Three-dimensional Particle Tracking Research Articles

Lagrangian coherent structures and entrainment near the turbulent/non-turbulent interface of a gravity current

In this paper, we employ the theory of Lagrangian coherent structures for three-dimensional vortex eduction and investigate the effect of large-scale vortical structures on the turbulent/non-turbulent interface (TNTI) and entrainment of a gravity current. The gravity current is realized experimentally and different levels of stratification are examined. For flow measurements, we use a multivolume three-dimensional particle tracking velocimetry technique. To identify vortical Lagrangian coherent structures (VLCSs), a fully automated three-dimensional extraction algorithm for multiple flow structures based on the so-called Lagrangian-averaged vorticity deviation method is implemented. The size, the orientation and the shape of the VLCSs are analysed and the results show that these characteristics depend only weakly on the strength of the stratification. Through conditional analysis, we provide evidence that VLCSs modulate the average TNTI height, consequently affecting the entrainment process. Furthermore, VLCSs influence the local entrainment velocity and organize the flow field on both the turbulent and non-turbulent sides of the gravity current boundary.

Performance analysis of the transcatheter aortic valve implantation on blood flow hemodynamics: An optical imaging-based in vitro study.

Cardiac implants may have a strong influence on the hemodynamics of the circulatory system. In this study, we aimed at investigating the impact of transcatheter aortic valve implantation (TAVI) devices on blood flow patterns that develop in the ascending aorta under physiological flow conditions in vitro. For this purpose, a noninvasive optical measurement tool, three-dimensional particle tracking velocimetry (3D-PTV), was used in a realistic compliant silicone aortic model. The performance and the influence of two TAVIs and one surgical valve on the aortic flow were investigated. Our results showed that valve design and materials may have a distinct influence on relevant hemodynamic properties, namely kinetic energy, production of turbulence, and shear stresses in the ascending aorta. All properties varied considerably between the different valve models. We found that the total aortic regurgitation composed of the closing volume, transvalvular and paravalvular leakages varied for the three valves investigated. Furthermore, peak mean kinetic energy (MKE) ranged from 61 to 116 J/m3 , whereas peak turbulent kinetic energy (TKE) ranged from 23 to 36 J/m3 . The analysis of shear showed that all the three studied devices had minimal overall risk for thrombus formation. We conclude that the characteristics and material designs of TAVI devices have strong influences on the hemodynamics in the ascending aorta.

Streamwise and spanwise slip over a superhydrophobic surface

The near-wall turbulent flow over a superhydrophobic surface (SHS) with random texture was studied using three-dimensional Lagrangian particle tracking velocimetry (3D-PTV). The channel was operated at a constant mass flow rate over the SHS and a smooth surface at a Reynolds number of 7000 based on the bulk velocity of $0.93~\text{m}~\text{s}^{-1}$ and the full channel height. The friction Reynolds number was 217, based on the friction velocity and half channel height. The 3D-PTV processing was based on the shake-the-box algorithm applied to images of fluorescent tracers recorded using four high-speed cameras. The SHS was obtained by spray coating, resulting in a root-mean-square roughness of $0.29\unicode[STIX]{x1D706}$ and an average texture width of $5.0\unicode[STIX]{x1D706}$, where $\unicode[STIX]{x1D706}=17~\unicode[STIX]{x03BC}\text{m}$ is the inner flow scale over the SHS. The 3D-PTV measurements confirmed an isotropic slip with a streamwise slip length of $5.9\unicode[STIX]{x1D706}$ and a spanwise slip length of $5.9\unicode[STIX]{x1D706}$. As a result, both the near-wall mean streamwise and spanwise velocity profiles over the SHS were higher than the smooth surface. The streamwise and spanwise slip velocities over the SHS were $0.27~\text{m}~\text{s}^{-1}$ and $0.018~\text{m}~\text{s}^{-1}$, respectively. The near-wall Reynolds stresses over the SHS were larger and shifted towards the wall when normalized by the corresponding inner scaling, despite the smaller friction Reynolds number of 180 over the SHS. The near-wall measurement of streamwise velocity showed that the shear-free pattern consists of streamwise-elongated regions with a length of $800\unicode[STIX]{x1D706}$ and a spanwise width of $300\unicode[STIX]{x1D706}$. The plastron dimensions correspond to the mean distance of the largest roughness peaks $(20~\unicode[STIX]{x03BC}\text{m})$ obtained from profilometry of the SHS. The drag reduction over the SHS was 30 %–38 % as estimated from pressure measurement and the flow field using the 3D-PTV.

Two-Dimensional and Three-Dimensional Single Particle Tracking of Upconverting Nanoparticles in Living Cells.

Lanthanide-doped upconversion nanoparticles (UCNPs) are inorganic nanomaterials in which the lanthanide cations embedded in the host matrix can convert incident near-infrared light to visible or ultraviolet light. These particles are often used for long-term and real-time imaging because they are extremely stable even when subjected to continuous irradiation for a long time. It is now possible to image their movement at the single particle level with a scale of a few nanometers and track their trajectories as a function of time with a scale of a few microseconds. Such UCNP-based single-particle tracking (SPT) technology provides information about the intracellular structures and dynamics in living cells. Thus far, most imaging techniques have been built on fluorescence microscopic techniques (epifluorescence, total internal reflection, etc.). However, two-dimensional (2D) images obtained using these techniques are limited in only being able to visualize those on the focal planes of the objective lens. On the contrary, if three-dimensional (3D) structures and dynamics are known, deeper insights into the biology of the thick cells and tissues can be obtained. In this review, we introduce the status of the fluorescence imaging techniques, discuss the mathematical description of SPT, and outline the past few studies using UCNPs as imaging probes or biologically functionalized carriers.

A quantitative study of track initialization of the four-frame best estimate algorithm for three-dimensional Lagrangian particle tracking

We introduce a method to improve three-dimensional particle tracking velocimetry (3D-PTV) algorithms. 3D-PTV is an experimental method used to measure the Lagrangian trajectories of individual particles over time. The trajectories are constructed by linking the particle positions from a sequence of images. Different 3D-PTV algorithms have been proposed in the literature, ranging from simply taking the nearest neighbor in the next frame to using multiframe schemes. This work focuses on the initialization of the four-frame best estimate (4BE) method introduced by Ouellette et al (2006 Exp. Fluids 40 301–13). Previously, tracking algorithms have been initialized by using the particle’s nearest neighbor(s) in the next frame or by using a velocity guess to predict the particle’s location in the next frame. We propose a more robust initialization, coupled with 4BE, that performs better than existing methods in the literature, in the sense of yielding a higher number of correct tracks. The performance of the proposed initialization method is compared to the 4BE method that uses nearest neighbor initialization by applying both methods on direct numerical simulation data from the Johns Hopkins turbulence databases. We show that the modified initialization greatly improves tracking in two canonical cases, homogeneous isotropic turbulence and turbulent channel flow (inhomogenous and anisotropic), greatly increasing the percentage of correct tracks found even under challenging seeding/particle displacement conditions.

Flow-induced motions of flexible plates: fluttering, twisting and orbital modes

The unsteady dynamics of wall-mounted flexible plates under inclined flows was fundamentally described using theoretical arguments and experiments under various Cauchy numbers $Ca=\unicode[STIX]{x1D70C}_{f}bL^{3}U_{0}^{2}/(EI)\in [7,81]$ (where $\unicode[STIX]{x1D70C}_{f}$ is the fluid density, $b$ and $L$ are the plate width and length, $U_{0}$ is the incoming velocity, $E$ is Young’s modulus and $I$ is the second moment of the area) and inclination angles $\unicode[STIX]{x1D6FC}$. Three-dimensional particle tracking velocimetry and a high-resolution force sensor were used to characterize the evolution of the plate dynamics and aerodynamic force. We show the existence of three distinctive, dominant modes of tip oscillations, which are modulated by the structure dynamic and flow instability. The first mode is characterized by small-amplitude, planar fluttering-like motions occurring under a critical Cauchy number, $Ca=Ca_{c}$. Past this condition, the motions are dominated by the second mode consisting of unsteady twisting superimposed onto the fluttering patterns. The onset of this mode is characterized by a sharp increase of the force fluctuation intensity. At sufficiently high $Ca$ and $\unicode[STIX]{x1D6FC}$, the plate may undergo a third mode given by large-scale tip orbits about the mean bending. Using the equation of motion and first-order approximations, we propose a formulation to estimate $Ca_{c}$ as a function of $\unicode[STIX]{x1D6FC}$; it exhibits solid agreement with experiments.

Metasurface integrated with double-helix point spread function and metalens for three-dimensional imaging

Abstract Metasurfaces are two-dimensional arrangements of antennas that control the propagation of electromagnetic waves with a subwavelength thickness and resolution. Previously, metasurfaces have been mostly used to obtain the function of a single optical element. Here, we demonstrate a plasmonic metasurface that represents the combination of a phase mask generating a double-helix point spread function (DH-PSF) and a metalens for imaging. DH-PSF has been widely studied in three-dimensional (3D) super-resolution imaging, biomedical imaging, and particle tracking, but the current DH-PSFs are inefficient, bulky, and difficult to integrate. The multielement metasurface, which we label as DH-metalens, enables a DH-PSF with transfer efficiency up to 70.3% and an ultrahigh level of optical system integration, three orders of magnitude smaller than those realized by conventional phase elements. Moreover, the demonstrated DH-metalens can work in broadband visible wavelengths and in multiple incident polarization states. Finally, we demonstrate the application of the DH-metalens in 3D imaging of point sources. These results pave ways for realizing integrated DH-PSFs, which have applications in 3D super-resolution microscopy, single particle tracking/imaging, and machine vision.

Calibration of astigmatic particle tracking velocimetry based on generalized Gaussian feature extraction

Flow and transport in porous media are driven by pore scale processes. Particle tracking in transparent porous media allows for the observation of these processes at the time scale of ms. We demonstrate an application of defocusing particle tracking using brightfield illumination and a CMOS camera sensor. The resulting images have relatively high noise levels. To address this challenge, we propose a new calibration for locating particles in the out-of-plane direction. The methodology relies on extracting features of particle images by fitting generalized Gaussian distributions to particle images. The resulting fitting parameters are then linked to the out-of-plane coordinates of particles using flexible machine learning tools. A workflow is presented which shows how to generate a training dataset of fitting parameters paired to known out-of-plane locations. Several regression models are tested on the resulting training dataset, of which a boosted regression tree ensemble produced the lowest cross-validation error. The efficacy of the proposed methodology is then examined in a laminar channel flow in a large measurement volume of 2048, 1152 and 3000 μm in length, width and depth respectively. The size of the test domain reflects the representative elementary volume of many fluid flow phenomena in porous media. Such large measurement depths require the collection of images at different focal levels. We acquired images at 21 focal levels 150 μm apart from each other. The error in predicting the out-of-plane location in a single slice of 240 μm thickness was found to be 7 μm, while in-plane locations were determined with sub-pixel resolution (below 0.8 μm). The mean relative error in the velocity measurement was obtained by comparing the experimental results to an analytic model of the flow. The estimated displacement errors in the axial direction of the flow were 0.21 pixel and 0.22 pixel at flows rates of 1.0 mL/h and 2.5 mL/h, respectively. These results demonstrate that it is possible to conduct three-dimensional particle tracking in a representative elementary volume based on a simple apparatus comprising a microscope with standard brightfield illumination and a camera with CMOS sensor.

Developing Noise-Resistant Three-Dimensional Single Particle Tracking Using Deep Neural Networks.

Three-dimensional single particle tracking (3D SPT) is a powerful tool in various chemical and biological studies. In 3D SPT, z sensitive point spread functions (PSFs) are frequently used to generate different patterns, from which the axial position of the probe can be recovered in addition to its xy coordinates. Conventional linear classifier-based methods, for example, the correlation coefficient method, perform poorly when the signal-to-noise ratio (S/N) drops. In this work, we test deep neural networks (DNNs) in recognizing and differentiating very similar image patterns incurred in 3D SPT. The training of the deep neural networks is optimized, and a procedure is established for 3D localization. We show that for high S/N images, both DNNs and conventional correlation coefficient-based method perform well. However, when the S/N drops close to 1, conventional methods completely fail while DNNs show strong resistance to both artificial and experimental noises. This noise resistance allows us to achieve a camera integration time of 50 μs for 200 nm fluorescent particles without losing accuracy significantly. This study sheds new light on developing robust image data analysis methods and on improving the time resolution of 3D SPT.

Extreme Small-Scale Clustering of Droplets in Turbulence Driven by Hydrodynamic Interactions.

We perform three-dimensional particle tracking measurements on droplets in a turbulent airflow. The droplets display the well-known preferential concentration of inertial particles, with an additional extreme clustering at the smallest scales. We explain this additional clustering phenomenon theoretically based on a Stokes-flow description of two spheres including their mutual hydrodynamic interaction and a perturbative small-inertia expansion.

Particle tracking by repetitive phase-shift interferometric super resolution microscopy.

Accurate and rapid particle tracking is essential for addressing many research problems in single molecule and cellular biophysics and colloidal soft condensed matter physics. We developed a novel three-dimensional interferometric fluorescent particle tracking approach that does not require any sample scanning. By periodically shifting the interferometer phase, the information stored in the interference pattern of the emitted light allows localizing particles positions with nanometer resolution. This tracking protocol was demonstrated by measuring a known trajectory of a fluorescent bead with sub-5nm axial localization error at 5Hz. The interferometric microscopy was used to track the RecA protein in Bacillus subtilis bacteria to demonstrate its compatibility with biological systems.

Single-camera three-dimensional tracking of natural particulate and zooplankton

We develop and characterize an image processing algorithm to adapt single-camera defocusing digital particle image velocimetry (DDPIV) for three-dimensional (3D) particle tracking velocimetry (PTV) of natural particulates, such as those present in the ocean. The conventional DDPIV technique is extended to facilitate tracking of non-uniform, non-spherical particles within a volume depth an order of magnitude larger than current single-camera applications (i.e. 10 cm × 10 cm × 24 cm depth) by a dynamic template matching method. This 2D cross-correlation method does not rely on precise determination of the centroid of the tracked objects. To accommodate the broad range of particle number densities found in natural marine environments, the performance of the measurement technique at higher particle densities has been improved by utilizing the time-history of tracked objects to inform 3D reconstruction. The developed processing algorithms were analyzed using synthetically generated images of flow induced by Hill’s spherical vortex, and the capabilities of the measurement technique were demonstrated empirically through volumetric reconstructions of the 3D trajectories of particles and highly non-spherical, 5 mm zooplankton.

Live-cell imaging reveals the dynamics and function of single-telomere TERRA molecules in cancer cells

ABSTRACTTelomeres cap the ends of eukaryotic chromosomes, protecting them from degradation and erroneous recombination events which may lead to genome instability. Telomeres are transcribed giving rise to telomeric repeat-containing RNAs, called TERRA. The TERRA long noncoding RNAs have been proposed to play important roles in telomere biology, including heterochromatin formation and telomere length homeostasis. While TERRA RNAs are predominantly nuclear and localize at telomeres, little is known about the dynamics and function of TERRA molecules expressed from individual telomeres. Herein, we developed an assay to image endogenous TERRA molecules expressed from a single telomere in living human cancer cells. We show that single-telomere TERRA can be detected as TERRA RNA single particles which freely diffuse within the nucleus. Furthermore, TERRA molecules aggregate forming TERRA clusters. Three-dimensional size distribution and single particle tracking analyses revealed distinct sizes and dynamics for TERRA RNA single particles and clusters. Simultaneous time lapse confocal imaging of TERRA particles and telomeres showed that TERRA clusters transiently co-localize with telomeres. Finally, we used chemically modified antisense oligonucleotides to deplete TERRA molecules expressed from a single telomere. Single-telomere TERRA depletion resulted in increased DNA damage at telomeres and elsewhere in the genome. These results suggest that single-telomere TERRA transcripts participate in the maintenance of genomic integrity in human cancer cells.

The drift chamber array at the external target facility in HIRFL-CSR

A drift chamber array at the External Target Facility in HIRFL-CSR has been constructed for three-dimensional particle tracking in high-energy radioactive ion beam experiments. The design, readout, track reconstruction program and calibration procedures for the detector are described. The drift chamber array was tested in a 311 AMeV 40Ar beam experiment. The detector performance based on the measurements of the beam test is presented. A spatial resolution of 230μm is achieved.

Three-dimensional particle tracking in concave structures made by ultraviolet nanoimprint via total internal reflection fluorescence microscopy and refractive-index-matching method

Total internal reflection fluorescence microscopy (TIRFM) is a promising method for measuring fluid flow close to a wall with nanoscale resolution in a process that is termed “multilayer nanoparticle image velocimetry” (MnPIV). TIRFM uses evanescent light that is generated on a substrate (typically a glass slide) by total internal reflection of light. Many researchers have previously studied x–y–z (3D) flows of water close to flat glass slides using MnPIV. On the other hand, a fluid flow close to a structured surface is also important. To measure flows of water near micro-patterns, we previously developed an MnPIV technique that uses a refractive-index-matching method. In previous study, the micropattern is made of a thermoplastic material with a refractive index that closely matches that of water. In this study, ultraviolet nanoimprint lithography was used for fabricating the appropriate micro-patterns because this technique can fabricate a pattern with a high resolution. As a result, we succeeded in performing MnPIV in water with a circular hole array pattern made by ultraviolet nanoimprint using a refractive-index-matching method. We believe that this technique will be helpful in elucidating fluid flows around microstructures.

Tracking microparticle motions in three-dimensional flow around a microcubic array fabricated on the wall surface

This paper describes the application of a microscopic defocusing image system to track 3D particle motions in microflow around a microcubic array near a microchannel wall surface. The measurement principle and calibration method were evaluated to provide accurate 3D microparticle location. Particle trajectories were measured in two microchannels. Measured velocity profiles of Hele–Shaw flows for two Reynolds numbers agreed well with theoretical profiles. Three-dimensional particle tracking in fluid flow around a microcubic array exhibited quasi-periodic and non-periodic trajectory modes. The experimental results indicated that 3D particle motions are spatially and time dependent even when the flow rate is constant, and microparticle trajectories may deviate from steady flow streamlines.

Three-dimensional microscale simulation of colloidal particle transport and deposition in model porous media with converging/diverging geometries

The microscale simulation of colloidal particle transport and deposition in porous media was achieved with a novel colloidal particle tracking model, called 3D-PTPO (Three-Dimensional Particle Tracking model by Python® and OpenFOAM®), using a Lagrangian method. Simulations were performed by considering the elementary pore structure as a capillary tube with converging/diverging geometries (tapered pipe and venturi tube). The particles are considered as a mass point during transport in the flow and their volume is reconstructed when they are deposited. The main feature of this novel model is to renew the flow field by reconstructing the pore structure by taking the volume of the deposited particles into account. The influence of the particle Péclet number (Pe) and the pore shape on the particle deposition therein is investigated. The results are analyzed in terms of deposition probability and dimensionless surface coverage as a function of the number of injected particles for a vast range of Péclet numbers thus allowing distinguishing the behavior in diffusion dominant and advection dominant regimes. Finally, the maximum dimensionless surface coverage Γfinal/ΓRSA is studied as a function of Pe. The declining trend observed for high Pe is in good agreement with experimental and simulation results found in the literature.

Three-dimensional particle tracking velocimetry algorithm based on tetrahedron vote

A particle tracking velocimetry algorithm based on tetrahedron vote, which is named TV-PTV, is proposed to overcome the limited selection problem of effective algorithms for 3D flow visualisation. In this new cluster-matching algorithm, tetrahedrons produced by the Delaunay tessellation are used as the basic units for inter-frame matching, which results in a simple algorithmic structure of only two independent preset parameters. Test results obtained using the synthetic test image data from the Visualisation Society of Japan show that TV-PTV presents accuracy comparable to that of the classical algorithm based on new relaxation method (NRX). Compared with NRX, TV-PTV possesses a smaller number of loops in programming and thus a shorter computing time, especially for large particle displacements and high particle concentration. TV-PTV is confirmed practically effective using an actual 3D wake flow.

A Protocol for Real-time 3D Single Particle Tracking

Real-time three-dimensional single particle tracking (RT-3D-SPT) has the potential to shed light on fast, 3D processes in cellular systems. Although various RT-3D-SPT methods have been put forward in recent years, tracking high speed 3D diffusing particles at low photon count rates remains a challenge. Moreover, RT-3D-SPT setups are generally complex and difficult to implement, limiting their widespread application to biological problems. This protocol presents a RT-3D-SPT system named 3D Dynamic Photon Localization Tracking (3D-DyPLoT), which can track particles with high diffusive speed (up to 20 µm2/s) at low photon count rates (down to 10 kHz). 3D-DyPLoT employs a 2D electro-optic deflector (2D-EOD) and a tunable acoustic gradient (TAG) lens to drive a single focused laser spot dynamically in 3D. Combined with an optimized position estimation algorithm, 3D-DyPLoT can lock onto single particles with high tracking speed and high localization precision. Owing to the single excitation and single detection path layout, 3D-DyPLoT is robust and easy to set up. This protocol discusses how to build 3D-DyPLoT step by step. First, the optical layout is described. Next, the system is calibrated and optimized by raster scanning a 190 nm fluorescent bead with the piezoelectric nanopositioner. Finally, to demonstrate real-time 3D tracking ability, 110 nm fluorescent beads are tracked in water.

Experimental study of the surface oscillations induced by a shallow flow past a lateral cavity

The present work presents an experimental study in which resonant surface oscillations inside a lateral cavity are reconstructed, often denoted as se- iching, which are excited by a shallow main stream flowing past the horizontal basin. Firstly, the flow configurations that trigger transverse and/or longitu- dinal seiching are studied using pressure measurements in the corners of the cavity, which shows that a transitional Froude number exists, approximately 0.63, at which the dominant seiching mode changes from transverse to longi- tudinal seiching. For both types of resonant conditions, the surface shape is analyzed in detail using a three-dimensional particle tracking velocimetry (3D- PTV) setup. Based upon floating seeding particles, the 3D surface is recon- structed with a superior spatial resolution compared to traditional measurement techniques, which confirms the multimodal aspect of the surface oscillations.