Crystal image analysis using 2D2D synchrosqueezed transforms

We propose efficient algorithms based on a band-limited version of 2D synchrosqueezed transforms to extract mesoscopic and microscopic information from atomic crystal images. The methods analyze atomic crystal images as an assemblage of non-overlapping segments of 2D general intrinsic mode type functions, which are superpositions of non-linear wave-like components. In particular, crystal defects are interpreted as the irregularity of local energy; crystal rotations are described as the angle deviation of local wave vectors from their references; the gradient of a crystal elastic deformation can be obtained by a linear system generated by local wave vectors. Several numerical examples of synthetic and real crystal images are provided to illustrate the efficiency, robustness, and reliability of our methods.Comment: 27 pages, 17 figure

A scale-space approach with wavelets to singularity estimation

This paper is concerned with the problem of determining the typical features of a curve when it is observed with noise. It has been shown that one can characterize the Lipschitz singularities of a signal by following the propagation across scales of the modulus maxima of its continuous wavelet transform. A nonparametric approach, based on appropriate thresholding of the empirical wavelet coefficients, is proposed to estimate the wavelet maxima of a signal observed with noise at various scales. In order to identify the singularities of the unknown signal, we introduce a new tool, "the structural intensity", that computes the "density" of the location of the modulus maxima of a wavelet representation along various scales. This approach is shown to be an effective technique for detecting the significant singularities of a signal corrupted by noise and for removing spurious estimates. The asymptotic properties of the resulting estimators are studied and illustrated by simulations. An application to a real data set is also proposed

A new view of nonlinear water waves: the Hilbert spectrum

We survey the newly developed Hilbert spectral analysis method and its applications to Stokes waves, nonlinear wave evolution processes, the spectral form of the random wave field, and turbulence. Our emphasis is on the inadequacy of presently available methods in nonlinear and nonstationary data analysis. Hilbert spectral analysis is here proposed as an alternative. This new method provides not only a more precise definition of particular events in time-frequency space than wavelet analysis, but also more physically meaningful interpretations of the underlying dynamic processes

Gaussian Process Morphable Models

Statistical shape models (SSMs) represent a class of shapes as a normal distribution of point variations, whose parameters are estimated from example shapes. Principal component analysis (PCA) is applied to obtain a low-dimensional representation of the shape variation in terms of the leading principal components. In this paper, we propose a generalization of SSMs, called Gaussian Process Morphable Models (GPMMs). We model the shape variations with a Gaussian process, which we represent using the leading components of its Karhunen-Loeve expansion. To compute the expansion, we make use of an approximation scheme based on the Nystrom method. The resulting model can be seen as a continuous analogon of an SSM. However, while for SSMs the shape variation is restricted to the span of the example data, with GPMMs we can define the shape variation using any Gaussian process. For example, we can build shape models that correspond to classical spline models, and thus do not require any example data. Furthermore, Gaussian processes make it possible to combine different models. For example, an SSM can be extended with a spline model, to obtain a model that incorporates learned shape characteristics, but is flexible enough to explain shapes that cannot be represented by the SSM. We introduce a simple algorithm for fitting a GPMM to a surface or image. This results in a non-rigid registration approach, whose regularization properties are defined by a GPMM. We show how we can obtain different registration schemes,including methods for multi-scale, spatially-varying or hybrid registration, by constructing an appropriate GPMM. As our approach strictly separates modelling from the fitting process, this is all achieved without changes to the fitting algorithm. We show the applicability and versatility of GPMMs on a clinical use case, where the goal is the model-based segmentation of 3D forearm images

Graph analysis of functional brain networks: practical issues in translational neuroscience

The brain can be regarded as a network: a connected system where nodes, or units, represent different specialized regions and links, or connections, represent communication pathways. From a functional perspective communication is coded by temporal dependence between the activities of different brain areas. In the last decade, the abstract representation of the brain as a graph has allowed to visualize functional brain networks and describe their non-trivial topological properties in a compact and objective way. Nowadays, the use of graph analysis in translational neuroscience has become essential to quantify brain dysfunctions in terms of aberrant reconfiguration of functional brain networks. Despite its evident impact, graph analysis of functional brain networks is not a simple toolbox that can be blindly applied to brain signals. On the one hand, it requires a know-how of all the methodological steps of the processing pipeline that manipulates the input brain signals and extract the functional network properties. On the other hand, a knowledge of the neural phenomenon under study is required to perform physiological-relevant analysis. The aim of this review is to provide practical indications to make sense of brain network analysis and contrast counterproductive attitudes