Image segmentation using voronoi polygons and MCMC, with application to muscle fibre images

We investigate a Bayesian method for the segmentation of muscle fibre images. The images are reasonably well approximated by a Dirichlet tessellation, and so we use a deformable template model based on Voronoi polygons to represent the segmented image. We consider various prior distributions for the parameters and suggest an appropriate likelihood. Following the Bayesian paradigm, the mathematical form for the posterior distribution is obtained (up to an integrating constant). We introduce a Metropolis-Hastings algorithm and a reversible jump Markov chain Monte Carlo algorithm (RJMCMC) for simulation from the posterior when the number of polygons is fixed or unknown. The particular moves in the RJMCMC algorithm are birth, death and position/colour changes of the point process which determines the location of the polygons. Segmentation of the true image was carried out using the estimated posterior mode and posterior mean. A simulation study is presented which is helpful for tuning the hyperparameters and to assess the accuracy. The algorithms work well on a real image of a muscle fibre cross-section image, and an additional parameter, which models the boundaries of the muscle fibres, is included in the final model.     

Efficient Bayesian analysis of multiple changepoint models with dependence across segments

We consider Bayesian analysis of a class of multiple changepoint models. While there are a variety of efficient ways to analyse these models if the parameters associated with each segment are independent, there are few general approaches for models where the parameters are dependent. Under the assumption that the dependence is Markov, we propose an efficient online algorithm for sampling from an approximation to the posterior distribution of the number and position of the changepoints. In a simulation study, we show that the approximation introduced is negligible. We illustrate the power of our approach through fitting piecewise polynomial models to data, under a model which allows for either continuity or discontinuity of the underlying curve at each changepoint. This method is competitive with, or outperform, other methods for inferring curves from noisy data; and uniquely it allows for inference of the locations of discontinuities in the underlying curve.     

Bayesian analysis of dynamic magnetic resonance breast images

Summary.  We describe an integrated methodology for analysing dynamic magnetic resonance images of the breast. The problems that motivate this methodology arise from a collaborative study with a tumour institute. The methods are developed within the Bayesian framework and comprise image restoration and classification steps. Two different approaches are proposed for the restoration. Bayesian inference is performed by means of Markov chain Monte Carlo algorithms. We make use of a Metropolis algorithm with a specially chosen proposal distribution that performs better than more commonly used proposals. The classification step is based on a few attribute images yielded by the restoration step that describe the essential features of the contrast agent variation over time. Procedures for hyperparameter estimation are provided, so making our method automatic. The results show the potential of the methodology to extract useful information from acquired dynamic magnetic resonance imaging data about tumour morphology and internal pathophysiological features.     

Bayesian texture segmentation of weed and crop images using reversible jump Markov chain Monte Carlo methods

Summary. A Bayesian method for segmenting weed and crop textures is described and implemented. The work forms part of a project to identify weeds and crops in images so that selective crop spraying can be carried out. An image is subdivided into blocks and each block is modelled as a single texture. The number of different textures in the image is assumed unknown. A hierarchical Bayesian procedure is used where the texture labels have a Potts model (colour Ising Markov random field) prior and the pixels within a block are distributed according to a Gaussian Markov random field, with the parameters dependent on the type of texture. We simulate from the posterior distribution by using a reversible jump Metropolis–Hastings algorithm, where the number of different texture components is allowed to vary. The methodology is applied to a simulated image and then we carry out texture segmentation on the weed and crop images that motivated the work.     

Hidden Markov mesh random field models in image analysis

This paper addresses the image modeling problem under the assumption that images can be represented by third-order, hidden Markov mesh random field models. The range of applications of the techniques described hereafter comprises the restoration of binary images, the modeling and compression of image data, as well as the segmentation of gray-level or multi-spectral images, and image sequences under the short-range motion hypothesis. We outline coherent approaches to both the problems of image modeling (pixel labeling) and estimation of model parameters (learning). We derive a real-time labeling algorithm-based on a maximum, marginal a posteriori probability criterion-for a hidden third-order Markov mesh random field model. Our algorithm achieves minimum time and space complexities simultaneously, and we describe what we believe to be the most appropriate data structures to implement it. Critical aspects of the computer simulation of a real-time implementation are discussed, down to the computer code level. We develop an (unsupervised) learning technique by which the model parameters can be estimated without ground truth information. We lay bare the conditions under which our approach can be made time-adaptive in order to be able to cope with short-range motion in dynamic image sequences. We present extensive experimental results for both static and dynamic images from a wide variety of sources. They comprise standard, infra-red and aerial images, as well as a sequence of ultrasound images of a fetus and a series of frames from a motion picture sequence. These experiments demonstrate that the method is subjectively relevant to the problems of image restoration, segmentation and modeling.     

ALLOCATION OF REMOTELY SENSED DATA USING MARKOV MODELS FOR IMAGE DATA AND PIXEL LABELS

For remotely sensed data, this paper reviews the Bayesian approach to the allocation of picture elements (pixels) to groups. Group labels are assumed a priori to be spatially correlated and, conditional on the labels, the image data are also assumed to be spatially correlated. The models considered have the property that the posterior distribution of the pixel labels given the image data inherits conditional independence constraints. Two allocation algorithms which exploit this fad are discussed. These algorithms are based on maximising the posterior distribution, and involve the use of neighbouring image and label data to update the label of any given pixel. The effect of spatial correlation in the image data on allocation performance is examined.     

An online Bayesian mixture labelling method by minimizing deviance of classification probabilities to reference labels

Solving label switching is crucial for interpreting the results of fitting Bayesian mixture models. The label switching originates from the invariance of posterior distribution to permutation of component labels. As a result, the component labels in Markov chain simulation may switch to another equivalent permutation, and the marginal posterior distribution associated with all labels may be similar and useless for inferring quantities relating to each individual component. In this article, we propose a new simple labelling method by minimizing the deviance of the class probabilities to a fixed reference labels. The reference labels can be chosen before running Markov chain Monte Carlo (MCMC) using optimization methods, such as expectation-maximization algorithms, and therefore the new labelling method can be implemented by an online algorithm, which can reduce the storage requirements and save much computation time. Using the Acid data set and Galaxy data set, we demonstrate the success of the proposed labelling method for removing the labelling switching in the raw MCMC samples.     

A finite mixture model for image segmentation

In this paper, we propose a model for image segmentation based on a finite mixture of Gaussian distributions. For each pixel of the image, prior probabilities of class memberships are specified through a Gibbs distribution, where association between labels of adjacent pixels is modeled by a class-specific term allowing for different interaction strengths across classes. We show how model parameters can be estimated in a maximum likelihood framework using Mean Field theory. Experimental performance on perturbed phantom and on real benchmark images shows that the proposed method performs well in a wide variety of empirical situations.     

Markov random field-based image subsampling method

The use of Bayesian models for the reconstruction of images degraded by both some blurring function H and the presence of noise has become popular in recent years. Making an analogy between classical degradation processes and resampling, we propose a Bayesian model for generating finer resolution images. The approach involves defining resampling, or aggregation, as a linear operator applied to an original picture to produce derived lower resolution data which represent our available experimental infor-mation. Within this framework, the operation of making inference on the orginal data can be viewed as an inverse linear transformation problem. This problem, formalized through Bayes' theorem, can be solved by the classical maximum a posteriori estimation procedure. Image local characteristics are assumed to follow a Gaussian Markov random field. Under some mild assumptions, simple, iterative and local operations are involved, making parallel 'relaxation' processing feasible. experimental results are shown on some images, for which good subsampling estimates are obtained.     

Review of the use of context in statistical image analysis

SUMMARY This paper is a review of the use of contextual information in statistical image analysis. After defining what we mean by 'context', we describe the Bayesian approach to high-level image analysis using deformable templates. We describe important aspects of work on character recognition and syntactic pattern recognition; in particular, aspects of the work which are relevant to scene understanding. We conclude with a review of some work on knowledge-based systems which use context to aid object recognition.     

Bayesian Analysis in Regression Models Using Pseudo-Likelihoods

This article deals with the issue of using a suitable pseudo-likelihood, instead of an integrated likelihood, when performing Bayesian inference about a scalar parameter of interest in the presence of nuisance parameters. The proposed approach has the advantages of avoiding the elicitation on the nuisance parameters and the computation of multidimensional integrals. Moreover, it is particularly useful when it is difficult, or even impractical, to write the full likelihood function.

We focus on Bayesian inference about a scalar regression coefficient in various regression models. First, in the context of non-normal regression-scale models, we give a theroetical result showing that there is no loss of information about the parameter of interest when using a posterior distribution derived from a pseudo-likelihood instead of the correct posterior distribution. Second, we present non trivial applications with high-dimensional, or even infinite-dimensional, nuisance parameters in the context of nonlinear normal heteroscedastic regression models, and of models for binary outcomes and count data, accounting also for possibile overdispersion. In all these situtations, we show that non Bayesian methods for eliminating nuisance parameters can be usefully incorporated into a one-parameter Bayesian analysis.     

Multi-source data fusion and super-resolution from astronomical images

Virtual observatories give us access to huge amounts of image data that are often redundant. Our goal is to take advantage of this redundancy by combining images of the same field of view into a single model. To achieve this goal, we propose to develop a multi-source data fusion method that relies on probability and band-limited signal theory. The target object is an image to be inferred from a number of blurred and noisy sources, possibly from different sensors under various conditions (i.e. resolution, shift, orientation, blur, noise...). We aim at the recovery of a compound model “image + uncertainties” that best relates to the observations and contains a maximum of useful information from the initial data set. Thus, in some cases, spatial super-resolution may be required in order to preserve the information. We propose to use a Bayesian inference scheme to invert a forward model, which describes the image formation process for each observation and takes into account some a priori knowledge (e.g. stars as point sources). This involves both automatic registration and spatial resampling, which are ill-posed inverse problems that are addressed within a rigorous Bayesian framework. The originality of the work is in devising a new technique of multi-image data fusion that provides us with super-resolution, self-calibration and possibly model selection capabilities. This approach should outperform existing methods such as resample-and-add or drizzling since it can handle different instrument characteristics for each input image and compute uncertainty estimates as well. Moreover, it is designed to also work in a recursive way, so that the model can be updated when new data become available.     

Detecting discontinuities in nonparametric regression curves and surfaces

The existence of a discontinuity in a regression function can be inferred by comparing regression estimates based on the data lying on different sides of a point of interest. This idea has been used in earlier research by Hall and Titterington (1992), Müller (1992) and later authors. The use of nonparametric regression allows this to be done without assuming linear or other parametric forms for the continuous part of the underlying regression function. The focus of the present paper is on assessing the evidence for the presence of a discontinuity within a regression function through examination of the standardised differences of ‘left’ and ‘right’ estimators at a variety of covariate values. The calculations for the test are carried out through distributional results on quadratic forms. A graphical method in the form of a reference band to highlight the sources of the evidence for discontinuities is proposed. The methods are also developed for the two covariate case where there are additional issues associated with the presence of a jump location curve. Methods for estimating this curve are also developed. All the techniques, for the one and two covariate situations, are illustrated through applications.     

Bayesian Robustness Modelling of Location and Scale Parameters

Abstract. The modelling process in Bayesian Statistics constitutes the fundamental stage of the analysis, since depending on the chosen probability laws the inferences may vary considerably. This is particularly true when conflicts arise between two or more sources of information. For instance, inference in the presence of an outlier (which conflicts with the information provided by the other observations) can be highly dependent on the assumed sampling distribution. When heavy‐tailed (e.g. t) distributions are used, outliers may be rejected whereas this kind of robust inference is not available when we use light‐tailed (e.g. normal) distributions. A long literature has established sufficient conditions on location‐parameter models to resolve conflict in various ways. In this work, we consider a location–scale parameter structure, which is more complex than the single parameter cases because conflicts can arise between three sources of information, namely the likelihood, the prior distribution for the location parameter and the prior for the scale parameter. We establish sufficient conditions on the distributions in a location–scale model to resolve conflicts in different ways as a single observation tends to infinity. In addition, for each case, we explicitly give the limiting posterior distributions as the conflict becomes more extreme.     

Performance of Variable Selection Methods in Regression Using Variations of the Bayesian Information Criterion

The Bayesian information criterion (BIC) is widely used for variable selection. We focus on the regression setting for which variations of the BIC have been proposed. A version that includes the Fisher Information matrix of the predictor variables performed best in one published study. In this article, we extend the evaluation, introduce a performance measure involving how closely posterior probabilities are approximated, and conclude that the version that includes the Fisher Information often favors regression models having more predictors, depending on the scale and correlation structure of the predictor matrix. In the image analysis application that we describe, we therefore prefer the standard BIC approximation because of its relative simplicity and competitive performance at approximating the true posterior probabilities.     

On Bayesian analyses and finite mixtures for proportions

When the results of biological experiments are tested for a possible difference between treatment and control groups, the inference is only valid if based upon a model that fits the experimental results satisfactorily. In dominant-lethal testing, foetal death has previously been assumed to follow a variety of models, including a Poisson, Binomial, Beta-binomial and various mixture models. However, discriminating between models has always been a particularly difficult problem. In this paper, we consider the data from 6 separate dominant-lethal assay experiments and discriminate between the competing models which could be used to describe them. We adopt a Bayesian approach and illustrate how a variety of different models may be considered, using Markov chain Monte Carlo (MCMC) simulation techniques and comparing the results with the corresponding maximum likelihood analyses. We present an auxiliary variable method for determining the probability that any particular data cell is assigned to a given component in a mixture and we illustrate the value of this approach. Finally, we show how the Bayesian approach provides a natural and unique perspective on the model selection problem via reversible jump MCMC and illustrate how probabilities associated with each of the different models may be calculated for each data set. In terms of estimation we show how, by averaging over the different models, we obtain reliable and robust inference for any statistic of interest.     

Tracking multiple moving objects in images using Markov Chain Monte Carlo

A new Bayesian state and parameter learning algorithm for multiple target tracking models with image observations are proposed. Specifically, a Markov chain Monte Carlo algorithm is designed to sample from the posterior distribution of the unknown time-varying number of targets, their birth, death times and states as well as the model parameters, which constitutes the complete solution to the specific tracking problem we consider. The conventional approach is to pre-process the images to extract point observations and then perform tracking, i.e. infer the target trajectories. We model the image generation process directly to avoid any potential loss of information when extracting point observations using a pre-processing step that is decoupled from the inference algorithm. Numerical examples show that our algorithm has improved tracking performance over commonly used techniques, for both synthetic examples and real florescent microscopy data, especially in the case of dim targets with overlapping illuminated regions.     

Bayesian variable selection and estimation in maximum entropy quantile regression

Quantile regression has gained increasing popularity as it provides richer information than the regular mean regression, and variable selection plays an important role in the quantile regression model building process, as it improves the prediction accuracy by choosing an appropriate subset of regression predictors. Unlike the traditional quantile regression, we consider the quantile as an unknown parameter and estimate it jointly with other regression coefficients. In particular, we adopt the Bayesian adaptive Lasso for the maximum entropy quantile regression. A flat prior is chosen for the quantile parameter due to the lack of information on it. The proposed method not only addresses the problem about which quantile would be the most probable one among all the candidates, but also reflects the inner relationship of the data through the estimated quantile. We develop an efficient Gibbs sampler algorithm and show that the performance of our proposed method is superior than the Bayesian adaptive Lasso and Bayesian Lasso through simulation studies and a real data analysis.     

A study of simulated annealing and a revised cascade algorithm for image reconstruction

We describe an image reconstruction problem and the computational difficulties arising in determining the maximum a posteriori (MAP) estimate. Two algorithms for tackling the problem, iterated conditional modes (ICM) and simulated annealing, are usually applied pixel by pixel. The performance of this strategy can be poor, particularly for heavily degraded images, and as a potential improvement Jubb and Jennison (1991) suggest the cascade algorithm in which ICM is initially applied to coarser images formed by blocking squares of pixels. In this paper we attempt to resolve certain criticisms of cascade and present a version of the algorithm extended in definition and implementation. As an illustration we apply our new method to a synthetic aperture radar (SAR) image. We also carry out a study of simulated annealing, with and without cascade, applied to a more tractable minimization problem from which we gain insight into the properties of cascade algorithms.     

Comparison of a genetic algorithm and simulated annealing in an application to statistical image reconstruction

Genetic algorithms (GAs) are adaptive search techniques designed to find near-optimal solutions of large scale optimization problems with multiple local maxima. Standard versions of the GA are defined for objective functions which depend on a vector of binary variables. The problem of finding the maximum a posteriori (MAP) estimate of a binary image in Bayesian image analysis appears to be well suited to a GA as images have a natural binary representation and the posterior image probability is a multi-modal objective function. We use the numerical optimization problem posed in MAP image estimation as a test-bed on which to compare GAs with simulated annealing (SA), another all-purpose global optimization method. Our conclusions are that the GAs we have applied perform poorly, even after adaptation to this problem. This is somewhat unexpected, given the widespread claims of GAs' effectiveness, but it is in keeping with work by Jennison and Sheehan (1995) which suggests that GAs are not adept at handling problems involving a great many variables of roughly equal influence.We reach more positive conclusions concerning the use of the GA's crossover operation in recombining near-optimal solutions obtained by other methods. We propose a hybrid algorithm in which crossover is used to combine subsections of image reconstructions obtained using SA and we show that this algorithm is more effective and efficient than SA or a GA individually.