The Microscope in a Computer: Image Synthesis from Three-Dimensional Full-Vector Solutions of Maxwell’s Equations at the Nanometer Scale

Capoglu, Ilker; Rogers, Jeremy D.; Taflove, Allen; Backman, Vadim

doi:10.1016/b978-0-44-459422-8.00001-1

Cited by 27 publications

(20 citation statements)

References 191 publications

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“…[5][6][7][8] It is based on the discretization of a 3-D volume into a Cartesian grid consisting of small compared to the wavelength cubic voxels, and the solution of Maxwell's equations for the evolution of the electric and magnetic field at discrete positions on this Cartesian grid. The core algorithm of the FDTD method was proposed by Yee 9 in 1966, and popularized by Taflove in the '80s and '90s, who also coined the term FDTD.…”

Section: Finite-difference Time-domain Simulationsmentioning

confidence: 99%

“…6,8 It can accurately calculate microscope images of arbitrary inhomogeneous samples under various imaging parameters, incorporating RI fluctuations as fine as 10 nm. 7 We have used Angora to synthesize all reported herein bright-field plane-wave epi-illumination microscope images at 30 different wavelengths between 500 and 700 nm, equally spaced in wave number space.…”

Section: Finite-difference Time-domain Simulationsmentioning

confidence: 99%

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Reconstruction of explicit structural properties at the nanoscale via spectroscopic microscopy

et al. 2016

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Abstract. The spectrum registered by a reflected-light bright-field spectroscopic microscope (SM) can quantify the microscopically indiscernible, deeply subdiffractional length scales within samples such as biological cells and tissues. Nevertheless, quantification of biological specimens via any optical measures most often reveals ambiguous information about the specific structural properties within the studied samples. Thus, optical quantification remains nonintuitive to users from the diverse fields of technique application. In this work, we demonstrate that the SM signal can be analyzed to reconstruct explicit physical measures of internal structure within label-free, weakly scattering samples: characteristic length scale and the amplitude of spatial refractive-index (RI) fluctuations. We present and validate the reconstruction algorithm via finite-difference time-domain solutions of Maxwell's equations on an example of exponential spatial correlation of RI. We apply the validated algorithm to experimentally measure structural properties within isolated cells from two genetic variants of HT29 colon cancer cell line as well as within a prostate tissue biopsy section. The presented methodology can lead to the development of novel biophotonics techniques that create two-dimensional maps of explicit structural properties within biomaterials: the characteristic size of macromolecular complexes and the variance of local mass density.

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Section: Finite-difference Time-domain Simulationsmentioning

confidence: 99%

Section: Finite-difference Time-domain Simulationsmentioning

confidence: 99%

Reconstruction of explicit structural properties at the nanoscale via spectroscopic microscopy

et al. 2016

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“…7. Using the scattered field outside the TF/SF boundary, and propagating it to the far (Fraunhofer) zone using a multilayer NFFFT [25], a numerical microscope image of the scatterer can be synthesized [27]. In Fig.…”

Section: Numerical Microscope Image Of a Scatterermentioning

confidence: 99%

Computation of tightly-focused laser beams in the FDTD method

Capoglu¹,

Taflove²,

Backman³

2013

Opt. Express

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Abstract:We demonstrate how a tightly-focused coherent TEM mn laser beam can be computed in the finite-difference time-domain (FDTD) method. The electromagnetic field around the focus is decomposed into a plane-wave spectrum, and approximated by a finite number of plane waves injected into the FDTD grid using the total-field/scattered-field (TF/SF) method. We provide an error analysis, and guidelines for the discrete approximation. We analyze the scattering of the beam from layered spaces and individual scatterers. The described method should be useful for the simulation of confocal microscopy and optical data storage. An implementation of the method can be found in our free and open source FDTD software ("Angora").

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“…The model was made possible by the use of rigorous numerical techniques, such as the finite-difference time-domain method, to calculate how light propagates in general samples. Capoglu et al [14] published a good review of rigorous computational models of optical microscopes. Few OCT models have used rigorous numerical techniques to model light propagation in the sample and those that do, do not rigorously model image formation.…”

Section: Introductionmentioning

confidence: 99%

Full wave model of image formation in optical coherence tomography applicable to general samples

Munro¹,

Curatolo²,

Sampson³

2015

Opt. Express

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Abstract:We demonstrate a highly realistic model of optical coherence tomography, based on an existing model of coherent optical microscopes, which employs a full wave description of light. A defining feature of the model is the decoupling of the key functions of an optical coherence tomography system: sample illumination, light-sample interaction and the collection of light scattered by the sample. We show how such a model can be implemented using the finite-difference time-domain method to model light propagation in general samples. The model employs vectorial focussing theory to represent the optical system and, thus, incorporates general illumination beam types and detection optics. To demonstrate its versatility, we model image formation of a stratified medium, a numerical point-spread function phantom and a numerical phantom, based upon a physical three-dimensional structured phantom employed in our laboratory. We show that simulated images compare well with experimental images of a three-dimensional structured phantom. Such a model provides a powerful means to advance all aspects of optical coherence tomography imaging.

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The Microscope in a Computer: Image Synthesis from Three-Dimensional Full-Vector Solutions of Maxwell’s Equations at the Nanometer Scale

Cited by 27 publications

References 191 publications

Reconstruction of explicit structural properties at the nanoscale via spectroscopic microscopy

Reconstruction of explicit structural properties at the nanoscale via spectroscopic microscopy

Computation of tightly-focused laser beams in the FDTD method

Full wave model of image formation in optical coherence tomography applicable to general samples

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