Calculation of high numerical aperture lightfield microscope point spread functions

Quicke, Peter; Howe, Carmel L.; Song, Pingfan; Jadan, Herman Verinaz; Dragotti, Pier Luigi; Knöpfel, Thomas; Foust, Amanda J.; Schultz, Simon R.; Neil, Mark A. A.

doi:10.1364/cosi.2019.cw4a.2

Cited by 6 publications

(7 citation statements)

References 6 publications

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“…To properly account for all the diffraction effects, it will be necessary to expand the simulation presented here with approaches that include wave optical effects. For fluorescence light field microscopy, this was done by Broxton et al and by Quicke et al, with the latter expanding the first treatment to allow for dipole emitters and high NA objective lenses [13,17].…”

Section: Discussionmentioning

confidence: 99%

Point spread function of the polarized light field microscope

Tran

Oldenbourg

2022

J. Opt. Soc. Am. A

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We examined the point spread function of the polarized light field microscope and established a computational framework to solve the forward problem in polarized light field imaging, for the purpose of furthering its use as a quantitative tool for measuring three-dimensional maps of the birefringence of transparent objects. We recorded experimental polarized light field images of small calcite crystals and of larger birefringent objects and compared our experimental results to numerical simulations based on polarized light ray tracing. We find good agreement between all our experiments and simulations, which leads us to propose polarized light ray tracing as one solution to the forward problem for the complex, nonlinear imaging mode of the polarized light field microscope. Solutions to the ill-posed inverse problem might be found in analytical methods and/or deep learning approaches that are based on training data generated by the forward solution presented here.

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Section: Discussionmentioning

confidence: 99%

Point spread function of the polarized light field microscope

Tran

Oldenbourg

2022

J. Opt. Soc. Am. A

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“…We calculated LFM PSFs differently to previously described, 53 using the method described by Quicke 52 and Quicke et al. 70 Briefly, to calculate the field at the MLA, we considered how a high-NA objective lens collects the field from an oscillating electric dipole at position

near the microscope focus,

, at the origin, calculating the Fourier transform of the field in the objective back focal plane. We assumed that we could model the behavior of a point source consisting of randomly oriented fluorescent molecules as the incoherent sum of dipoles along three orthogonal directions.…”

Section: Methodsmentioning

confidence: 99%

“…We compare and evaluate deconvolution and synthetic refocusing for different GEVI imaging applications, while using a coarse deconvolution approach with no lateral oversampling to reduce computational cost. We also apply a recently developed LFM PSF calculation 70 for high-NA objectives. We show that LFM enables 3-D localization of dendritic and somatic GEVI fluorescence transients and compare the extent to which refocused and deconvolved light fields enable lateral and axial transient localization.…”

Section: Introductionmentioning

confidence: 99%

Subcellular resolution three-dimensional light-field imaging with genetically encoded voltage indicators

et al. 2020

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Significance: Light-field microscopy (LFM) enables high signal-to-noise ratio (SNR) and light efficient volume imaging at fast frame rates. Voltage imaging with genetically encoded voltage indicators (GEVIs) stands to particularly benefit from LFM's volumetric imaging capability due to high required sampling rates and limited probe brightness and functional sensitivity. Aim: We demonstrate subcellular resolution GEVI light-field imaging in acute mouse brain slices resolving dendritic voltage signals in three spatial dimensions. Approach: We imaged action potential-induced fluorescence transients in mouse brain slices sparsely expressing the GEVI VSFP-Butterfly 1.2 in wide-field microscopy (WFM) and LFM modes. We compared functional signal SNR and localization between different LFM reconstruction approaches and between LFM and WFM. Results: LFM enabled three-dimensional (3-D) localization of action potential-induced fluorescence transients in neuronal somata and dendrites. Nonregularized deconvolution decreased SNR with increased iteration number compared to synthetic refocusing but increased axial and lateral signal localization. SNR was unaffected for LFM compared to WFM. Conclusions: LFM enables 3-D localization of fluorescence transients, therefore eliminating the need for structures to lie in a single focal plane. These results demonstrate LFM's potential for studying dendritic integration and action potential propagation in three spatial dimensions.

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“…Stacks from the same light field images were also calculated using Richardson-Lucy deconvolution. The 3D light field PSF was calculated using the method described in [8], by considering how a light field microscope collects fluorescence from a dipole oscillating with a wavelength of 550 nm. The total PSF was calculated as an incoherent sum of dipoles oriented along x, y, and z. PSF values were calculated on a 5 × 5 grid relative to the microlens.…”

Section: Light Field Volume Reconstructionmentioning

confidence: 99%

“…However, similar to widefield imaging, this technique lacks optical sectioning such that out-of-focus sources reduce the contrast of in-focus sources. In contrast, 3D deconvolution reconstructs a volume by deconvolving its light-field measurements with a 3D light-field Point Spread Function (PSF) based on a wave optics model 9 of the LFM. This can be achieved by using iterative deconvolution methods, such as the Richardson-Lucy 10,11 or Image Space Reconstruction Algorithms.…”

Section: Introductionmentioning

confidence: 99%

Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light-fields

Howe

Quicke

Song

et al. 2020

Preprint

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Light field microscopy (LFM) enables fast, light efficient, volumetric imaging of neuronal activity with functional fluorescence indicators. Here we apply LFM to single-cell and bulk-labeled imaging of the red calcium dye, CaSiR-1 in acute mouse brain slices. We compare two common light field volume reconstruction algorithms: synthetic refocusing and Richardson-Lucy 3D deconvolution. We compare temporal signal-to-noise ratio (SNR) and spatial signal confinement between the two LFM algorithms and conventional widefield image series. Both algorithms can resolve calcium signals from neuronal processes in three dimensions. Increasing deconvolution iteration number improves spatial signal confinement but reduces SNR compared to synthetic refocusing.

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Calculation of high numerical aperture lightfield microscope point spread functions

Cited by 6 publications

References 6 publications

Point spread function of the polarized light field microscope

Point spread function of the polarized light field microscope

Subcellular resolution three-dimensional light-field imaging with genetically encoded voltage indicators

Comparing synthetic refocusing to deconvolution for the extraction of neuronal calcium transients from light-fields

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