Estimating the granularity coefficient of a Potts-Markov random field within an MCMC algorithm

This paper addresses the problem of estimating the Potts parameter B jointly with the unknown parameters of a Bayesian model within a Markov chain Monte Carlo (MCMC) algorithm. Standard MCMC methods cannot be applied to this problem because performing inference on B requires computing the intractable normalizing constant of the Potts model. In the proposed MCMC method the estimation of B is conducted using a likelihood-free Metropolis-Hastings algorithm. Experimental results obtained for synthetic data show that estimating B jointly with the other unknown parameters leads to estimation results that are as good as those obtained with the actual value of B. On the other hand, assuming that the value of B is known can degrade estimation performance significantly if this value is incorrect. To illustrate the interest of this method, the proposed algorithm is successfully applied to real bidimensional SAR and tridimensional ultrasound images

Variational bayes for estimating the parameters of a hidden Potts model

Hidden Markov random field models provide an appealing representation of images and other spatial problems. The drawback is that inference is not straightforward for these models as the normalisation constant for the likelihood is generally intractable except for very small observation sets. Variational methods are an emerging tool for Bayesian inference and they have already been successfully applied in other contexts. Focusing on the particular case of a hidden Potts model with Gaussian noise, we show how variational Bayesian methods can be applied to hidden Markov random field inference. To tackle the obstacle of the intractable normalising constant for the likelihood, we explore alternative estimation approaches for incorporation into the variational Bayes algorithm. We consider a pseudo-likelihood approach as well as the more recent reduced dependence approximation of the normalisation constant. To illustrate the effectiveness of these approaches we present empirical results from the analysis of simulated datasets. We also analyse a real dataset and compare results with those of previous analyses as well as those obtained from the recently developed auxiliary variable MCMC method and the recursive MCMC method. Our results show that the variational Bayesian analyses can be carried out much faster than the MCMC analyses and produce good estimates of model parameters. We also found that the reduced dependence approximation of the normalisation constant outperformed the pseudo-likelihood approximation in our analysis of real and synthetic datasets

Filter-Based Probabilistic Markov Random Field Image Priors: Learning, Evaluation, and Image Analysis

Markov random fields (MRF) based on linear filter responses are one of the most popular forms for modeling image priors due to their rigorous probabilistic interpretations and versatility in various applications. In this dissertation, we propose an application-independent method to quantitatively evaluate MRF image priors using model samples. To this end, we developed an efficient auxiliary-variable Gibbs samplers for a general class of MRFs with flexible potentials. We found that the popular pairwise and high-order MRF priors capture image statistics quite roughly and exhibit poor generative properties. We further developed new learning strategies and obtained high-order MRFs that well capture the statistics of the inbuilt features, thus being real maximum-entropy models, and other important statistical properties of natural images, outlining the capabilities of MRFs. We suggest a multi-modal extension of MRF potentials which not only allows to train more expressive priors, but also helps to reveal more insights of MRF variants, based on which we are able to train compact, fully-convolutional restricted Boltzmann machines (RBM) that can model visual repetitive textures even better than more complex and deep models. The learned high-order MRFs allow us to develop new methods for various real-world image analysis problems. For denoising of natural images and deconvolution of microscopy images, the MRF priors are employed in a pure generative setting. We propose efficient sampling-based methods to infer Bayesian minimum mean squared error (MMSE) estimates, which substantially outperform maximum a-posteriori (MAP) estimates and can compete with state-of-the-art discriminative methods. For non-rigid registration of live cell nuclei in time-lapse microscopy images, we propose a global optical flow-based method. The statistics of noise in fluorescence microscopy images are studied to derive an adaptive weighting scheme for increasing model robustness. High-order MRFs are also employed to train image filters for extracting important features of cell nuclei and the deformation of nuclei are then estimated in the learned feature spaces. The developed method outperforms previous approaches in terms of both registration accuracy and computational efficiency

Rich probabilistic models for semantic labeling

Das Ziel dieser Monographie ist es die Methoden und Anwendungen des semantischen Labelings zu erforschen. Unsere Beiträge zu diesem sich rasch entwickelten Thema sind bestimmte Aspekte der Modellierung und der Inferenz in probabilistischen Modellen und ihre Anwendungen in den interdisziplinären Bereichen der Computer Vision sowie medizinischer Bildverarbeitung und Fernerkundung

Statistical modeling and processing of high frequency ultrasound images: application to dermatologic oncology

Cette thèse étudie le traitement statistique des images d’ultrasons de haute fréquence, avec application à l’exploration in-vivo de la peau humaine et l’évaluation non invasive de lésions. Des méthodes Bayésiennes sont considérées pour la segmentation d’images échographiques de la peau. On y établit que les ultrasons rétrodiffusés par la peau convergent vers un processus aléatoire complexe de type Levy-Flight, avec des statistiques non Gaussiennes alpha-stables. L’enveloppe du signal suit une distribution Rayleigh généralisée à queue lourde. A partir de ces résultats, il est proposé de modéliser l’image ultrason de multiples tissus comme un mélange spatialement cohérent de lois Rayleigh à queues lourdes. La cohérence spatiale inhérente aux tissus biologiques est modélisée par un champ aléatoire de Potts-Markov pour représenter la dépendance locale entre les composantes du mélange. Un algorithme Bayésien original combiné à une méthode Monte Carlo par chaine de Markov (MCMC) est proposé pour conjointement estimer les paramètres du modèle et classifier chaque voxel dans un tissu. L’approche proposée est appliquée avec succès à la segmentation de tumeurs de la peau in-vivo dans des images d’ultrasons de haute fréquence en 2D et 3D. Cette méthode est ensuite étendue en incluant l’estimation du paramètre B de régularisation du champ de Potts dans la chaine MCMC. Les méthodes MCMC classiques ne sont pas directement applicables à ce problème car la vraisemblance du champ de Potts ne peut pas être évaluée. Ce problème difficile est traité en adoptant un algorithme Metropolis-Hastings “sans vraisemblance” fondé sur la statistique suffisante du Potts. La méthode de segmentation non supervisée, ainsi développée, est appliquée avec succès à des images échographiques 3D. Finalement, le problème du calcul de la borne de Cramer-Rao (CRB) du paramètre B est étudié. Cette borne dépend des dérivées de la constante de normalisation du modèle de Potts, dont le calcul est infaisable. Ce problème est résolu en proposant un algorithme Monte Carlo original, qui est appliqué avec succès au calcul de la borne CRB des modèles d’Ising et de Potts. ABSTRACT : This thesis studies statistical image processing of high frequency ultrasound imaging, with application to in-vivo exploration of human skin and noninvasive lesion assessment. More precisely, Bayesian methods are considered in order to perform tissue segmentation in ultrasound images of skin. It is established that ultrasound signals backscattered from skin tissues converge to a complex Levy Flight random process with non-Gaussian _-stable statistics. The envelope signal follows a generalized (heavy-tailed) Rayleigh distribution. Based on these results, it is proposed to model the distribution of multiple-tissue ultrasound images as a spatially coherent finite mixture of heavy-tailed Rayleigh distributions. Spatial coherence inherent to biological tissues is modeled by a Potts Markov random field. An original Bayesian algorithm combined with a Markov chain Monte Carlo method is then proposed to jointly estimate the mixture parameters and a label-vector associating each voxel to a tissue. The proposed method is successfully applied to the segmentation of in-vivo skin tumors in high frequency 2D and 3D ultrasound images. This method is subsequently extended by including the estimation of the Potts regularization parameter B within the Markov chain Monte Carlo (MCMC) algorithm. Standard MCMC methods cannot be applied to this problem because the likelihood of B is intractable. This difficulty is addressed by using a likelihood-free Metropolis-Hastings algorithm based on the sufficient statistic of the Potts model. The resulting unsupervised segmentation method is successfully applied to tridimensional ultrasound images. Finally, the problem of computing the Cramer-Rao bound (CRB) of B is studied. The CRB depends on the derivatives of the intractable normalizing constant of the Potts model. This is resolved by proposing an original Monte Carlo algorithm, which is successfully applied to compute the CRB of the Ising and Potts models

Probabilistic Models for Joint Segmentation, Detection and Tracking

Migrace buněk a buněčných částic hraje důležitou roli ve fungování živých organismů. Systematický výzkum buněčné migrace byl umožněn v posledních dvaceti letech rychlým rozvojem neinvazivních zobrazovacích technik a digitálních snímačů. Moderní zobrazovací systémy dovolují studovat chování buněčných populací složených z mnoha ticíců buněk. Manuální analýza takového množství dat by byla velice zdlouhavá, protože některé experimenty vyžadují analyzovat tvar, rychlost a další charakteristiky jednotlivých buněk. Z tohoto důvodu je ve vědecké komunitě velká poptávka po automatických metodách.Migration of cells and subcellular particles plays a crucial role in many processes in living organisms. Despite its importance a systematic research of cell motility has only been possible in last two decades due to rapid development of non-invasive imaging techniques and digital cameras. Modern imaging systems allow to study large populations with thousands of cells. Manual analysis of the acquired data is infeasible, because in order to gain insight into underlying biochemical processes it is sometimes necessary to determine shape, velocity and other characteristics of individual cells. Thus there is a high demand for automatic methods