Artifact-free deconvolution in light field microscopy

Stefanoiu, Anca; Page, Josue; Symvoulidis, Panagiotis; Westmeyer, Gil G.; Lasser, Tobias

doi:10.1364/oe.27.031644

Cited by 47 publications

(74 citation statements)

References 38 publications

(107 reference statements)

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“…There are various works in computer vision demonstrating computational super-resolution through combining multiple aliased low-resolution images acquired at sub-pixel camera movements [32][33][34][35][36][37]. In light field photography and conventional light field microscopy, computational super-resolution was addressed by exploiting sub-lenslet sampling [16,17,21,22,38,39]. In Fourier light field microscopy, the EIs form behind the micro-lenses at specific translational offsets with respect to their corresponding micro-lens centers.…”

Section: Aliasing and Computational Super-resolutionmentioning

confidence: 99%

“…is the complex transmittance function of a lenslet and (x l , y l ) are the local lenslet coordinates, while P(x l , y l ) is the lenslet pupil function [16,17].…”

Section: Light Field Point Spread Function Modelmentioning

confidence: 99%

“…Naturally, the technology was also adopted in optical microscopy, where Levoy et al [12] introduced it as light field microscopy (LFM); it is also referred to as integral microscopy (IMic) in the literature [13,14]. It has since emerged as a very capable scan-less optical imaging modality well-suited for highly-dynamic fluorescent biological specimens, allowing for subsequent 3D reconstruction [15][16][17]. LFM has been demonstrated in various biomedical application, including recording neuro-dynamics in vertebrate model organisms [18,19] or live cell imaging [20].…”

Section: Introductionmentioning

confidence: 99%

“…This effect is particularly strong around the native object plane (NOP), which is commonly referred to as the zero plane [16,18]. While the zero plane artifacts in the reconstruction have been very recently addressed in [17] via a resampling strategy during the deconvolution process, the recoverable resolution is ultimately limited by the design of the microscope and the resolution at the NOP remains low.…”

Section: Introductionmentioning

confidence: 99%

“…To address this limitation, there is a considerable amount of research which proposes various approaches. Examples include defocused plenoptic configurations [17,20,24] which manipulate the sampling pattern by altering the relative distances in the optical path (e.g. MLA to sensor), various hardware variations like wavefront coding techniques [25], hybrid systems combining a light field with a wide field acquisition [26] or simultaneous dual LFM setups [19] with complementary acquisition parameters.…”

Section: Introductionmentioning

confidence: 99%

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What about computational super-resolution in fluorescence Fourier light field microscopy?

et al. 2020

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Recently, Fourier light field microscopy was proposed to overcome the limitations in conventional light field microscopy by placing a micro-lens array at the aperture stop of the microscope objective instead of the image plane. In this way, a collection of orthographic views from different perspectives are directly captured. When inspecting fluorescent samples, the sensitivity and noise of the sensors are a major concern and large sensor pixels are required to cope with low-light conditions, which implies under-sampling issues. In this context, we analyze the sampling patterns in Fourier light field microscopy to understand to what extent computational super-resolution can be triggered during deconvolution in order to improve the resolution of the 3D reconstruction of the imaged data.

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Section: Aliasing and Computational Super-resolutionmentioning

confidence: 99%

“…is the complex transmittance function of a lenslet and (x l , y l ) are the local lenslet coordinates, while P(x l , y l ) is the lenslet pupil function [16,17].…”

Section: Light Field Point Spread Function Modelmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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What about computational super-resolution in fluorescence Fourier light field microscopy?

et al. 2020

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An experimental method to characterize the relationship between aperture image and ray directions in microscope optics

Tran

Oldenbourg

2020

Microscopy Res & Technique

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We propose a direct experimental method to calibrate the relationship between ray directions in object space and their positions in the aperture plane of a light field microscope. The calibration improves the interpretation of light field images, which contain information from both types of image planes, the field plane and the aperture plane of the ray path in the microscope. Our method is based on the diffraction of line gratings of known periodicities and provides accurate results with subpixel resolution. The method can be custom-tailored to most any optical configuration, including standard light microscopy setups, whenever correct mapping between ray parameters in the object/image plane and the aperture plane is needed.

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3-D visualization of transparent fluid flows from snapshot light field data

2021

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This paper presents the use of light field data, recorded in a snapshot from a single plenoptic camera, for 3-D visualization of transparent fluid flows. We demonstrate the transfer of light field deconvolution, a method so far used only in microscopy, to macroscopic scales with a photographic setup. This technique is suitable for optically thin media without any additional particles or tracers and allows volumetric investigation of non-stationary flows with a simple single camera setup. An experimental technique for the determination of the shift-variant point spread functions is presented, which is a key for applications using a photographic optical system. The paper shows results from different test cases with increasing complexity. Reconstruction of the 3-D positions of randomly distributed light points demonstrates the achievable high accuracy of the technique. Gas flames and droplets of a fluorescent liquid show the feasibility of the proposed method for the visualization of transparent, luminous flows. The visualizations exhibit high quality and resolution in low-contrast flows, where standard plenoptic software based on computer vision fails. Axial resolution depends on the data and is about an order of magnitude lower than the lateral resolution for simple point objects. The technique also allows the time-resolved analysis of flow structures and the generation of 3D3C-velocity fields from a sequence of exposures. Graphical Abstract

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Artifact-free deconvolution in light field microscopy

Cited by 47 publications

References 38 publications

What about computational super-resolution in fluorescence Fourier light field microscopy?

What about computational super-resolution in fluorescence Fourier light field microscopy?

An experimental method to characterize the relationship between aperture image and ray directions in microscope optics

3-D visualization of transparent fluid flows from snapshot light field data

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