PIVlab – Towards User-friendly, Affordable and Accurate Digital Particle Image Velocimetry in MATLAB
TL;DR: The accuracy of several algorithms was determined and the best performing methods were implemented in a user-friendly open-source tool for performing DPIV flow analysis in Matlab.
Abstract: Digital particle image velocimetry (DPIV) is a non-intrusive analysis technique that is very popular for mapping flows quantitatively. To get accurate results, in particular in complex flow fields, a number of challenges have to be faced and solved: The quality of the flow measurements is affected by computational details such as image pre-conditioning, sub-pixel peak estimators, data validation procedures, interpolation algorithms and smoothing methods. The accuracy of several algorithms was determined and the best performing methods were implemented in a user-friendly open-source tool for performing DPIV flow analysis in Matlab.
Citations
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01 Jan 1992
TL;DR: In this article, cross-correlation methods of interrogation of successive single-exposure frames can be used to measure the separation of pairs of particle images between successive frames, which can be optimized in terms of spatial resolution, detection rate, accuracy and reliability.
Abstract: To improve the performance of particle image velocimetry in measuring instantaneous velocity fields, direct cross-correlation of image fields can be used in place of auto-correlation methods of interrogation of double- or multiple-exposure recordings. With improved speed of photographic recording and increased resolution of video array detectors, cross-correlation methods of interrogation of successive single-exposure frames can be used to measure the separation of pairs of particle images between successive frames. By knowing the extent of image shifting used in a multiple-exposure and by a priori knowledge of the mean flow-field, the cross-correlation of different sized interrogation spots with known separation can be optimized in terms of spatial resolution, detection rate, accuracy and reliability.
1,101 citations
TL;DR: This study is the first approach to establish a system for in vitro microfluidic ADME profiling and repeated dose systemic toxicity testing of drug candidates over 28 days in co-culture, and assures near to physiological fluid-to-tissue ratios.
Abstract: Systemic absorption and metabolism of drugs in the small intestine, metabolism by the liver as well as excretion by the kidney are key determinants of efficacy and safety for therapeutic candidates. However, these systemic responses of applied substances lack in most in vitro assays. In this study, a microphysiological system maintaining the functionality of four organs over 28 days in co-culture has been established at a minute but standardized microsystem scale. Preformed human intestine and skin models have been integrated into the four-organ-chip on standard cell culture inserts at a size 100 000-fold smaller than their human counterpart organs. A 3D-based spheroid, equivalent to ten liver lobules, mimics liver function. Finally, a barrier segregating the media flow through the organs from fluids excreted by the kidney has been generated by a polymeric membrane covered by a monolayer of human proximal tubule epithelial cells. A peristaltic on-chip micropump ensures pulsatile media flow interconnecting the four tissue culture compartments through microfluidic channels. A second microfluidic circuit ensures drainage of the fluid excreted through the kidney epithelial cell layer. This four-organ-chip system assures near to physiological fluid-to-tissue ratios. In-depth metabolic and gene analysis revealed the establishment of reproducible homeostasis among the co-cultures within two to four days, sustainable over at least 28 days independent of the individual human cell line or tissue donor background used for each organ equivalent. Lastly, 3D imaging two-photon microscopy visualised details of spatiotemporal segregation of the two microfluidic flows by proximal tubule epithelia. To our knowledge, this study is the first approach to establish a system for in vitro microfluidic ADME profiling and repeated dose systemic toxicity testing of drug candidates over 28 days.
612 citations
TL;DR: A mechanism for apoptotic cell extrusion is proposed: spontaneously formed topological defects in epithelia govern cell fate, and the ability to control extrusion hotspots by geometrically inducing defects through microcontact printing of patterned monolayers is demonstrated.
Abstract: Epithelial tissues (epithelia) remove excess cells through extrusion, preventing the accumulation of unnecessary or pathological cells. The extrusion process can be triggered by apoptotic signalling, oncogenic transformation and overcrowding of cells. Despite the important linkage of cell extrusion to developmental, homeostatic and pathological processes such as cancer metastasis, its underlying mechanism and connections to the intrinsic mechanics of the epithelium are largely unexplored. We approach this problem by modelling the epithelium as an active nematic liquid crystal (that has a long range directional order), and comparing numerical simulations to strain rate and stress measurements within monolayers of MDCK (Madin Darby canine kidney) cells. Here we show that apoptotic cell extrusion is provoked by singularities in cell alignments in the form of comet-shaped topological defects. We find a universal correlation between extrusion sites and positions of nematic defects in the cell orientation field in different epithelium types. The results confirm the active nematic nature of epithelia, and demonstrate that defect-induced isotropic stresses are the primary precursors of mechanotransductive responses in cells, including YAP (Yes-associated protein) transcription factor activity, caspase-3-mediated cell death, and extrusions. Importantly, the defect-driven extrusion mechanism depends on intercellular junctions, because the weakening of cell-cell interactions in an α-catenin knockdown monolayer reduces the defect size and increases both the number of defects and extrusion rates, as is also predicted by our model. We further demonstrate the ability to control extrusion hotspots by geometrically inducing defects through microcontact printing of patterned monolayers. On the basis of these results, we propose a mechanism for apoptotic cell extrusion: spontaneously formed topological defects in epithelia govern cell fate. This will be important in predicting extrusion hotspots and dynamics in vivo, with potential applications to tissue regeneration and the suppression of metastasis. Moreover, we anticipate that the analogy between the epithelium and active nematic liquid crystals will trigger further investigations of the link between cellular processes and the material properties of epithelia.
556 citations
TL;DR: In this article, a tissue-engineered ray was constructed from rat cardiomyocytes on an elastomeric body enclosing a microfabricated gold skeleton to mimic the fin deflection patterns of batoid fish.
Abstract: Inspired by the relatively simple morphological blueprint provided by batoid fish such as stingrays and skates, we created a biohybrid system that enables an artificial animal—a tissue-engineered ray—to swim and phototactically follow a light cue. By patterning dissociated rat cardiomyocytes on an elastomeric body enclosing a microfabricated gold skeleton, we replicated fish morphology at 1 10 scale and captured basic fin deflection patterns of batoid fish. Optogenetics allows for phototactic guidance, steering, and turning maneuvers. Optical stimulation induced sequential muscle activation via serpentine-patterned muscle circuits, leading to coordinated undulatory swimming. The speed and direction of the ray was controlled by modulating light frequency and by independently eliciting right and left fins, allowing the biohybrid machine to maneuver through an obstacle course.
471 citations
Journal Article•
TL;DR: Inspired by the relatively simple morphological blueprint provided by batoid fish such as stingrays and skates, a biohybrid system that enables an artificial animal—a tissue-engineered ray—to swim and phototactically follow a light cue is created.
405 citations
References
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24 Jan 2005
TL;DR: It is shown that such an approach can yield an implementation of the discrete Fourier transform that is competitive with hand-optimized libraries, and the software structure that makes the current FFTW3 version flexible and adaptive is described.
Abstract: FFTW is an implementation of the discrete Fourier transform (DFT) that adapts to the hardware in order to maximize performance. This paper shows that such an approach can yield an implementation that is competitive with hand-optimized libraries, and describes the software structure that makes our current FFTW3 version flexible and adaptive. We further discuss a new algorithm for real-data DFTs of prime size, a new way of implementing DFTs by means of machine-specific single-instruction, multiple-data (SIMD) instructions, and how a special-purpose compiler can derive optimized implementations of the discrete cosine and sine transforms automatically from a DFT algorithm.
5,172 citations
"PIVlab – Towards User-friendly, Aff..." refers methods in this paper
...For the FFT calculations, FFTW is used [17] which accepts inputs of arbitrary size, but is slow for sizes that are prime or which have large prime factors (note the peaks in the graph)....
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Book•
11 Jun 2002TL;DR: In this paper, the authors present a practical guide for the planning, performance and understanding of experiments employing the PIV technique, which is primarily intended for engineers, scientists and students, who already have some basic knowledge of fluid mechanics and nonintrusive optical measurement techniques.
Abstract: This practical guide intends to provide comprehensive information on the PIV technique that in the past decade has gained significant popularity
throughout engineering and scientific fields involving fluid mechanics. Relevant theoretical background information directly support the practical
aspects associated with the planning, performance and understanding of experiments employing the PIV technique. The second edition includes
extensive revisions taking into account significant progress on the technique as well as the continuously broadening range of possible
applications which are illustrated by a multitude of examples. Among the new topics covered are high-speed imaging, three-component methods,
advanced evaluation and post-processing techniques as well as microscopic PIV, the latter made possible by extending the group of authors by
an internationally recognized expert. This book is primarily intended for engineers, scientists and students, who already have some basic
knowledge of fluid mechanics and non-intrusive optical measurement techniques. It shall guide researchers and engineers to design and perform
their experiment successfully without requiring them to first become specialists in the field. Nonetheless many of the basic properties of PIV are
provided as they must be well understood before a correct interpretation of the results is possible.
4,811 citations
TL;DR: A review of these methods can be found in articles by Lauterborn & Vogel (1984), Adrian (1986a), Hesselink (1988), and Dudderar et al..
Abstract: An important achievement of modern experimental fluid mechanics is the invention and development of techniques for the measurement of whole, instantaneous fields of scalars and vectors. These techniques include tomographic interferometry (Hesselink 1988) and planar laser-induced fluorescence for scalars (Hassa et al 1987), and nuclear-magnetic-resonance imaging (Lee et al 1987), planar laser-induced fluorescence, laser-speckle velocimetry, particle-tracking velocimetry, molecular-tracking velocimetry (Miles et al 1989), and particle-image velocimetry for velocity fields. Reviews of these methods can be found in articles by Lauterborn & Vogel (1984), Adrian (1986a), Hesselink (1988), and Dudderar et al (1988), in books written by Merzkirch (1987) and edited by Chiang & Reid (1988) and Gad-el-Hak (1989).
3,413 citations
01 Sep 1987-Graphical Models \/graphical Models and Image Processing \/computer Vision, Graphics, and Image Processing
TL;DR: It is concluded that clipped ahe should become a method of choice in medical imaging and probably also in other areas of digital imaging, and that clip ahe can be made adequately fast to be routinely applied in the normal display sequence.
Abstract: Adaptive histogram equalization (ahe) is a contrast enhancement method designed to be broadly applicable and having demonstrated effectiveness. However, slow speed and the overenhancement of noise it produces in relatively homogeneous regions are two problems. We report algorithms designed to overcome these and other concerns. These algorithms include interpolated ahe, to speed up the method on general purpose computers; a version of interpolated ahe designed to run in a few seconds on feedback processors; a version of full ahe designed to run in under one second on custom VLSI hardware; weighted ahe, designed to improve the quality of the result by emphasizing pixels' contribution to the histogram in relation to their nearness to the result pixel; and clipped ahe, designed to overcome the problem of overenhancement of noise contrast. We conclude that clipped ahe should become a method of choice in medical imaging and probably also in other areas of digital imaging, and that clipped ahe can be made adequately fast to be routinely applied in the normal display sequence.
3,041 citations
TL;DR: In this article, the directional ambiguity associated with PIV and LSV is resolved by implementing local spatial cross-correlations between two sequential single-exposed particle images, and the recovered velocity data are used to compute the spatial and temporal vorticity distribution and the circulation of the vortex ring.
Abstract: Digital particle image velocimetry (DPIV) is the digital counterpart of conventional laser speckle velocitmetry (LSV) and particle image velocimetry (PIV) techniques. In this novel, two-dimensional technique, digitally recorded video images are analyzed computationally, removing both the photographic and opto-mechanical processing steps inherent to PIV and LSV. The directional ambiguity generally associated with PIV and LSV is resolved by implementing local spatial cross-correlations between two sequential single-exposed particle images. The images are recorded at video rate (30 Hz or slower) which currently limits the application of the technique to low speed flows until digital, high resolution video systems with higher framing rates become more economically feasible. Sequential imaging makes it possible to study unsteady phenomena like the temporal evolution of a vortex ring described in this paper. The spatial velocity measurements are compared with data obtained by direct measurement of the separation of individual particle pairs. Recovered velocity data are used to compute the spatial and temporal vorticity distribution and the circulation of the vortex ring.
1,976 citations