Variational models and numerical algorithms for selective image segmentation

This thesis deals with the numerical solution of nonlinear partial differential equations and their application in image processing. The differential equations we deal with here arise from the minimization of variational models for image restoration techniques (such as denoising) and recognition of objects techniques (such as segmentation). Image denoising is a technique aimed at restoring a digital image that has been contaminated by noise while segmentation is a fundamental task in image analysis responsible for partitioning an image as sub-regions or representing the image into something that is more meaningful and easier to analyze such as extracting one or more specific objects of interest in images based on relevant information or a desired feature. Although there has been a lot of research in the restoration of images, the performance of such methods is still poor, especially when the images have a high level of noise or when the algorithms are slow. Task of the segmentation is even more challenging problem due to the difficulty of delineating, even manually, the contours of the objects of interest. The problems are often due to low contrast, fuzzy contours, similar intensities with adjacent objects, or the objects to be extracted having no real contours. The first objective of this work is to develop fast image restoration and segmentation methods which provide better denoising and fast and robust performance for image segmentation. The contribution presented here is the development of a restarted homotopy analysis method which has been designed to be easily adaptable to various types of image processing problems. As a second research objective we propose a framework for image selective segmentation which partitions an image based on the information known in advance of the object/objects to be extracted (for example the left kidney is the target to be extracted in a CT image and the prior knowledge is a few markers in this object of interest). This kind of segmentation appears especially in medical applications. Medical experts usually estimate and manually draw the boundaries of the organ/organs based on their experience. Our aim is to introduce automatic segmentation of the object of interest as a contribution not only to the way doctors and surgeons diagnose and operate but to other fields as well. The proposed methods showed success in segmenting different objects and perform well in different types of images not only in two-dimensional but in three-dimensional images as well

Automated Vessel Segmentation Using Infinite Perimeter Active Contour Model with Hybrid Region Information with Application to Retinal Images

Automated detection of blood vessel structures is becoming of crucial interest for better management of vascular disease. In this paper, we propose a new infinite active contour model that uses hybrid region information of the image to approach this problem. More specifically, an infinite perimeter regularizer, provided by using L 2 Lebesgue measure of the γ-neighborhood of boundaries, allows for better detection of small oscillatory (branching) structures than the traditional models based on the length of a feature's boundaries (i.e., H 1 Hausdorff measure). Moreover, for better general segmentation performance, the proposed model takes the advantage of using different types of region information, such as the combination of intensity information and local phase based enhancement map. The local phase based enhancement map is used for its superiority in preserving vessel edges while the given image intensity information will guarantee a correct feature's segmentation. We evaluate the performance of the proposed model by applying it to three public retinal image datasets (two datasets of color fundus photography and one fluorescein angiography dataset). The proposed model outperforms its competitors when compared with other widely used unsupervised and supervised methods. For example, the sensitivity (0.742), specificity (0.982) and accuracy (0.954) achieved on the DRIVE dataset are very close to those of the second observer's annotations

An improved model for joint segmentation and registration based on linear curvature smoother

Image segmentation and registration are two of the most challenging tasks in medical imaging. They are closely related because both tasks are often required simultaneously. In this article, we present an improved variational model for a joint segmentation and registration based on active contour without edges and the linear curvature model. The proposed model allows large deformation to occur by solving in this way the difficulties other jointly performed segmentation and registration models have in case of encountering multiple objects into an image or their highly dependence on the initialisation or the need for a pre-registration step, which has an impact on the segmentation results. Through different numerical results, we show that the proposed model gives correct registration results when there are different features inside the object to be segmented or features that have clear boundaries but without fine details in which the old model would not be able to cope. </jats:p

Coupled shape priors for dynamic segmentation of dendritic spines

Segmentation of biomedical images is a challenging task, especially when there is low quality or missing data. The use of prior information can provide significant assistance for obtaining more accurate results. In this paper we propose a new approach for dendritic spine segmentation from microscopic images over time, which is motivated by incorporating shape information from previous time points to segment a spine in the current time point. In particular, using a training set consisting of spines in two consecutive time points to construct coupled shape priors, and given the segmentation in the previous time point, we can improve the segmentation process of the spine in the current time point. Our approach has been evaluated on 2-photon microscopy images of dendritic spines and its effectiveness has been demonstrated by both visual and quantitative results

Automatic dendritic spine detection using multiscale dot enhancement filters and sift features

Statistical characterization of morphological changes of dendritic spines is becoming of crucial interest in the field of neurobiology. Automatic detection and segmentation of dendritic spines promises significant reductions on the time spent by the scientists and reduces the subjectivity concerns. In this paper, we present two approaches for automated detection of dendritic spines in 2-photon laser scanning microscopy (2pLSM) images. The first method combines the idea of dot enhancement filters with information from the dendritic skeleton. The second method learns an SVM classifier by utilizing some pre-labeled SIFT feature descriptors and uses the classifier to detect dendritic spines in new images. For the segmentation of detected spines, we employ a watershed-variational segmentation algorithm. We evaluate the proposed approaches by comparing with manual segmentations of domain experts and the results of a noncommercial software, NeuronIQ. Our methods produce promising detection rate with high segmentation accuracy thus can serve as a useful tool for spine analysis

Nonparametric joint shape and feature priors for segmentation of dendritic spines

Multimodal shape density estimation is a challenging task in many biomedical image segmentation problems. Existing techniques in the literature estimate the underlying shape distribution by extending Parzen density estimator to the space of shapes. Such density estimates are only expressed in terms of distances between shapes which may not be sufficient for ensuring accurate segmentation when the observed intensities provide very little information about the object boundaries. In such scenarios, employing additional shape-dependent discriminative features as priors and exploiting both shape and feature priors can aid to the segmentation process. In this paper, we propose a segmentation algorithm that uses nonparametric joint shape and feature priors using Parzen density estimator. The joint prior density estimate is expressed in terms of distances between shapes and distances between features. We incorporate the learned joint shape and feature prior distribution into a maximum a posteriori estimation framework for segmentation. The resulting optimization problem is solved using active contours. We present experimental results on dendritic spine segmentation in 2-photon microscopy images which involve a multimodal shape density

Automated dendritic spine tracking on 2-photon microscopic images (2-Foton mikroskopi görüntülerinde otomatik dendritik diken takibi)

The rapid and spontaneous morphological changes of dendritic spines have been an important observation to understand how information is stored in brain. Manual assessment of spine structure has been a useful tool to understand the differences between wild type (normal) and diseased cases. In order to perform a more through analysis, automatic tools need to be developed due to the immense amount of image data collected throughout the experiments. Additionally, dendritic spines are very dynamic structures and florescence microscopy contains high level of noise, blur and shift due to the optical properties. In this study, we track locations of dendritic spines in a full series of a time-lapse two photon microscopic images. To achieve this we propose a combined detection and tracking framework. For the detection we use a SIFT based algorithm, while the tracking requires a combination of registration and distance based spine matching. Experimental results show that this technique helps to track detected spines in time series even though the noise or blur deformed the image and complicated the detection

Image-selective segmentation model for multi-regions within the object of interest with application to medical disease

Detection and extraction of an object of interest and accurate boundaries segmentation in a given image has been of interest in the last decades due to its application in different fields. To successfully segment a single object, interactive/selective segmentation techniques has been developed as a supplement to the existing global segmentation techniques. Even though existing interactive/selective segmentation techniques perform well in segmenting the images with prominent edges, those methods are less efficient or even fail in segmenting images having multi-regions of different intensity scale. In this paper, we design a new variational selective segmentation model which incorporates the idea of area-based fitting term along with a signed pressure force function based on a generalized average into a variational energy function. The new model is capable to capture the object of interest which can be single or multi-region within the object of interest. To evaluate the performance of our new model, we compare our results with state of the art models by showing same efficiency and reliability on detecting single-region and an outperforming for multi-region selective segmentation. Comparison tests were carried out on synthetic and real data images