A Variational Model for Object Segmentation Using Boundary Information and Shape Prior Driven by the Mumford-Shah Functional

In this paper, we propose a new variational model to segment an object belonging to a given shape space using the active contour method, a geometric shape prior and the Mumford-Shah functional. The core of our model is an energy functional composed by three complementary terms. The first one is based on a shape model which constrains the active contour to get a shape of interest. The second term detects object boundaries from image gradients. And the third term drives globally the shape prior and the active contour towards a homogeneous intensity region. The segmentation of the object of interest is given by the minimum of our energy functional. This minimum is computed with the calculus of variations and the gradient descent method that provide a system of evolution equations solved with the well-known level set method. We also prove the existence of this minimum in the space of functions with bounded variation. Applications of the proposed model are presented on synthetic and medical image

Level Set KSVD

We present a new algorithm for image segmentation - Level-set KSVD. Level-set KSVD merges the methods of sparse dictionary learning for feature extraction and variational level-set method for image segmentation. Specifically, we use a generalization of the Chan-Vese functional with features learned by KSVD. The motivation for this model is agriculture based. Aerial images are taken in order to detect the spread of fungi in various crops. Our model is tested on such images of cotton fields. The results are compared to other methods.Comment: 25 pages, 14 figures. Submitted to IJC

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

Image segmentation with variational active contours

An important branch of computer vision is image segmentation. Image segmentation aims at extracting meaningful objects lying in images either by dividing images into contiguous semantic regions, or by extracting one or more specific objects in images such as medical structures. The image segmentation task is in general very difficult to achieve since natural images are diverse, complex and the way we perceive them vary according to individuals. For more than a decade, a promising mathematical framework, based on variational models and partial differential equations, have been investigated to solve the image segmentation problem. This new approach benefits from well-established mathematical theories that allow people to analyze, understand and extend segmentation methods. Moreover, this framework is defined in a continuous setting which makes the proposed models independent with respect to the grid of digital images. This thesis proposes four new image segmentation models based on variational models and the active contours method. The active contours or snakes model is more and more used in image segmentation because it relies on solid mathematical properties and its numerical implementation uses the efficient level set method to track evolving contours. The first model defined in this dissertation proposes to determine global minimizers of the active contour/snake model. Despite of great theoretic properties, the active contours model suffers from the existence of local minima which makes the initial guess critical to get satisfactory results. We propose to couple the geodesic/geometric active contours model with the total variation functional and the Mumford-Shah functional to determine global minimizers of the snake model. It is interesting to notice that the merging of two well-known and "opposite" models of geodesic/geometric active contours, based on the detection of edges, and active contours without edges provides a global minimum to the image segmentation algorithm. The second model introduces a method that combines at the same time deterministic and statistical concepts. We define a non-parametric and non-supervised image classification model based on information theory and the shape gradient method. We show that this new segmentation model generalizes, in a conceptual way, many existing models based on active contours, statistical and information theoretic concepts such as mutual information. The third model defined in this thesis is a variational model that extracts in images objects of interest which geometric shape is given by the principal components analysis. The main interest of the proposed model is to combine the three families of active contours, based on the detection of edges, the segmentation of homogeneous regions and the integration of geometric shape prior, in order to use simultaneously the advantages of each family. Finally, the last model presents a generalization of the active contours model in scale spaces in order to extract structures at different scales of observation. The mathematical framework which allows us to define an evolution equation for active contours in scale spaces comes from string theory. This theory introduces a mathematical setting to process a manifold such as an active contour embedded in higher dimensional Riemannian spaces such as scale spaces. We thus define the energy functional and the evolution equation of the multiscale active contours model which can evolve in the most well-known scale spaces such as the linear or the curvature scale space

A Variational Model for Object Segmentation Using Boundary Information, Statistical Shape Prior and the Mumford-Shah Functional

In this paper, we propose a variational model to segment an object belonging to a given scale space using the active contour method, a geometric shape prior and the Mumford-Shah functional. We define an energy functional composed by three complementary terms. The first one detects object boundaries from image gradients. The second term constrains the active contour to get a shape compatible with a statistical shape model of the shape of interest. And the third part drives globally the shape prior and the active contour towards a homogeneous intensity region. The segmentation of the object of interest is given by the minimum of our energy functional. This minimum is computed with the calculus of variations and the gradient descent method that provide a system of evolution equations solved with the well-known level set method. We also prove the existence of this minimum in the space of functions with bounded variation. Applications of the proposed model are presented on synthetic and medical images

Segmentation of brain tumors in MRI images using three-dimensional active contour without edge

Brain tumor segmentation in magnetic resonance imaging (MRI) is considered a complex procedure because of the variability of tumor shapes and the complexity of determining the tumor location, size, and texture. Manual tumor segmentation is a time-consuming task highly prone to human error. Hence, this study proposes an automated method that can identify tumor slices and segment the tumor across all image slices in volumetric MRI brain scans. First, a set of algorithms in the pre-processing stage is used to clean and standardize the collected data. A modified gray-level co-occurrence matrix and Analysis of Variance (ANOVA) are employed for feature extraction and feature selection, respectively. A multi-layer perceptron neural network is adopted as a classifier, and a bounding 3D-box-based genetic algorithm is used to identify the location of pathological tissues in the MRI slices. Finally, the 3D active contour without edge is applied to segment the brain tumors in volumetric MRI scans. The experimental dataset consists of 165 patient images collected from the MRI Unit of Al-Kadhimiya Teaching Hospital in Iraq. Results of the tumor segmentation achieved an accuracy of 89% +/- 4.7% compared with manual processes

Monitoring of lung cancer patients during radiotherapy using combined texture and level set analysis of CBCT images

In the UK, radiotherapy (RT) contributes to a large amount of lung cancer treatment while its imaging information is limited to computed tomography (CT) and cone beam CT (CBCT) images. The oncologists defines the gross tumour volume (GTV) manually on the planning-CT images before any treatment starts. Manual contouring suffers from many disadvantages and the bad quality of CBCT images makes it very challenging for the clinicians to observe tumour behaviour in the time of treatment. CBCT is the only kind of image available throughout the whole course of RT which is used in the mechanical procedure of adjusting patient position before starting each session of treatment and is not generally used by clinicians for monitoring the tumour. The goal of this thesis is to develop a tumour detection model of non-small cell lung tumours on CBCT images in the course of treatment. By developing this process clinicians will be greatly aided in their role, helping them to detect lung tumours to allow better diagnosis and improving patient treatment outcome. Therefore a new segmentation approach is proposed as combined texture analysis and level set model. It has the potential capability to track the variation of the tumour shape over time of treatment solely using CBCT images, and evaluate the accountability of RT for different patients. The texture analysis, second-order statistics obtained from gray level co-occurrence matrices (GLCM), highlight the tumour boundary and help Chan-Vese and Li level set models convergence in the segmentation process. Further on a new parallel level sets model is proposed by combining Chan-Vese and Li models in the concept of vector-valued image level set. This new approach overcomes the difficulties in the parameter settings of current models by giving more freedom of choice in tuning parameters as well as selecting level set models. All proposed models were evaluated on the dataset of fifty different patients suffered from non-small cell lung cancer. For the validation procedure, qualitative analysis was carried out by an oncologist as there is no ground truth in each CBCT image during RT. The decision of the oncologist based on patient history has proven the results of this work. For quantitative analysis, the Dice coefficient is used to evaluate the tumour segmentation results on CBCT compared to GTV on CT images prior to treatment to evaluate the amount of changes especially after one third of RT on CBCT #10. Additionally, the proposed segmentation models had the accuracy of almost 90% to the GTV delineated by the oncologist for the only one patient in the dataset having GTV on CBCT images which proved the ability of these models for further analysis during the absence of GTV on CBCTs. For improving this research and helping the clinicians at most, the proposed segmentation model can be used as a notification model to assist clinicians for a better understanding of the tumour during RT and subsequent use in offline adaptive radiotherapy (ART)

A comparative evaluation for liver segmentation from spir images and a novel level set method using signed pressure force function

Thesis (Doctoral)--Izmir Institute of Technology, Electronics and Communication Engineering, Izmir, 2013Includes bibliographical references (leaves: 118-135)Text in English; Abstract: Turkish and Englishxv, 145 leavesDeveloping a robust method for liver segmentation from magnetic resonance images is a challenging task due to similar intensity values between adjacent organs, geometrically complex liver structure and injection of contrast media, which causes all tissues to have different gray level values. Several artifacts of pulsation and motion, and partial volume effects also increase difficulties for automatic liver segmentation from magnetic resonance images. In this thesis, we present an overview about liver segmentation methods in magnetic resonance images and show comparative results of seven different liver segmentation approaches chosen from deterministic (K-means based), probabilistic (Gaussian model based), supervised neural network (multilayer perceptron based) and deformable model based (level set) segmentation methods. The results of qualitative and quantitative analysis using sensitivity, specificity and accuracy metrics show that the multilayer perceptron based approach and a level set based approach which uses a distance regularization term and signed pressure force function are reasonable methods for liver segmentation from spectral pre-saturation inversion recovery images. However, the multilayer perceptron based segmentation method requires a higher computational cost. The distance regularization term based automatic level set method is very sensitive to chosen variance of Gaussian function. Our proposed level set based method that uses a novel signed pressure force function, which can control the direction and velocity of the evolving active contour, is faster and solves several problems of other applied methods such as sensitivity to initial contour or variance parameter of the Gaussian kernel in edge stopping functions without using any regularization term