Recent Advances in Single-Particle Tracking: Experiment and Analysis

This Special Issue of Entropy, titled “Recent Advances in Single-Particle Tracking: Experiment and Analysis”, contains a collection of 13 papers concerning different aspects of single-particle tracking, a popular experimental technique that has deeply penetrated molecular biology and statistical and chemical physics. Presenting original research, yet written in an accessible style, this collection will be useful for both newcomers to the field and more experienced researchers looking for some reference. Several papers are written by authorities in the field, and the topics cover aspects of experimental setups, analytical methods of tracking data analysis, a machine learning approach to data and, finally, some more general issues related to diffusion

Estimation of anisotropic Gaussian fields through Radon transform

26 pagesInternational audienceWe estimate the anisotropic index of an anisotropic fractional Brownian field. For all directions, we give a convergent estimator of the value of the anisotropic index in this direction, based on generalized quadratic variations. We also prove a central limit theorem. First we present a result of identification that relies on the asymptotic behavior of the spectral density of a process. Then, we define Radon transforms of the anisotropic fractional Brownian field and prove that these processes admit a spectral density satisfying the previous assumptions. Finally we use simulated fields to test the proposed estimator in different anisotropic and isotropic cases. Results show that the estimator behaves similarly in all cases and is able to detect anisotropy quite accurately

An Information Theoretic Approach For Feature Selection And Segmentation In Posterior Fossa Tumors

Posterior Fossa (PF) is a type of brain tumor located in or near brain stem and cerebellum. About 55% - 70 % pediatric brain tumors arise in the posterior fossa, compared with only 15% - 20% of adult tumors. For segmenting PF tumors we should have features to study the characteristics of tumors. In literature, different types of texture features such as Fractal Dimension (FD) and Multifractional Brownian Motion (mBm) have been exploited for measuring randomness associated with brain and tumor tissues structures, and the varying appearance of tissues in magnetic resonance images (MRI). For selecting best features techniques such as neural network and boosting methods have been exploited. However, neural network cannot descirbe about the properties of texture features. We explore methods such as information theroetic methods which can perform feature selection based on properties of texture features. The primary contribution of this dissertation is investigating efficacy of different image features such as intensity, fractal texture, and level - set shape in segmentation of PF tumor for pediatric patients. We explore effectiveness of using four different feature selection and three different segmentation techniques respectively to discriminate tumor regions from normal tissue in multimodal brain MRI. Our research suggest that Kullback - Leibler Divergence (KLD) measure for feature ranking and selection and Expectation Maximization (EM) algorithm for feature fusion and tumor segmentation offer the best performance for the patient data in this study. To improve segmentation accuracy, we need to consider abnormalities such as cyst, edema and necrosis which surround tumors. In this work, we exploit features which describe properties of cyst and technique which can be used to segment it. To achieve this goal, we extend the two class KLD techniques to multiclass feature selection techniques, so that we can effectively select features for tumor, cyst and non tumor tissues. We compute segemntation accuracy by computing number of pixels segemented to total number of pixels for the best features. For automated process we integrate the inhomoheneity correction, feature selection using KLD and segmentation in an integrated EM framework. To validate results we have used similarity coefficients for computing the robustness of segmented tumor and cyst

The Contour Extraction of Cup in Fundus Images for Glaucoma Detection

Glaucoma is the second leading cause of blindness in the world; therefore the detection of glaucoma is required. The detection of glaucoma is used to distinguish whether a patient's eye is normal or glaucoma. An expert observed the structure of the retina using fundus image to detect glaucoma. In this research, we propose feature extraction method based on cup area contour using fundus images to detect glaucoma. Our proposed method has been evaluated on 44 fundus images consisting of 23 normal and 21 glaucoma. The data is divided into two parts: firstly, used to the learning phase and secondly, used to the testing phase. In order to identify the fundus images including the class of normal or glaucoma, we applied Support Vector Machines (SVM) method. The performance of our method achieves the accuracy of 94.44%

2D Shape Recognition Using Information Theoretic Kernels

In this paper, a novel approach for contour-based 2D shape recognition is proposed, using a recently intro-duced class of information theoretic kernels. This kind of kernels, based on a non-extensive generalization of the classical Shannon information theory, are defined on probability measures. In the proposed approach, chain code representations are first extracted from the contours; then n-gram statistics are computed and used as input to the information theoretic kernels. We tested different versions of such kernels, using support vector machine and nearest neighbor classifiers. An experi-mental evaluation on the chicken pieces dataset shows that the proposed approach outperforms the current state-of-the-art methods. 1

The Scale Invariant Wigner Spectrum Estimation of Gaussian Locally Self-Similar Processes

We study locally self-similar processes (LSSPs) in Silverman's sense. By deriving the minimum mean-square optimal kernel within Cohen's class counterpart of time-frequency representations, we obtain an optimal estimation for the scale invariant Wigner spectrum (SIWS) of Gaussian LSSPs. The class of estimators is completely characterized in terms of kernels, so the optimal kernel minimizes the mean-square error of the estimation. We obtain the SIWS estimation for two cases: global and local, where in the local case, the kernel is allowed to vary with time and frequency. We also introduce two generalizations of LSSPs: the locally self-similar chrip process and the multicomponent locally self-similar process, and obtain their optimal kernels. Finally, the performance and accuracy of the estimation is studied via simulation.Comment: 28 page

Self-similar random fields and rescaled random balls models

International audienceWe study generalized random fields which arise as rescaling limits of spatial configurations of uniformly scattered random balls as the mean radius of the balls tends to 0 or infinity. Assuming that the radius distribution has a power law behavior, we prove that the centered and renormalized random balls field admits a limit with strong spatial dependence. In particular, our approach provides a unified framework to obtain all self-similar, stationary and isotropic Gaussian fields. In addition to investigating stationarity and self-similarity properties, we give L^2-representations of the asymptotic generalized random fields viewed as continuous random linear functionals

Feature-Guided Deep Radiomics for Glioblastoma Patient Survival Prediction

Glioblastoma is recognized as World Health Organization (WHO) grade IV glioma with an aggressive growth pattern. The current clinical practice in diagnosis and prognosis of Glioblastoma using MRI involves multiple steps including manual tumor sizing. Accurate identification and segmentation of multiple abnormal tissues within tumor volume in MRI is essential for precise survival prediction. Manual tumor and abnormal tissue detection and sizing are tedious, and subject to inter-observer variability. Consequently, this work proposes a fully automated MRI-based glioblastoma and abnormal tissue segmentation, and survival prediction framework. The framework includes radiomics feature-guided deep neural network methods for tumor tissue segmentation; followed by survival regression and classification using these abnormal tumor tissue segments and other relevant clinical features. The proposed multiple abnormal tumor tissue segmentation step effectively fuses feature-based and feature-guided deep radiomics information in structural MRI. The survival prediction step includes two representative survival prediction pipelines that combine different feature selection and regression approaches. The framework is evaluated using two recent widely used benchmark datasets from Brain Tumor Segmentation (BraTS) global challenges in 2017 and 2018. The best overall survival pipeline in the proposed framework achieves leave-one-out cross-validation (LOOCV) accuracy of 0.73 for training datasets and 0.68 for validation datasets, respectively. These training and validation accuracies for tumor patient survival prediction are among the highest reported in literature. Finally, a critical analysis of radiomics features and efficacy of these features in segmentation and survival prediction performance is presented as lessons learned