ex-vivo zebrafish muscle tissue.

physics.optics↗

arXiv2023

Tracing multiple scattering trajectories for deep optical imaging in scattering media

Multiple light scattering hampers imaging objects in complex scattering media. Approaches used in real practices mainly aim to filter out multiple scattering obscuring the ballistic waves that travel straight through the scattering medium. Here, we propose a method that makes the deterministic use of multiple scattering for microscopic imaging of an object embedded deep within scattering media. The proposed method finds a stack of multiple complex phase plates that generate similar light trajectories as the original scattering medium. By implementing the inverse scattering using the identified phase plates, our method rectifies multiple scattering and amplifies ballistic waves by almost 600 times, which leads to a substantial increase in imaging depth. Our study marks an important milestone in solving the longstanding high-order inverse scattering problems.

physics.optics↗

arXiv2021

High-throughput volumetric adaptive optical imaging using compressed time-reversal matrix

Deep-tissue optical imaging suffers from the reduction of resolving power due to tissue-induced optical aberrations and multiple scattering noise. Reflection matrix approaches recording the maps of backscattered waves for all the possible orthogonal input channels have provided formidable solutions for removing severe aberrations and recovering the ideal diffraction-limited spatial resolution without relying on fluorescence labeling and guide stars. However, measuring the full input-output response of the tissue specimen is time-consuming, making the real-time image acquisition difficult. Here, we present the use of a time-reversal matrix, instead of the reflection matrix, for fast high-resolution volumetric imaging of a mouse brain. The time-reversal matrix reduces two-way problem to one-way problem, which effectively relieves the requirement for the coverage of input channels. Using a newly developed aberration correction algorithm designed for the time-reversal matrix, we demonstrated the correction of complex aberrations using as small as 2 % of the complete basis while maintaining the image reconstruction fidelity comparable to the fully sampled reflection matrix. Due to nearly 100-fold reduction in the matrix recording time, we could achieve real-time aberration-correction imaging for a field of view of 40 x 40 microns (176 x 176 pixels) at a frame rate of 80 Hz. Furthermore, we demonstrated high-throughput volumetric adaptive optical imaging of a mouse brain by recording a volume of 128 x 128 x 125 microns (568 x 568 x 125 voxels) in 3.58 s, correcting tissue aberrations at each and every 1-micron depth section, and visualizing myelinated axons with a lateral resolution of 0.45 microns and an axial resolution of 2 microns.

physics.optics↗

arXiv2019

Laser scanning reflection-matrix microscopy for label-free in vivo imaging of a mouse brain through an intact skull

We present a laser scanning reflection-matrix microscopy combining the scanning of laser focus and the wide-field mapping of the electric field of the backscattered waves for eliminating higher-order aberrations even in the presence of strong multiple light scattering noise. Unlike conventional confocal laser scanning microscopy, we record the amplitude and phase maps of reflected waves from the sample not only at the confocal pinhole, but also at other non-confocal points. These additional measurements lead us to constructing a time-resolved reflection matrix, with which the sample-induced aberrations for the illumination and detection pathways are separately identified and corrected. We realized in vivo reflectance imaging of myelinated axons through an intact skull of a living mouse with the spatial resolution close to the ideal diffraction limit. Furthermore, we demonstrated near-diffraction-limited multiphoton imaging through an intact skull by physically correcting the aberrations identified from the reflection matrix. The proposed method is expected to extend the range of applications, where the knowledge of the detailed microscopic information deep within biological tissues is critical.

physics.bio-ph↗

arXiv2017

Observation of a non-equilibrium steady state of cold atoms in a moving optical lattice

We investigated non-equilibrium atomic dynamics in a moving optical lattice via observation of atomic resonance fluorescence spectrum. A three-dimensional optical lattice was generated in a phase-stabilized magneto-optical trap (MOT) and the lattice was made to move by introducing a detuning between the counter-propagating trap lasers. A non-equilibrium steady states (NESS's) of atoms was then established in the hybrid of the moving optical lattice and the surrounding MOT. A part of atoms were localized and transported in the moving optical lattice and the rest were not localized in the lattice while trapped as a cold gas in the MOT. These motional states coexisted with continuous transition between them. As the speed of the lattice increased, the population of the non-localized state increased in a stepwise fashion due to the existence of bound states at the local minima of the lattice potential. A deterministic rate-equation model for atomic populations in those motional states was introduced in order to explain the experimental results. The model calculations then well reproduced the key features of the experimental observations, confirming the existence of an NESS in the cold atom system.

physics.atom-ph↗

arXiv2017

Fluorescence detection of single lithium atoms in an optical lattice using Doppler-cooling beams

We demonstrate in situ fluorescence detection of $^7$Li atoms in a 1D optical lattice with single atom precision. Even though illuminated lithium atoms tend to boil out, when the lattice is deep, molasses beams without extra cooling retain the atoms while producing sufficient fluorescent photons for detection. When the depth of the potential well at an antinode is 2.4 mK, an atom remains trapped for 30 s while scattering probe photons at the rate of $1.7 \times 10^5$ s$^{-1}$. We propose a simple model that describes the dependence of the lifetime of an atom on well depth. When the number of trapped atoms is reduced, a clear stepwise change is observed in integrated fluorescence, indicating the detection of a single atom. At a photon-collecting efficiency of only 1.3% owing to small numerical aperture, the presence or absence of an atom is determined within 300 ms with an error of less than $5 \times 10^{-4}$.

physics.atom-ph↗

arXiv2015

Fluorescence spectra of atoms in a phase-stabilized magneto-optical trap as an optical lattice

We present a study on characteristics of a magneto-optical trap (MOT) as an optical lattice. Fluorescence spectra of atoms trapped in a MOT with a passively phase-stabilized beam configuration have been measured by means of the photon-counting heterodyne spectroscopy. We observe a narrow Rayleigh peak and well-resolved Raman sidebands in the fluorescence spectra which clearly show that the MOT itself behaves as a three-dimensional optical lattice. Optical-lattice-like properties of the phase-stabilized MOT such as vibrational frequencies and lineshapes of Rayleigh peak and Raman sidebands are investigated systematically for various trap conditions.

physics.atom-ph↗

arXiv2015

Cavity-Modified Collective Rayleigh Scattering of Two Atoms

We report on the observation of cooperative radiation of exactly two neutral atoms strongly coupled to the single mode field of an optical cavity, which is close to the lossless-cavity limit. Monitoring the cavity output power, we observe constructive and destructive interference of collective Rayleigh scattering for certain relative distances between the two atoms. Because of cavity backaction onto the atoms, the cavity output power for the constructive two-atom case ($N=2$) is almost equal to the single-emitter case ($N=1$), which is in contrast to free-space where one would expect an $N^2$ scaling of the power. These effects are quantitatively explained by a classical model as well as by a quantum mechanical model based on Dicke states. We extract information on the relative phases of the light fields at the atom positions and employ advanced cooling to reduce the jump rate between the constructive and destructive atom configurations. Thereby we improve the control over the system to a level where the implementation of two-atom entanglement schemes involving optical cavities becomes realistic.

quant-ph↗

arXiv2014

Carrier-free Raman manipulation of trapped neutral atoms

We experimentally realize an enhanced Raman control scheme for neutral atoms that features an intrinsic suppression of the two-photon carrier transition, but retains the sidebands which couple to the external degrees of freedom of the trapped atoms. This is achieved by trapping the atom at the node of a blue detuned standing wave dipole trap, that acts as one field for the two-photon Raman coupling. The improved ratio between cooling and heating processes in this configuration enables a five times lower fundamental temperature limit for resolved sideband cooling. We apply this method to perform Raman cooling to the two-dimensional vibrational ground state and to coherently manipulate the atomic motion. The presented scheme requires minimal additional resources and can be applied to experiments with challenging optical access, as we demonstrate by our implementation for atoms strongly coupled to an optical cavity.

physics.atom-ph↗

arXiv2014

EIT-control of single-atom motion in an optical cavity

We demonstrate cooling of the motion of a single atom confined by a dipole trap inside a high-finesse optical resonator. Cooling of the vibrational motion results from EIT-like interference in an atomic Λ-type configuration, where one transition is strongly coupled to the cavity mode and the other is driven by an external control laser. Good qualitative agreement with the theoretical predictions is found for the explored parameter ranges. The role of the cavity in the cooling dynamics is confirmed by means of a direct comparison with EIT-cooling performed in the dipole trap in free space. These results set the basis to the realization of an efficient photonic interface based on single atoms.

quant-ph↗

arXiv2012

Bayesian feedback control of a two-atom spin-state in an atom-cavity system

We experimentally demonstrate real-time feedback control of the joint spin-state of two neutral Caesium atoms inside a high finesse optical cavity. The quantum states are discriminated by their different cavity transmission levels. A Bayesian update formalism is used to estimate state occupation probabilities as well as transition rates. We stabilize the balanced two-atom mixed state, which is deterministically inaccessible, via feedback control and find very good agreement with Monte-Carlo simulations. On average, the feedback loops achieves near optimal conditions by steering the system to the target state marginally exceeding the time to retrieve information about its state.

quant-ph↗

arXiv2006

Dependence of fluorescence-level statistics on bin time size in a few-atom magneto-optical trap

We have analyzed the statistical distribution of the fluorescence signal levels in a magneto-optical trap containing a few atoms and observed that it strongly depends on the relative size of the bin time with respect to the trap decay time. We derived analytic expressions for the signal distributions in two limiting cases, long and short bin time limits, and found good agreement with numerical simulations performed regardless of the size of the bin time. We found an optimal size of the bin time for minimizing the probability of indeterminate atom numbers while providing accurate information on the instantaneous number of atoms in the trap. These theoretical results are compared with actual experimental data. We observed super-Poisson counting statistics for the fluorescence from trapped atoms, which might be attributed to uncorrelated motion of trapped atoms in the inhomogeneous magnetic field in the trap.

physics.atom-ph↗

arXiv2006

The dependence of transverse and longitudinal resolutions on incident Gaussian beam widths in the illumination part of optical scanning microscopy

We studied both theoretically and experimentally the intensity distribution of a Gaussian laser beam when it was focussed by an objective lens with its numerical-aperture (NA) up to 0.95. Approximate formulae for full widths at half maximum (FWHM) of the intensity distribution at focus were derived for very large and very small initial beam waists with respect to the entrance pupil radius of the objective lens. In experiments the energy flux through a 0.5 micron pinhole was measured for various pinhole positions. We found that the FWHM's at focus in the transverse and the longitudinal directions do not increase much from the ultimate FWHM's until the input beam waist is reduced below the half of the entrance pupil radius. In addition, we observed significance of the spatial distribution of the input beam against a true Gaussian beam profile in the case of small initial beam waist. For high NA with resulting focal beam waists comparable to or smaller than the wavelength of the laser, the interaction between the electric field and the conducting surface of the pinhole caused the transverse FWHM to be measured slightly smaller than FWHM of the unperturbed intensity distribution convoluted with the pinhole opening.

physics.optics↗

arXiv2006

Analysis of the atom-number correlation function in a few-atom trap

Stochastic properties of loading and loss mechanism in a few atom trap are analyzed. An approximate formula is derived for the atom-number correlation function for the trapped atoms in the limit of reasonably small two-atom loss rate. Validity of the approximate formula is confirmed by numerical simulations.

physics.atom-ph↗