22,432 research outputs found
Diffusion Maps Kalman Filter for a Class of Systems with Gradient Flows
In this paper, we propose a non-parametric method for state estimation of
high-dimensional nonlinear stochastic dynamical systems, which evolve according
to gradient flows with isotropic diffusion. We combine diffusion maps, a
manifold learning technique, with a linear Kalman filter and with concepts from
Koopman operator theory. More concretely, using diffusion maps, we construct
data-driven virtual state coordinates, which linearize the system model. Based
on these coordinates, we devise a data-driven framework for state estimation
using the Kalman filter. We demonstrate the strengths of our method with
respect to both parametric and non-parametric algorithms in three tracking
problems. In particular, applying the approach to actual recordings of
hippocampal neural activity in rodents directly yields a representation of the
position of the animals. We show that the proposed method outperforms competing
non-parametric algorithms in the examined stochastic problem formulations.
Additionally, we obtain results comparable to classical parametric algorithms,
which, in contrast to our method, are equipped with model knowledge.Comment: 15 pages, 12 figures, submitted to IEEE TS
Improving Fiber Alignment in HARDI by Combining Contextual PDE Flow with Constrained Spherical Deconvolution
We propose two strategies to improve the quality of tractography results
computed from diffusion weighted magnetic resonance imaging (DW-MRI) data. Both
methods are based on the same PDE framework, defined in the coupled space of
positions and orientations, associated with a stochastic process describing the
enhancement of elongated structures while preserving crossing structures. In
the first method we use the enhancement PDE for contextual regularization of a
fiber orientation distribution (FOD) that is obtained on individual voxels from
high angular resolution diffusion imaging (HARDI) data via constrained
spherical deconvolution (CSD). Thereby we improve the FOD as input for
subsequent tractography. Secondly, we introduce the fiber to bundle coherence
(FBC), a measure for quantification of fiber alignment. The FBC is computed
from a tractography result using the same PDE framework and provides a
criterion for removing the spurious fibers. We validate the proposed
combination of CSD and enhancement on phantom data and on human data, acquired
with different scanning protocols. On the phantom data we find that PDE
enhancements improve both local metrics and global metrics of tractography
results, compared to CSD without enhancements. On the human data we show that
the enhancements allow for a better reconstruction of crossing fiber bundles
and they reduce the variability of the tractography output with respect to the
acquisition parameters. Finally, we show that both the enhancement of the FODs
and the use of the FBC measure on the tractography improve the stability with
respect to different stochastic realizations of probabilistic tractography.
This is shown in a clinical application: the reconstruction of the optic
radiation for epilepsy surgery planning
Real-Time analysis and visualization for single-molecule based super-resolution microscopy
Accurate multidimensional localization of isolated fluorescent emitters is a time consuming process in single-molecule based super-resolution microscopy. We demonstrate a functional method for real-time reconstruction with automatic feedback control, without compromising the localization accuracy. Compatible with high frame rates of EM-CCD cameras, it relies on a wavelet segmentation algorithm, together with a mix of CPU/GPU implementation. A combination with Gaussian fitting allows direct access to 3D localization. Automatic feedback control ensures optimal molecule density throughout the acquisition process. With this method, we significantly improve the efficiency and feasibility of localization-based super-resolution microscopy
Inferring Latent States and Refining Force Estimates via Hierarchical Dirichlet Process Modeling in Single Particle Tracking Experiments
Optical microscopy provides rich spatio-temporal information characterizing
in vivo molecular motion. However, effective forces and other parameters used
to summarize molecular motion change over time in live cells due to latent
state changes, e.g., changes induced by dynamic micro-environments,
photobleaching, and other heterogeneity inherent in biological processes. This
study focuses on techniques for analyzing Single Particle Tracking (SPT) data
experiencing abrupt state changes. We demonstrate the approach on GFP tagged
chromatids experiencing metaphase in yeast cells and probe the effective forces
resulting from dynamic interactions that reflect the sum of a number of
physical phenomena. State changes are induced by factors such as microtubule
dynamics exerting force through the centromere, thermal polymer fluctuations,
etc. Simulations are used to demonstrate the relevance of the approach in more
general SPT data analyses. Refined force estimates are obtained by adopting and
modifying a nonparametric Bayesian modeling technique, the Hierarchical
Dirichlet Process Switching Linear Dynamical System (HDP-SLDS), for SPT
applications. The HDP-SLDS method shows promise in systematically identifying
dynamical regime changes induced by unobserved state changes when the number of
underlying states is unknown in advance (a common problem in SPT applications).
We expand on the relevance of the HDP-SLDS approach, review the relevant
background of Hierarchical Dirichlet Processes, show how to map discrete time
HDP-SLDS models to classic SPT models, and discuss limitations of the approach.
In addition, we demonstrate new computational techniques for tuning
hyperparameters and for checking the statistical consistency of model
assumptions directly against individual experimental trajectories; the
techniques circumvent the need for "ground-truth" and subjective information.Comment: 25 pages, 6 figures. Differs only typographically from PLoS One
publication available freely as an open-access article at
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.013763
VNect: Real-time 3D Human Pose Estimation with a Single RGB Camera
We present the first real-time method to capture the full global 3D skeletal
pose of a human in a stable, temporally consistent manner using a single RGB
camera. Our method combines a new convolutional neural network (CNN) based pose
regressor with kinematic skeleton fitting. Our novel fully-convolutional pose
formulation regresses 2D and 3D joint positions jointly in real time and does
not require tightly cropped input frames. A real-time kinematic skeleton
fitting method uses the CNN output to yield temporally stable 3D global pose
reconstructions on the basis of a coherent kinematic skeleton. This makes our
approach the first monocular RGB method usable in real-time applications such
as 3D character control---thus far, the only monocular methods for such
applications employed specialized RGB-D cameras. Our method's accuracy is
quantitatively on par with the best offline 3D monocular RGB pose estimation
methods. Our results are qualitatively comparable to, and sometimes better
than, results from monocular RGB-D approaches, such as the Kinect. However, we
show that our approach is more broadly applicable than RGB-D solutions, i.e. it
works for outdoor scenes, community videos, and low quality commodity RGB
cameras.Comment: Accepted to SIGGRAPH 201
Multi-Bernoulli Sensor-Control via Minimization of Expected Estimation Errors
This paper presents a sensor-control method for choosing the best next state
of the sensor(s), that provide(s) accurate estimation results in a multi-target
tracking application. The proposed solution is formulated for a multi-Bernoulli
filter and works via minimization of a new estimation error-based cost
function. Simulation results demonstrate that the proposed method can
outperform the state-of-the-art methods in terms of computation time and
robustness to clutter while delivering similar accuracy
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