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Multiresolution-based weighted regularization for denoised image interpolation from scattered samples with application to confocal microscopy

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JOURNAL OF THE OPTICAL SOCIETY OF AMERICA A-OPTICS IMAGE SCIENCE AND VISION 2018年第10期35卷 1749-1759页

作者： Francis, Bibin Mathew, Manoj Arigovindan, Muthuvel Indian Inst Sci IISc Imaging Syst Lab Elect Engn Bangalore 560012 Karnataka India Natl Ctr Biol Sci Cent Imaging & Flow Cytometry Facil Bangalore 560065 Karnataka India

The problem of reconstructing an image from nonuniformly spaced, spatial point measurements is frequently encountered in bioimaging and other scientific disciplines. The most successful class of methods in handling this problem uses the regularization approach involving the minimization of a derivative-based roughness functional. It has been well demonstrated, in the presence of noise, that nonquadratic roughness functionals such as l(1), measure yield better performance compared to the quadratic ones in inverse problems in general and in deconvolution in particular. However, for the present problem, all well-evaluated methods use quadratic roughness measures;indeed, l(1) performs worse than the quadratic roughness when the sampling density is low. This is due to the fact that the mutual incoherence between the measurement operator (dirac-delta) and the regularization operator (derivative) is low in the present problem. Here we develop a new multiresolution-based roughness functional that performs better than l(1) and quadratic functionals under a wide range of sampling densities. We also propose an efficient iterative method for minimizing the resulting cost function. We demonstrate the superiority of the proposed regularization functional in the context of reconstructing full images from nonuniformly undersampled data obtained from a confocal microscope. (C) 2018 Optical Society of America

关键词： computation methods Confocal microscopy Functional imaging Image reconstruction Imaging noise Inverse problems

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Visualizing topical drug uptake with conventional fluorescence microscopy and deep learning

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BIOMEDICAL OPTICS EXPRESS 2020年第12期11卷 6864-6880页

作者： Evans, Conor L. Hermsmeier, Maiko Yamamoto, Akira Chan, Kin F. Massachusetts Gen Hosp Wellman Ctr Photomed Boston MA 02114 USA BioPharmX Inc 115 Nicholson Ln San Jose CA 95134 USA Simpson Intervent Inc Woodside CA 94062 USA

Mapping the uptake of topical drugs and quantifying dermal pharmacokinetics (PK) presents numerous challenges. Though high resolution and high precision methods such as mass spectrometry offer the means to quantify drug concentration in tissue, these tools are complex and often expensive, limiting their use in routine experiments. For the many topical drugs that are naturally fluorescent, tracking fluorescence emission can be a means to gather critical PK parameters. However, skin autofluorescence can often overwhelm drug fluorescence signatures. Here we demonstrate the combination of standard epi-fluorescence imaging with deep learning for the visualization and quantification of fluorescent drugs in human skin. By training a U-Net convolutional neural network on a dataset of annotated images, drug uptake from both high "infinite" dose and daily clinical dose regimens can be measured and quantified. This approach has the potential to simplify routine topical product development in the laboratory. (c) 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

关键词： computation methods Fluorescence microscopy Image quality Imaging techniques Mass spectrometry Neural networks

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Signal model and granular-noise analysis of computational image reconstruction for curved integral imaging systems

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APPLIED OPTICS 2009年第5期48卷 827-833页

作者： Shin, Dong-Hak Yoo, Hoon Sangmyung Univ Div Digital Media Technol Seoul 110743 South Korea Dongseo Univ Dept Visual Content Pusan 617716 South Korea

In this paper, we propose an improved analysis on the signal property of curved computational integral imaging reconstruction (C-CIIR). In the proposed model and analysis, we explain a general analysis of computational integral imaging by introducing a curvature effect that is obtained by the additional use of a large-aperture (LA) lens. Based on the proposed signal model in C-CIIR, we analyze the characteristics of the granular noise (GN) and conduct preliminary experiments to show the feasibility of our model. Experimental results indicate that the GN caused by the nonuniform overlapping gets reduced and that the GN is diminished as the focal length of the additional LA lens used decreases in C-CIIR. Also, the proposed model and analysis are considered to be generalized versions of the signal model and analysis of the previous computational integral imaging systems. (C) 2009 Optical Society of America

关键词： Analytical techniques computation methods Image processing Image reconstruction Imaging systems Three dimensional imaging

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Application of the three-component bidirectional reflectance distribution function model to Monte Carlo calculation of spectral effective emissivities of nonisothermal blackbody cavities

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APPLIED OPTICS 2012年第33期51卷 8003-8012页

作者： Prokhorov, Alexander Prokhorova, Nina I. Virial Int LLC Gaithersburg MD 20878 USA

We applied the bidirectional reflectance distribution function (BRDF) model consisting of diffuse, quasi-specular, and glossy components to the Monte Carlo modeling of spectral effective emissivities for nonisothermal cavities. A method for extension of a monochromatic three-component (3C) BRDF model to a continuous spectral range is proposed. The initial data for this method are the BRDFs measured in the plane of incidence at a single wavelength and several incidence angles and directional-hemispherical reflectance measured at one incidence angle within a finite spectral range. We proposed the Monte Carlo algorithm for calculation of spectral effective emissivities for nonisothermal cavities whose internal surface is described by the wavelength-dependent 3C BRDF model. The results obtained for a cylindroconical nonisothermal cavity are discussed and compared with results obtained using the conventional specular-diffuse model. (C) 2012 Optical Society of America

关键词： Bidirectional reflectance distribution function computation methods Diffuse reflectance Fresnel reflection Optical properties Ray tracing

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Discrete dipole approximation for time-domain computation of optical forces on magnetodielectric scatterers

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OPTICS EXPRESS 2011年第3期19卷 2466-2475页

作者： Chaumet, Patrick C. Belkebir, Kamal Rahmani, Adel Univ Paul Cezanne Inst Fresnel UMR 6133 F-13397 Marseille 20 France Univ Technol Sydney Dept Math Sci Broadway NSW 2007 Australia

We present a general approach, based on the discrete dipole approximation (DDA), for the computation of the exchange of momentum between light and a magnetodielectric, three-dimensional object with arbitrary geometry and linear permittivity and permeability tensors in time domain. The method can handle objects with an arbitrary shape, including objects with dispersive dielectric and/or magnetic material responses. (C) 2011 Optical Society of America

关键词： computation methods Light scattering Optical force Spontaneous emission Surface plasmon resonance Transient phenomena

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Differentiable scattering matrix for optimization of photonic structures

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OPTICS EXPRESS 2020年第25期28卷 37773-37787页

作者： Zhu, Ziwei Zheng, Changxi Columbia Univ Dept Comp Sci New York NY 10027 USA

The scattering matrix, which quantifies the optical reflection and transmission of a photonic structure, is pivotal for understanding the performance of the structure. In many photonic design tasks, it is also desired to know how the structure's optical performance changes with respect to design parameters, that is, the scattering matrix's derivatives (or gradient). Here we address this need. We present a new algorithm for computing scattering matrix derivatives accurately and robustly. In particular, we focus on the computation in semi-analytical methods (such as rigorous coupled-wave analysis). To compute the scattering matrix of a structure, these methods must solve an eigen-decomposition problem. However, when it comes to computing scattering matrix derivatives, differentiating the eigen-decomposition poses significant numerical difficulties. We show that the differentiation of the eigen-decomposition problem can be completely sidestepped, and thereby propose a robust algorithm. To demonstrate its efficacy, we use our algorithm to optimize metasurface structures and reach various optical design goals. (C) 2020 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

关键词： computation methods Light transmission Mode conversion Phase shift Photonic crystals Wave propagation

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Improved resolution in 3D structured illumination microscopy using 3D model-based restoration with positivity-constraint

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BIOMEDICAL OPTICS EXPRESS 2021年第12期12卷 7717-7731页

作者： Van, Cong T. S. Preza, Chrysanthe Univ Memphis Dept Elect & Comp Engn Computat Imaging Res Lab Memphis TN 38152 USA

The performance of structured illumination microscopy (SIM) systems depends on the computational method used to process the raw data. In this paper, we present a regularized three-dimensional (3D) model-based (MB) restoration method with positivity constraint (PC) for 3D processing of data from 3D-SIM (or 3-beam interference SIM), in which the structured illumination pattern varies laterally and axially. The proposed 3D-MBPC method introduces positivity in the solution through the reconstruction of an auxiliary function using a conjugate-gradient method that minimizes the mean squared error between the data and the 3D imaging model. The 3D-MBPC method provides axial super resolution, which is not the same as improved optical sectioning demonstrated with model-based approaches based on the 2D-SIM (or 2-beam interference SIM) imaging model, for either 2D or 3D processing of a single plane from a 3D-SIM dataset. Results obtained with our 3D-MBPC method show improved 3D resolution over what is achieved by the standard generalized Wiener filter method, the first known method that performs 3D processing of 3D-SIM data. Noisy simulation results quantify the achieved 3D resolution, which is shown to match theoretical predictions. Experimental verification of the 3D-MBPC method with biological data demonstrates successful application to data volumes of different sizes.

关键词： computation methods Inverse problems Optical imaging Structured illumination microscopy Three dimensional imaging Three dimensional microscopy

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Feature issue introduction: advanced computational nanophotonics: from materials to devices

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OPTICAL MATERIALS EXPRESS 2019年第4期9卷 1967-1970页

作者： Kildishev, Alexander, V Hu, Juejun Martin, Olivier J. F. Werner, Douglas H. Purdue Univ Birck Nanotechnol Ctr Sch Elect & Comp Engn W Lafayette IN 47907 USA MIT Dept Mat Sci & Engn Cambridge MA 02139 USA Swiss Fed Inst Technol Lausanne EPFL Nanophoton & Metrol Lab CH-1015 Lausanne Switzerland Penn State Univ Dept Elect Engn University Pk PA 16802 USA

computational nanophotonics has already made a disruptive impact on the photonic and optoelectronic industries and has dramatically influenced the ways today's optical engineers create, optimize, and use innovative materials and computer-aided services. This Feature Issue presents a set of eleven papers combined under the joint title of Advanced computational Nanophotonics: From Materials to Devices. The science and art of computational photonics have a long established history, yet interest in new approaches to advanced multiphysics modeling at the nanoscale and hence to innovatory multi-objective optimization techniques for nanophotonics have been growing exponentially in the last decade, and are now the subject of intense cross-disciplinary research efforts. The papers selected for the Feature Issue present a diverse palette of topics that, for example, include a comprehensive review of new optimization techniques, a fundamental theoretical concept of photonic Dirac monopoles, along with new multiphysics approaches to full-wave material modeling in non-linear nanophotonics and, in particular, to innovative modeling of photonic neural networks. Applications of advanced computational methods are additionally showcased with space-time light control by dynamic metasurfaces, polarization control with structured color all-dielectric metafilms, and an optofluidic system driven by a thermoplasmonic element. (C) 2019 Optical Society of America under the terms of the OSA Open Access Publishing Agreement

关键词： computation methods Evanescent waves Polarization control Quantum information processing Rigorous coupled wave analysis Total internal reflection

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Limited possibility for quantifying mean particle size by logarithmic light-scattering spectroscopy

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APPLIED OPTICS 2003年第16期42卷 2968-2971页

作者： Johns, M Liu, HL Univ Texas Dept Biomed Engn Arlington TX 76019 USA

Recent studies have shown that the slope of logarithmic scattering spectroscopy of a turbid medium is related to the sizes of the scattering particles within the turbid medium. Mie theory can be used to generate a logarithmic plot of the reduced-scattering coefficient versus wavelength. According to Nilsson et al. [Appl. Opt. 37, 1256 (1998)], the slope value of a linear fit of the logarithmic scattering spectroscopy between 600 and 1050 nm can be used for direct determination of particle size. We performed similar calculations using the Rayleigh-Gans approximation and obtained an analogous overall shape with additional sinusoidal features. Our calculations indicate a possible relationship between the slope and the particle size when the size is used to calculate the slope, namely, in the forward calculation. However, because of the sinusoidal pattern, the inverse calculation to obtain the particle size from the slope may be applied only for particles with a radius of <0.13 mum in combination with 650-1050-nm light. Caution should be exercised when inverse calculation is performed to determine the scattering particle sizes in the range of radii >0.13 mum, with the slope of logarithmic scattering spectroscopy within 650-1050 nm. (C) 2003 Optical Society of America.

关键词： computation methods Mie theory Particle scattering Scattering Scattering measurement Turbid media

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High-efficiency and broadband photonic polarization rotator based on multilevel shape optimization

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OPTICS LETTERS 2019年第8期44卷 1960-1963页

作者： Lebbe, Nicolas Gliere, Alain Hassan, Karim Univ Grenoble Alpes CEA LETI F-38000 Grenoble France Univ Grenoble Alpes LJK F-38000 Grenoble France

We report on a novel photonic polarization rotator design obtained by multilevel shape optimization. The numerical method consists of a topological optimization scheme, improving iteratively the efficiency of the component by modifying its shape on two discrete levels along the etching direction. We numerically show that, compared to state-of-the-art single-level shape optimization, the performances can be drastically improved for a given device length. Next, the polarization conversion efficiency can be further improved up to a computed value of 98.5% with less than 0.35 dB insertion losses on a 100 nm bandwidth for a 6 mu m x 1 mu m footprint. (C) 2019 Optical Society of America

关键词： computation methods Electric fields Extinction ratios Finite element method Genetic algorithms Polarization

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