Fast and accurate three-dimensional point spread function computation for fluorescence microscopy

Li, Jizhou; Xue, Feng; Blu, Thierry

doi:10.1364/josaa.34.001029

Cited by 46 publications

(22 citation statements)

References 30 publications

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“…Its limitations, however, are its computation speed. Recently, a fast and yet accurate implementation was proposed [53]. Table 1 gives an overview of the required optical input parameters.…”

Section: Methodsmentioning

confidence: 99%

“…Unlike the tesa stacks, multiple particle positions could only be realized in separate calibration samples. The height of all individual layers was measured with a [53]. Parameters: z p = 54 µm, n s = 1.472, N A = 0.95, t * g = 150 µm, t g = 144 µm.…”

Section: Methodsmentioning

confidence: 99%

“…Cross-section image stitched with ImageJ. (b) Simulation with fast Gibson-Lanni model implementation[53]. Dashed line indicates the best focus at z obj,exp = 34 µm and z obj,sim = 33.5 µm, respectively.…”

mentioning

confidence: 99%

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Calibration Routine for Quantitative Three-Dimensional Flow Field Measurements in Drying Polymer Solutions Subject to Marangoni Convection

Tönsmann

Kröhl

Cavadini

et al. 2019

Colloids and Interfaces

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Surface-tension induced flows may have a significant impact on the surface topography of thin films or small printed structures derived from polymer solution processing. Despite a century of research on Marangoni convection, the community lacks quantitative experimental flow field data, especially from within drying solutions. We utilize multifocal micro particle tracking velocimetry (µPTV) to obtain these data and show a calibration routine based on point spread function (PSF) simulations as well as experimental data. The results account for a varying sample refractive index, beneficial cover-glass correction collar settings as well as a multifocal lens system. Finally, the calibration procedure is utilized exemplarily to reconstruct a three-dimensional, transient flow field within a poly(vinyl acetate)-methanol solution dried with inhomogeneous boundary conditions.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Calibration Routine for Quantitative Three-Dimensional Flow Field Measurements in Drying Polymer Solutions Subject to Marangoni Convection

Tönsmann

Kröhl

Cavadini

et al. 2019

Colloids and Interfaces

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“…TensorFlow. Cytokit also includes support for automatically generating Point Spread Functions based on an experiment configuration through a fast Gibson-Lanni kernel approximation method [20].…”

Section: Operationsmentioning

confidence: 99%

Cytokit: A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging

Czech

Aksoy

et al. 2018

Preprint

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BackgroundMultiplexed in-situ fluorescent imaging offers several advantages over single-cell assays that do not preserve the spatial characteristics of biological samples. This spatial information, in addition to morphological properties and extensive intracellular or surface marker profiling, comprise promising avenues for rapid advancements in the understanding of disease progression and diagnosis. As protocols for conducting such imaging experiments continue to improve, it is the intent of this study to provide and validate software for processing the large quantity of associated data in kind. ResultsCytokit offers (i) an end-to-end, GPU-accelerated image processing pipeline; (ii) efficient input/output (I/O) strategies for operations specific to high dimensional microscopy; and (iii) an interactive user interface for cross filtering of spatial, graphical, expression, and morphological cell properties within the 100+ GB image datasets common to multiplexed immunofluorescence.Image processing operations supported in Cytokit are generally sourced from existing deep learning models or are at least in part adapted from open source packages to run in a single or multi-GPU environment. The efficacy of these operations is demonstrated through several imaging experiments that pair Cytokit results with those from an independent but comparable assay. A further validation also demonstrates that previously published results can be reproduced from a publicly available multiplexed image dataset.

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“…3(b). The point spread function used for the deconvolution was estimated numerically based on the model of Gibson and Lanni [13,23].…”

mentioning

confidence: 99%

Single-step fabrication of surface waveguides in fused silica with few-cycle laser pulses

Furch¹,

Engel²,

Witting³

et al. 2019

Opt. Lett.

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Direct laser writing of surface waveguides with ultrashort pulses is a crucial achievement towards all-laser manufacturing of photonic integrated circuits sensitive to their environment. In this Letter, few-cycle laser pulses (with a sub-10 fs duration) are used to produce subsurface waveguides in a non-doped, non-coated fused silica substrate. The fabrication technique relies on laser-induced microdensification below the threshold for nanopore formation. The optical losses of the fabricated waveguides are governed by the optical properties of the superstrate. We have measured losses ranging from less than 0.1 dB/mm (air superstrate) up to 2.8 dB/mm when immersion oil is applied on top of the waveguide.

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Fast and accurate three-dimensional point spread function computation for fluorescence microscopy

Cited by 46 publications

References 30 publications

Calibration Routine for Quantitative Three-Dimensional Flow Field Measurements in Drying Polymer Solutions Subject to Marangoni Convection

Calibration Routine for Quantitative Three-Dimensional Flow Field Measurements in Drying Polymer Solutions Subject to Marangoni Convection

Cytokit: A single-cell analysis toolkit for high dimensional fluorescent microscopy imaging

Single-step fabrication of surface waveguides in fused silica with few-cycle laser pulses

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