44,427 research outputs found
Automated visual tracking for studying the ontogeny of zebrafish swimming
The zebrafish Danio rerio is a widely used model organism in studies of genetics, developmental biology, and recently, biomechanics. In order to quantify changes in swimming during all stages of development, we have developed a visual tracking system that estimates the posture of fish. Our current approach assumes planar motion of the fish, given image sequences taken from a top view. An accurate geometric fish model is automatically designed and fit to the images at each time frame. Our approach works across a range of fish shapes and sizes and is therefore well suited for studying the ontogeny of fish swimming, while also being robust to common environmental occlusions. Our current analysis focuses on measuring the influence of vertebra development on the swimming capabilities of zebrafish. We examine wild-type zebrafish and mutants with stiff vertebrae (stocksteif) and quantify their body kinematics as a function of their development from larvae to adult (mutants made available by the Hubrecht laboratory, The Netherlands). By tracking the fish, we are able to measure the curvature and net acceleration along the body that result from the fish's body wave. Here, we demonstrate the capabilities of the tracking system for the escape response of wild-type zebrafish and stocksteif mutant zebrafish. The response was filmed with a digital high-speed camera at 1500 frames s–1. Our approach enables biomechanists and ethologists to process much larger datasets than possible at present. Our automated tracking scheme can therefore accelerate insight in the swimming behavior of many species of (developing) fish
Identification of a spatio-temporal model of crystal growth based on boundary curvature
A new method of identifying the spatio-temporal transition rule of crystal growth is introduced based on the connection between growth kinetics and dentritic
morphology. Using a modified three-point-method, curvatures of the considered crystal branch are calculated and curvature direction is used to measure growth
velocity. A polynomial model is then produced based on a curvature-velocity relationship to represent the spatio-temporal growth process. A very simple simulation
example is used initially to clearly explain the methodology. The results of identifying a model from a real crystal growth experiment show that the proposed
method can produce a good representation of crystal growth
Adaptive Smoothing for Trajectory Reconstruction
Trajectory reconstruction is the process of inferring the path of a moving
object between successive observations. In this paper, we propose a smoothing
spline -- which we name the V-spline -- that incorporates position and velocity
information and a penalty term that controls acceleration. We introduce a
particular adaptive V-spline designed to control the impact of irregularly
sampled observations and noisy velocity measurements. A cross-validation scheme
for estimating the V-spline parameters is given and we detail the performance
of the V-spline on four particularly challenging test datasets. Finally, an
application of the V-spline to vehicle trajectory reconstruction in two
dimensions is given, in which the penalty term is allowed to further depend on
known operational characteristics of the vehicle.Comment: 25 pages, submitte
Application of Monte Carlo Algorithms to the Bayesian Analysis of the Cosmic Microwave Background
Power spectrum estimation and evaluation of associated errors in the presence
of incomplete sky coverage; non-homogeneous, correlated instrumental noise; and
foreground emission is a problem of central importance for the extraction of
cosmological information from the cosmic microwave background. We develop a
Monte Carlo approach for the maximum likelihood estimation of the power
spectrum. The method is based on an identity for the Bayesian posterior as a
marginalization over unknowns. Maximization of the posterior involves the
computation of expectation values as a sample average from maps of the cosmic
microwave background and foregrounds given some current estimate of the power
spectrum or cosmological model, and some assumed statistical characterization
of the foregrounds. Maps of the CMB are sampled by a linear transform of a
Gaussian white noise process, implemented numerically with conjugate gradient
descent. For time series data with N_{t} samples, and N pixels on the sphere,
the method has a computational expense $KO[N^{2} +- N_{t} +AFw-log N_{t}],
where K is a prefactor determined by the convergence rate of conjugate gradient
descent. Preconditioners for conjugate gradient descent are given for scans
close to great circle paths, and the method allows partial sky coverage for
these cases by numerically marginalizing over the unobserved, or removed,
region.Comment: submitted to Ap
Fitting Effective Diffusion Models to Data Associated with a "Glassy Potential": Estimation, Classical Inference Procedures and Some Heuristics
A variety of researchers have successfully obtained the parameters of low
dimensional diffusion models using the data that comes out of atomistic
simulations. This naturally raises a variety of questions about efficient
estimation, goodness-of-fit tests, and confidence interval estimation. The
first part of this article uses maximum likelihood estimation to obtain the
parameters of a diffusion model from a scalar time series. I address numerical
issues associated with attempting to realize asymptotic statistics results with
moderate sample sizes in the presence of exact and approximated transition
densities. Approximate transition densities are used because the analytic
solution of a transition density associated with a parametric diffusion model
is often unknown.I am primarily interested in how well the deterministic
transition density expansions of Ait-Sahalia capture the curvature of the
transition density in (idealized) situations that occur when one carries out
simulations in the presence of a "glassy" interaction potential. Accurate
approximation of the curvature of the transition density is desirable because
it can be used to quantify the goodness-of-fit of the model and to calculate
asymptotic confidence intervals of the estimated parameters. The second part of
this paper contributes a heuristic estimation technique for approximating a
nonlinear diffusion model. A "global" nonlinear model is obtained by taking a
batch of time series and applying simple local models to portions of the data.
I demonstrate the technique on a diffusion model with a known transition
density and on data generated by the Stochastic Simulation Algorithm.Comment: 30 pages 10 figures Submitted to SIAM MMS (typos removed and slightly
shortened
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