Comparison of phase retrieval methods for optical diffraction tomography

Wedberg, Torolf C.; Stamnes, Jakob J.

doi:10.1088/0963-9659/4/1/005

Cited by 38 publications

(13 citation statements)

References 6 publications

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“…While some of these works examine phase retrieval as a reconstruction algorithm, they must either shift the focal plane [22,24] or source [25] axially between each measurement, or must assume constraints on the sample [19,20,23,26] to successfully recover the phase. These prior works do not connect DT to ptychographic phase retrieval (i.e., they do not recover the phase by using diversity between the variably illuminated DT images).…”

Section: Related Workmentioning

confidence: 99%

Diffraction tomography with Fourier ptychography

Horstmeyer

Chung

et al. 2016

Optica

237

128

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This paper presents a technique to image the complex index of refraction of a sample across three dimensions. The only required hardware is a standard microscope and an array of LEDs. The method, termed Fourier ptychographic tomography (FPT), first captures a sequence of intensity-only images of a sample under angularly varying illumination. Then, using principles from ptychography and diffraction tomography, it computationally solves for the sample structure in three dimensions. The experimental microscope demonstrates a lateral spatial resolution of 0.39 μm and an axial resolution of 3.7 μm at the Nyquist–Shannon sampling limit (0.54 and 5.0 μm at the Sparrow limit, respectively) across a total imaging depth of 110 μm. Unlike competing methods, this technique quantitatively measures the volumetric refractive index of primarily transparent and contiguous sample features without the need for interferometry or any moving parts. Wide field-of-view reconstructions of thick biological specimens suggest potential applications in pathology and developmental biology.

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Section: Related Workmentioning

confidence: 99%

Diffraction tomography with Fourier ptychography

Horstmeyer

Chung

et al. 2016

Optica

237

128

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“…Filling the data in the missing cone is a signal recovery problem, where the missing spots in Fourier space are to be recovered using a priori information about the object under consideration. Phase retrieval, another signal recovery problem, has attracted a lot of interest (Fienup, 1982;Saldin et al, 2001;Wedberg and Stamnes, 1999;Yan et al, 2011). In this case, the phase of a complex-valued function with known modulus has to be estimated.…”

Section: Retrieval Of Missing Amplitudes and Phases By Pcomentioning

confidence: 99%

Image processing techniques for high-resolution structure determination from badly ordered 2D crystals

Biyani

Scherer

Righetto

et al. 2017

Preprint

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Abstract2D electron crystallography can be used to study small membrane proteins in their native environment. Obtaining highly ordered 2D crystals is difficult and time-consuming.However, 2D crystals diffracting to only 10-12 Å can be prepared relatively conveniently in most cases. We have developed image-processing algorithms allowing to generate a high resolution 3D structure from cryo-electron crystallography images of badly ordered crystals.These include movie-mode unbending, refinement over sub-tiles of the images in order to locally refine the sample tilt geometry; implementation of different CTF correction schemes;and an iterative method to apply known constraints in the real and reciprocal space to approximate amplitudes and phases in the so-called missing cone regions. These algorithms applied to a dataset of the potassium channel MloK1 show significant resolution improvements to approximately 5Å.. CC-BY-NC 4.0 International license It is made available under a (which was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint . http://dx.doi.org/10.1101/113415 doi: bioRxiv preprint first posted online Mar. 3, 2017; Biyani et al., Image processing techniques for high-resolution 2D electron crystallography 3

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“…To overcome this problem, intensity-only diffraction tomography techniques [30][31][32][33], phase retrieval algorithms [34] or alternative methods such as the phase-shifting holography [35] can be employed. In this study, we assume that the phase information of the measured scattered fields is available through such a phase retrieval algorithm, and therefore intensity-only ODT techniques are ignored while performing reconstructions and comparisons.…”

Section: Optical Diffraction Tomographymentioning

confidence: 99%

Modal-based tomographic imaging from far-zone observations

Karbeyaz

Rappaport

2008

J. Opt. Soc. Am. A

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A novel method of optical diffraction tomography (ODT) to image weakly scattering, electrically large two dimensional (2D) objects using the far-zone scattered field data is presented. The proposed technique is based on the expansion of the target object function in terms of Fourier-Bessel basis functions, and an alternative approximation for the total electric field within the support of the investigated scatterer. Analytical (Mie) plane-wave scattering by a layered, circularly symmetric, lossy dielectric cylinder, and finite-difference time-domain simulations involving plane-wave scattering first by a more general, lossless dielectric phantom and then by embryo models involving various mitochondrial distributions are utilized to compare the performance of the proposed method with that of the standard ODT techniques which are based on the Born/Rytov approximations and Fourier diffraction theorem. Quantitative and qualitative superiority of the presented method is demonstrated. The proposed method can be used without being confined to far-zone observations with a proper (cylindrical-spherical) receiver configuration, and can be easily modified to handle multi-frequency data for a wideband reconstruction whenever applicable. The proposed 2D technique can be readily extended to more realistic three dimensional scenarios, and can be used in tomographic microscopy for various purposes, such as the cell-embryo health assessment for in vitro fertilization procedures.

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Comparison of phase retrieval methods for optical diffraction tomography

Cited by 38 publications

References 6 publications

Diffraction tomography with Fourier ptychography

Diffraction tomography with Fourier ptychography

Image processing techniques for high-resolution structure determination from badly ordered 2D crystals

Modal-based tomographic imaging from far-zone observations

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