scholarly journals Inferring cellular forces from image stacks

2017 ◽  
Vol 372 (1720) ◽  
pp. 20160261 ◽  
Author(s):  
Jim H. Veldhuis ◽  
Ahmad Ehsandar ◽  
Jean-Léon Maître ◽  
Takashi Hiiragi ◽  
Simon Cox ◽  
...  
Keyword(s):  
Cancer Metastasis ◽  
Three Dimensional ◽  
Synthetic Data ◽  
Cellular Systems ◽  
Force Balance ◽  
Three Dimensions ◽  
Surface Evolver ◽  
Force Microscopy ◽  
Wide Range ◽  
Cellular Forces

Although the importance of cellular forces to a wide range of embryogenesis and disease processes is widely recognized, measuring these forces is challenging, especially in three dimensions. Here, we introduce CellFIT-3D, a force inference technique that allows tension maps for three-dimensional cellular systems to be estimated from image stacks. Like its predecessors, video force microscopy and CellFIT, this cell mechanics technique assumes boundary-specific interfacial tensions to be the primary drivers, and it constructs force-balance equations based on triple junction (TJ) dihedral angles. The technique involves image processing, segmenting of cells, grouping of cell outlines, calculation of dihedral planes, averaging along three-dimensional TJs, and matrix equation assembly and solution. The equations tend to be strongly overdetermined, allowing indistinct TJs to be ignored and solution error estimates to be determined. Application to clean and noisy synthetic data generated using Surface Evolver gave tension errors of 1.6–7%, and analyses of eight-cell murine embryos gave estimated errors smaller than the 10% uncertainty of companion aspiration experiments. Other possible areas of application include morphogenesis, cancer metastasis and tissue engineering. This article is part of the themed issue ‘Systems morphodynamics: understanding the development of tissue hardware’.

Turbulent three-dimensional dielectric electrohydrodynamic convection between two plates

2012 ◽  
Vol 696 ◽  
pp. 228-262 ◽  
Author(s):  
A. Kourmatzis ◽  
J. S. Shrimpton
Keyword(s):  
Spatial Data ◽  
Three Dimensional ◽  
Reynolds Numbers ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Energy Budgets ◽  
Turbulent Regime ◽  
Scalar Flux ◽  
Wide Range ◽  
Scalar Variance

AbstractThe fundamental mechanisms responsible for the creation of electrohydrodynamically driven roll structures in free electroconvection between two plates are analysed with reference to traditional Rayleigh–Bénard convection (RBC). Previously available knowledge limited to two dimensions is extended to three-dimensions, and a wide range of electric Reynolds numbers is analysed, extending into a fully inherently three-dimensional turbulent regime. Results reveal that structures appearing in three-dimensional electrohydrodynamics (EHD) are similar to those observed for RBC, and while two-dimensional EHD results bear some similarities with the three-dimensional results there are distinct differences. Analysis of two-point correlations and integral length scales show that full three-dimensional electroconvection is more chaotic than in two dimensions and this is also noted by qualitatively observing the roll structures that arise for both low (${\mathit{Re}}_{E} = 1$) and high electric Reynolds numbers (up to ${\mathit{Re}}_{E} = 120$). Furthermore, calculations of mean profiles and second-order moments along with energy budgets and spectra have examined the validity of neglecting the fluctuating electric field ${ E}_{i}^{\ensuremath{\prime} } $ in the Reynolds-averaged EHD equations and provide insight into the generation and transport mechanisms of turbulent EHD. Spectral and spatial data clearly indicate how fluctuating energy is transferred from electrical to hydrodynamic forms, on moving through the domain away from the charging electrode. It is shown that ${ E}_{i}^{\ensuremath{\prime} } $ is not negligible close to the walls and terms acting as sources and sinks in the turbulent kinetic energy, turbulent scalar flux and turbulent scalar variance equations are examined. Profiles of hydrodynamic terms in the budgets resemble those in the literature for RBC; however there are terms specific to EHD that are significant, indicating that the transfer of energy in EHD is also attributed to further electrodynamic terms and a strong coupling exists between the charge flux and variance, due to the ionic drift term.

scholarly journals The magnetorotational instability prefers three dimensions

2020 ◽  
Vol 476 (2233) ◽  
pp. 20190622
Author(s):  
Jeffrey S. Oishi ◽  
Geoffrey M. Vasil ◽  
Morgan Baxter ◽  
Andrew Swan ◽  
Keaton J. Burns ◽  
...  
Keyword(s):  
Shear Rate ◽  
Angular Velocity ◽  
Laboratory Experiments ◽  
Three Dimensional ◽  
Linear Instability ◽  
Three Dimensions ◽  
Two Dimensional ◽  
Magnetorotational Instability ◽  
Dynamo Action ◽  
Wide Range

The magnetorotational instability (MRI) occurs when a weak magnetic field destabilizes a rotating, electrically conducting fluid with inwardly increasing angular velocity. The MRI is essential to astrophysical disc theory where the shear is typically Keplerian. Internal shear layers in stars may also be MRI-unstable, and they take a wide range of profiles, including near-critical. We show that the fastest growing modes of an ideal magnetofluid are three-dimensional provided the shear rate, S , is near the two-dimensional onset value, S c . For a Keplerian shear, three-dimensional modes are unstable above S  ≈ 0.10 S c , and dominate the two-dimensional modes until S  ≈ 2.05 S c . These three-dimensional modes dominate for shear profiles relevant to stars and at magnetic Prandtl numbers relevant to liquid-metal laboratory experiments. Significant numbers of rapidly growing three-dimensional modes remainy well past 2.05 S c . These finding are significant in three ways. First, weakly nonlinear theory suggests that the MRI saturates by pushing the shear rate to its critical value. This can happen for systems, such as stars and laboratory experiments, that can rearrange their angular velocity profiles. Second, the non-normal character and large transient growth of MRI modes should be important whenever three-dimensionality exists. Finally, three-dimensional growth suggests direct dynamo action driven from the linear instability.

scholarly journals Nanoscopic changes in the lattice structure of striated muscle sarcomeres involved in the mechanism of spontaneous oscillatory contraction (SPOC)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Fumiaki Kono ◽  
Seitaro Kawai ◽  
Yuta Shimamoto ◽  
Shin’ichi Ishiwata
Keyword(s):  
Structural Changes ◽  
Striated Muscle ◽  
Lattice Structure ◽  
Three Dimensional ◽  
Force Balance ◽  
Dynamic Force ◽  
Structural Requirement ◽  
Oscillatory Dynamics ◽  
Contractile System ◽  
Wide Range

Abstract Muscles perform a wide range of motile functions in animals. Among various types are skeletal and cardiac muscles, which exhibit a steady auto-oscillation of force and length when they are activated at an intermediate level of contraction. This phenomenon, termed spontaneous oscillatory contraction or SPOC, occurs devoid of cell membranes and at fixed concentrations of chemical substances, and is thus the property of the contractile system per se. We have previously developed a theoretical model of SPOC and proposed that the oscillation emerges from a dynamic force balance along both the longitudinal and lateral axes of sarcomeres, the contractile units of the striated muscle. Here, we experimentally tested this hypothesis by developing an imaging-based analysis that facilitates detection of the structural changes of single sarcomeres at unprecedented spatial resolution. We found that the sarcomere width oscillates anti-phase with the sarcomere length in SPOC. We also found that the oscillatory dynamics can be altered by osmotic compression of the myofilament lattice structure of sarcomeres, but they are unchanged by a proteolytic digestion of titin/connectin—the spring-like protein that provides passive elasticity to sarcomeres. Our data thus reveal the three-dimensional mechanical dynamics of oscillating sarcomeres and suggest a structural requirement of steady auto-oscillation.

Application of 3D Traction Force Microscopy to Mechanotransduction of Cell Clusters

2011 ◽  
Vol 70 ◽  
pp. 21-27 ◽  
Author(s):  
Jacob Notbohm ◽  
Jin Hong Kim ◽  
Anand Asthagiri ◽  
Guruswami Ravichandran
Keyword(s):  
Finite Element ◽  
Three Dimensional ◽  
Traction Force ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Cell Contact ◽  
Traction Force Microscopy ◽  
Inhibition Of Proliferation ◽  
Force Microscopy ◽  
Cell Clusters

With increasing understanding of the important role mechanics plays in cell behavior, the experimental technique of traction force microscopy has grown in popularity over the past decade. While researchers have assumed that cells on a flat substrate apply tractions in only two dimensions, a finite element simulation is discussed here that demonstrates how cells apply tractions in all three dimensions. Three dimensional traction force microscopy is then used to experimentally confirm the finite element results. Finally, the implications that the traction distributions of cell clusters have on the study of inhibition of proliferation due to cell contact and scattering of cells in a cluster are discussed.

scholarly journals Divergent excitation two photon microscopy for 3D random access mesoscale imaging at single cell resolution

2019 ◽  
Author(s):  
FK Janiak ◽  
P Bartel ◽  
MR Bale ◽  
T Yoshimatsu ◽  
E Komulainen ◽  
...  
Keyword(s):  
Single Cell ◽  
Neuronal Activity ◽  
Low Cost ◽  
Three Dimensional ◽  
Random Access ◽  
Field Of View ◽  
Three Dimensions ◽  
Two Photon ◽  
Wide Range ◽  
Effective Excitation

ABSTACTIn neuroscience, diffraction limited two-photon (2P) microscopy is a cornerstone technique that permits minimally invasive optical monitoring of neuronal activity. However, most conventional 2P microscopes impose significant constraints on the size of the imaging field-of-view and the specific shape of the effective excitation volume, thus limiting the scope of biological questions that can be addressed and the information obtainable. Here, employing ‘divergent beam optics’ (DBO), we present an ultra-low-cost, easily implemented and flexible solution to address these limitations, offering a several-fold expanded three-dimensional field of view that also maintains single-cell resolution. We show that this implementation increases both the space-bandwidth product and effective excitation power, and allows for straight-forward tailoring of the point-spread-function. Moreover, rapid laser-focus control via an electrically tunable lens now allows near-simultaneous imaging of remote regions separated in three dimensions and permits the bending of imaging planes to follow natural curvatures in biological structures. Crucially, our core design is readily implemented (and reversed) within a matter of hours, and fully compatible with a wide range of existing 2P customizations, making it highly suitable as a base platform for further development. We demonstrate the application of our system for imaging neuronal activity in a variety of examples in mice, zebrafish and fruit flies.

scholarly journals 3D Magnetic Reconnection

2010 ◽  
Vol 6 (S271) ◽  
pp. 227-238 ◽  
Author(s):  
Clare E. Parnell ◽  
Rhona C. Maclean ◽  
Andrew L. Haynes ◽  
Klaus Galsgaard
Keyword(s):  
Magnetic Reconnection ◽  
Energy State ◽  
Single Point ◽  
Three Dimensional ◽  
Two Dimensions ◽  
Three Dimensions ◽  
Wide Range ◽  
Field Lines ◽  
Magnetohydrodynamic Models ◽  
The Magnetic Field

AbstractMagnetic reconnection is an important process that is prevalent in a wide range of astrophysical bodies. It is the mechanism that permits magnetic fields to relax to a lower energy state through the global restructuring of the magnetic field and is thus associated with a range of dynamic phenomena such as solar flares and CMEs. The characteristics of three-dimensional reconnection are reviewed revealing how much more diverse it is than reconnection in two dimensions. For instance, three-dimensional reconnection can occur both in the vicinity of null points, as well as in the absence of them. It occurs continuously and continually throughout a diffusion volume, as opposed to at a single point, as it does in two dimensions. This means that in three-dimensions field lines do not reconnect in pairs of lines making the visualisation and interpretation of three-dimensional reconnection difficult.By considering particular numerical 3D magnetohydrodynamic models of reconnection, we consider how magnetic reconnection can lead to complex magnetic topologies and current sheet formation. Indeed, it has been found that even simple interactions, such as the emergence of a flux tube, can naturally give rise to ‘turbulent-like’ reconnection regions.

scholarly journals A Comprehensive Observational Study of Graupel and Hail Terminal Velocity, Mass Flux, and Kinetic Energy

2018 ◽  
Vol 75 (11) ◽  
pp. 3861-3885 ◽  
Author(s):  
Andrew Heymsfield ◽  
Miklós Szakáll ◽  
Alexander Jost ◽  
Ian Giammanco ◽  
Robert Wright
Keyword(s):  
Reynolds Number ◽  
Kinetic Energy ◽  
Mass Flux ◽  
Three Dimensional ◽  
Acrylonitrile Butadiene Styrene ◽  
Terminal Velocity ◽  
Three Dimensions ◽  
Cross Sectional ◽  
Wide Range ◽  
3D Volume

Abstract This study uses novel approaches to estimate the fall characteristics of hail, covering a size range from about 0.5 to 7 cm, and the drag coefficients of lump and conical graupel. Three-dimensional (3D) volume scans of 60 hailstones of sizes from 2.5 to 6.7 cm were printed in three dimensions using acrylonitrile butadiene styrene (ABS) plastic, and their terminal velocities were measured in the Mainz, Germany, vertical wind tunnel. To simulate lump graupel, 40 of the hailstones were printed with maximum dimensions of about 0.2, 0.3, and 0.5 cm, and their terminal velocities were measured. Conical graupel, whose three dimensions (maximum dimension 0.1–1 cm) were estimated from an analytical representation and printed, and the terminal velocities of seven groups of particles were measured in the tunnel. From these experiments, with printed particle densities from 0.2 to 0.9 g cm−3, together with earlier observations, relationships between the drag coefficient and the Reynolds number and between the Reynolds number and the Best number were derived for a wide range of particle sizes and heights (pressures) in the atmosphere. This information, together with the combined total of more than 2800 hailstones for which the mass and the cross-sectional area were measured, has been used to develop size-dependent relationships for the terminal velocity, the mass flux, and the kinetic energy of realistic hailstones.

Characterizing three‐dimensional wavefields with high‐resolution spectra

Geophysics ◽  
1992 ◽  
Vol 57 (4) ◽  
pp. 522-531
Author(s):  
R. A. Meek ◽  
A. A. Vassiliou
Keyword(s):  
Fourier Transform ◽  
Maximum Entropy ◽  
Fourier Transforms ◽  
Spectral Estimation ◽  
Three Dimensional ◽  
Estimation Method ◽  
Synthetic Data ◽  
Estimation Algorithm ◽  
Three Dimensions ◽  
Coherent Noise

Three‐dimensional spectra (frequency‐x‐wavenumber‐y‐wavenumber or [Formula: see text] spectra) can be used to determine the frequency content, velocity, and direction of waves entering an array of receivers. This information is important in detecting aliasing problems, understanding coherent noise, designing arrays, and determining parameters for coherent noise filters. Because of the limited spatial dimensions of most arrays the discrete Fourier transform produces an estimate of the three‐dimensional (3-D) spectrum with severe wavenumber distortion. We extend a 2-D hybrid spectral estimation method to three dimensions by combining a temporal Fourier transform with a spatial 2-D maximum entropy spectral estimation technique. The method produces [Formula: see text] spectra with higher wavenumber resolution and less spectral distortion than corresponding 3-D Fourier spectra. The 2-D maximum entropy spectral estimation algorithm uses a sequence of Fourier transforms to extrapolate the estimated autocorrelation function of the data. We assume the wavenumber spectrum of the data comprises a sum of a few poles. Field and synthetic data are used to demonstrate how 3-D wavefields can be characterized with this method of spectral analysis. From these results we conclude that the method gives excellent wavenumber resolution but performs poorly in detecting small signals in the presence of high amplitude signals. We feel this limitation is not serious for characterizing strong amplitude coherent energy recorded by an array of receivers.

scholarly journals Volume-CLEM: a method for correlative light and electron microscopy in three dimensions

2019 ◽  
Vol 317 (6) ◽  
pp. L778-L784 ◽  
Author(s):  
Jan Hegermann ◽  
Christoph Wrede ◽  
Susanne Fassbender ◽  
Ronja Schliep ◽  
Matthias Ochs ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Light And Electron Microscopy ◽  
Three Dimensional ◽  
Fluorescent Labeling ◽  
Three Dimensions ◽  
Data Sets ◽  
New Approach ◽  
3D Data ◽  
Wide Range ◽  
3D Em

Generation of three-dimensional (3D) data sets from serial sections of tissues imaged by light microscopy (LM) allows identification of rare structures by morphology or fluorescent labeling. Here, we demonstrate a workflow for correlative LM and electron microscopy (EM) from 3D LM to 3D EM, using the same sectioned material for both methods consecutively. The new approach is easy to reproduce in routine EM laboratories and applicable to a wide range of organs and research questions.

scholarly journals Simultaneous measurements of three-dimensional trajectories and wingbeat frequencies of birds in the field

2018 ◽  
Vol 15 (147) ◽  
pp. 20180653 ◽  
Author(s):  
Hangjian Ling ◽  
Guillam E. Mclvor ◽  
Geoff Nagy ◽  
Sepehr MohaimenianPour ◽  
Richard T. Vaughan ◽  
...  
Keyword(s):  
Stereo Matching ◽  
Imaging System ◽  
Three Dimensional ◽  
Bird Species ◽  
Three Dimensions ◽  
Natural Environments ◽  
Flight Performance ◽  
Stereo Imaging ◽  
Wingbeat Frequency ◽  
Wide Range

Tracking the movements of birds in three dimensions is integral to a wide range of problems in animal ecology, behaviour and cognition. Multi-camera stereo-imaging has been used to track the three-dimensional (3D) motion of birds in dense flocks, but precise localization of birds remains a challenge due to imaging resolution in the depth direction and optical occlusion. This paper introduces a portable stereo-imaging system with improved accuracy and a simple stereo-matching algorithm that can resolve optical occlusion. This system allows us to decouple body and wing motion, and thus measure not only velocities and accelerations but also wingbeat frequencies along the 3D trajectories of birds. We demonstrate these new methods by analysing six flocking events consisting of 50 to 360 jackdaws ( Corvus monedula ) and rooks ( Corvus frugilegus ) as well as 32 jackdaws and 6 rooks flying in isolated pairs or alone. Our method allows us to (i) measure flight speed and wingbeat frequency in different flying modes; (ii) characterize the U-shaped flight performance curve of birds in the wild, showing that wingbeat frequency reaches its minimum at moderate flight speeds; (iii) examine group effects on individual flight performance, showing that birds have a higher wingbeat frequency when flying in a group than when flying alone and when flying in dense regions than when flying in sparse regions; and (iv) provide a potential avenue for automated discrimination of bird species. We argue that the experimental method developed in this paper opens new opportunities for understanding flight kinematics and collective behaviour in natural environments.

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