Real-Time Adaptive Video Compression

Compressive sensing has been widely applied to problems in signal and imaging processing. In this work, we present an algorithm for predicting optimal real-time compression rates for video. The video data we consider is spatially compressed during the acquisition process, unlike in many of the standard methods. Rather than temporally compressing the frames at a fixed rate, our algorithm adaptively predicts the compression rate given the behavior of a few previous compressed frames. The algorithm uses polynomial fitting and simple filters, making it computationally feasible and easy to implement in hardware. Based on numerical simulations of real videos, the algorithm is able to capture object motion and approximate dynamics within the compressed frames. The adaptive video compression improves the quality of the reconstructed video (as compared to an equivalent fixed rate compression scheme) by several dB of peak signal-to-noise ratio without increasing the amount of information stored, as seen in numerical simulations presented here

Surface reconstruction from microscopic images in optical lithography

We propose a shape-from-shading method to reconstruct surfaces of silicon wafers from images of printed circuits taken with scanning electron microscope. Our method combines the physical model of the optical acquisition system with prior knowledge about the shapes of the patterns in the circuit. The reconstruction of the surface is formulated as an optimization problem with a combined criterion based on the irradiance equation and a shape prior that constrains the shape of the surface to agree with the expected shape of the pattern. To account for the variability of the manufacturing process, the model allows a non-linear elastic deformation between the expected patterns and the reconstructed surface. Our method provides two outputs: a reconstructed surface and a deformation field. The reconstructed surface is derived from the shading observed in the images and the prior knowledge about circuit patterns, which results in a shape-from-shading technique stable and robust to noise. The deformation field produces a mapping between the expected shape and the reconstructed surface, which provides a measure of deviation between the models and the real manufacturing process

Image processing methods for human brain connectivity analysis from in-vivo diffusion MRI

In this PhD Thesis proposal, the principles of diffusion MRI (dMRI) in its application to the human brain mapping of connectivity are reviewed. The background section covers the fundamentals of dMRI, with special focus on those related to the distortions caused by susceptibility inhomogeneity across tissues. Also, a deep survey of available correction methodologies for this common artifact of dMRI is presented. Two methodological approaches to improved correction are introduced. Finally, the PhD proposal describes its objectives, the research plan, and the necessary resources

Model and Appearance Based Analysis of Neuronal Morphology from Different Microscopy Imaging Modalities

The neuronal morphology analysis is key for understanding how a brain works. This process requires the neuron imaging system with single-cell resolution; however, there is no feasible system for the human brain. Fortunately, the knowledge can be inferred from the model organism, Drosophila melanogaster, to the human system. This dissertation explores the morphology analysis of Drosophila larvae at single-cell resolution in static images and image sequences, as well as multiple microscopy imaging modalities. Our contributions are on both computational methods for morphology quantification and analysis of the influence of the anatomical aspect. We develop novel model-and-appearance-based methods for morphology quantification and illustrate their significance in three neuroscience studies. Modeling of the structure and dynamics of neuronal circuits creates understanding about how connectivity patterns are formed within a motor circuit and determining whether the connectivity map of neurons can be deduced by estimations of neuronal morphology. To address this problem, we study both boundary-based and centerline-based approaches for neuron reconstruction in static volumes. Neuronal mechanisms are related to the morphology dynamics; so the patterns of neuronal morphology changes are analyzed along with other aspects. In this case, the relationship between neuronal activity and morphology dynamics is explored to analyze locomotion procedures. Our tracking method models the morphology dynamics in the calcium image sequence designed for detecting neuronal activity. It follows the local-to-global design to handle calcium imaging issues and neuronal movement characteristics. Lastly, modeling the link between structural and functional development depicts the correlation between neuron growth and protein interactions. This requires the morphology analysis of different imaging modalities. It can be solved using the part-wise volume segmentation with artificial templates, the standardized representation of neurons. Our method follows the global-to-local approach to solve both part-wise segmentation and registration across modalities. Our methods address common issues in automated morphology analysis from extracting morphological features to tracking neurons, as well as mapping neurons across imaging modalities. The quantitative analysis delivered by our techniques enables a number of new applications and visualizations for advancing the investigation of phenomena in the nervous system

Intégration des données de sismique 4D dans les modèles de réservoir (recalage d'images fondé sur l'élasticité non linéraire)

Dans une première partie, nous proposons une méthodologie innovante pour la comparaison d'images en ingénierie de réservoir. L'objectif est de pouvoir comparer des cubes sismiques obtenus par simulation avec ceux observés sur un champ pétrolier, dans le but de construire un modèle représentatif de la réalité. Nous développons une formulation fondée sur du filtrage, de la classification statistique et de la segmentation d'images. Ses performances sont mises en avant sur des cas réalistes. Dans une seconde partie, nous nous intéressons aux méthodes de recalage d'images utilisées en imagerie médicale pour mettre en correspondance des images. Nous introduisons deux nouveaux modèles de recalage fondés sur l'élasticité non linéaire, où les formes sont appréhendées comme des matériaux de type Saint Venant-Kirchhoff et Ciarlet-Geymonat. Nous justifions théoriquement l'existence de solutions ainsi que la résolution numérique. Le potentiel de ces méthodes est illustré sur des images médicales.In a first part, we propose an innovative methodology for image matching in the context of reservoir simulation. In order to build a model consistent with data collected on the field, we need to evaluate the error between seismic cubes obtained by simulation and seismic cubes acquired in the oil field. Using image processing tools, we develop a new formulation of the error. The application of this new formulation on synthetic reservoir cases demonstrates its efficiency. In a second part, we address the issue of designing two theoretically well-motivated registration models capable of handling large deformations since they are based on nonlinear elasticity. The shape to be matched are viewed as Ciarlet-Geymonat materials for the first model and as Saint-Venant Kirchhoff materials for the second one. We investigate the efficiency of the proposed matching model for the registration of mouse brain gene expression data to a neuroanatomical mouse atlas.ROUEN-INSA Madrillet (765752301) / SudocSudocFranceF

A combined segmentation and registration framework with a nonlinear elasticity smoother

In this paper, we present a new non-parametric combined segmentation and registration method. The problem is cast as an optimization one, combining a matching criterion based on the active contour without edges [4] for segmentation, and a nonlinear-elasticity-based smoother on the displacement vector field. This modeling is twofold: first, registration is jointly performed with segmentation since guided by the segmentation process; it means that the algorithm produces both a smooth mapping between the two shapes and the segmentation of the object contained in the reference image. Secondly, the use of a nonlinear-elasticity-type regularizer allows large deformations to occur, which makes the model comparable in this point with the viscous fluid registration method [7]. Several applications are proposed to demonstrate the potential of this method to both segmentation of one single image and to registration between two images

Geometric Variational Models for Inverse Problems in Imaging

This dissertation develops geometric variational models for different inverse problems in imaging that are ill-posed, designing at the same time efficient numerical algorithms to compute their solutions. Variational methods solve inverse problems by the following two steps: formulation of a variational model as a minimization problem, and design of a minimization algorithm to solve it. This dissertation is organized in the same manner. It first formulates minimization problems associated with geometric models for different inverse problems in imaging, and it then designs efficient minimization algorithms to compute their solutions. The minimization problem summarizes both the data available from the measurements and the prior knowledge about the solution in its objective functional; this naturally leads to the combination of a measurement or data term and a prior term. Geometry can play a role in any of these terms, depending on the properties of the data acquisition system or the object being imaged. In this context, each chapter of this dissertation formulates a variational model that includes geometry in a different manner in the objective functional, depending on the inverse problem at hand. In the context of compressed sensing, the first chapter exploits the geometric properties of images to include an alignment term in the sparsity prior of compressed sensing; this additional prior term aligns the normal vectors of the level curves of the image with the reconstructed signal, and it improves the quality of reconstruction. A two-step recovery method is designed for that purpose: first, it estimates the normal vectors to the level curves of the image; second, it reconstructs an image matching the compressed sensing measurements, the geometric alignment of normals, and the sparsity constraint of compressed sensing. The proposed method is extended to non-local operators in graphs for the recovery of textures. The harmonic active contours of Chapter 2 make use of differential geometry to interpret the segmentation of an image as a minimal surface manifold. In this case, geometry is exploited in both the measurement term, by coupling the different image channels in a robust edge detector, and in the prior term, by imposing smoothness in the segmentation. The proposed technique generalizes existing active contours to higher dimensional spaces and non-flat images; in the plane, it improves the segmentation of images with inhomogeneities and weak edges. Shape-from-shading is investigated in Chapter 3 for the reconstruction of a silicon wafer from images of printed circuits taken with a scanning electron microscope. In this case, geometry plays a role in the image acquisition system, that is, in the measurement term of the objective functional. The prior term involves a smoothness constraint on the surface and a shape prior on the expected pattern in the circuit. The proposed reconstruction method also estimates a deformation field between the ideal pattern design and the reconstructed surface, substituting the model of shape variability necessary in shape priors with an elastic deformation field that quantifies deviations in the manufacturing process. Finally, the techniques used for the design of efficient numerical algorithms are explained with an example problem based on the level set method. To this purpose, Chapter 4 develops an efficient algorithm for the level set method when the level set function is constrained to remain a signed distance function. The distance function is preserved by the introduction of an explicit constraint in the minimization problem, the minimization algorithm is efficient by the adequate use of variable-splitting and augmented Lagrangian techniques. These techniques introduce additional variables, constraints, and Lagrange multipliers in the original minimization problem, and they decompose it into sub-optimization problems that are simple and can be efficiently solved. As a result, the proposed algorithm is five to six times faster than the original algorithm for the level set method

Statistical analysis for longitudinal MR imaging of dementia

Serial Magnetic Resonance (MR) Imaging can reveal structural atrophy in the brains of subjects with neurodegenerative diseases such as Alzheimer’s Disease (AD). Methods of computational neuroanatomy allow the detection of statistically significant patterns of brain change over time and/or over multiple subjects. The focus of this thesis is the development and application of statistical and supporting methodology for the analysis of three-dimensional brain imaging data. There is a particular emphasis on longitudinal data, though much of the statistical methodology is more general. New methods of voxel-based morphometry (VBM) are developed for serial MR data, employing combinations of tissue segmentation and longitudinal non-rigid registration. The methods are evaluated using novel quantitative metrics based on simulated data. Contributions to general aspects of VBM are also made, and include a publication concerning guidelines for reporting VBM studies, and another examining an issue in the selection of which voxels to include in the statistical analysis mask for VBM of atrophic conditions. Research is carried out into the statistical theory of permutation testing for application to multivariate general linear models, and is then used to build software for the analysis of multivariate deformation- and tensor-based morphometry data, efficiently correcting for the multiple comparison problem inherent in voxel-wise analysis of images. Monte Carlo simulation studies extend results available in the literature regarding the different strategies available for permutation testing in the presence of confounds. Theoretical aspects of longitudinal deformation- and tensor-based morphometry are explored, such as the options for combining within- and between-subject deformation fields. Practical investigation of several different methods and variants is performed for a longitudinal AD study

Proceedings of the Second International Workshop on Mathematical Foundations of Computational Anatomy (MFCA'08) - Geometrical and Statistical Methods for Modelling Biological Shape Variability

International audienceThe goal of computational anatomy is to analyze and to statistically model the anatomy of organs in different subjects. Computational anatomic methods are generally based on the extraction of anatomical features or manifolds which are then statistically analyzed, often through a non-linear registration. There are nowadays a growing number of methods that can faithfully deal with the underlying biomechanical behavior of intra-subject deformations. However, it is more difficult to relate the anatomies of different subjects. In the absence of any justified physical model, diffeomorphisms provide a general mathematical framework that enforce topological consistency. Working with such infinite dimensional space raises some deep computational and mathematical problems, in particular for doing statistics. Likewise, modeling the variability of surfaces leads to rely on shape spaces that are much more complex than for curves. To cope with these, different methodological and computational frameworks have been proposed (e.g. smooth left-invariant metrics, focus on well-behaved subspaces of diffeomorphisms, modeling surfaces using courants, etc.) The goal of the Mathematical Foundations of Computational Anatomy (MFCA) workshop is to foster the interactions between the mathematical community around shapes and the MICCAI community around computational anatomy applications. It targets more particularly researchers investigating the combination of statistical and geometrical aspects in the modeling of the variability of biological shapes. The workshop aims at being a forum for the exchange of the theoretical ideas and a source of inspiration for new methodological developments in computational anatomy. A special emphasis is put on theoretical developments, applications and results being welcomed as illustrations. Following the very successful first edition of this workshop in 2006 (see http://www.inria.fr/sophia/asclepios/events/MFCA06/), the second edition was held in New-York on September 6, in conjunction with MICCAI 2008. Contributions were solicited in Riemannian and group theoretical methods, Geometric measurements of the anatomy, Advanced statistics on deformations and shapes, Metrics for computational anatomy, Statistics of surfaces. 34 submissions were received, among which 9 were accepted to MICCAI and had to be withdrawn from the workshop. Each of the remaining 25 paper was reviewed by three members of the program committee. To guaranty a high level program, 16 papers only were selected