An Automatic Level Set Based Liver Segmentation from MRI Data Sets

A fast and accurate liver segmentation method is a challenging work in medical image analysis area. Liver segmentation is an important process for computer-assisted diagnosis, pre-evaluation of liver transplantation and therapy planning of liver tumors. There are several advantages of magnetic resonance imaging such as free form ionizing radiation and good contrast visualization of soft tissue. Also, innovations in recent technology and image acquisition techniques have made magnetic resonance imaging a major tool in modern medicine. However, the use of magnetic resonance images for liver segmentation has been slow when we compare applications with the central nervous systems and musculoskeletal. The reasons are irregular shape, size and position of the liver, contrast agent effects and similarities of the gray values of neighbor organs. Therefore, in this study, we present a fully automatic liver segmentation method by using an approximation of the level set based contour evolution from T2 weighted magnetic resonance data sets. The method avoids solving partial differential equations and applies only integer operations with a two-cycle segmentation algorithm. The efficiency of the proposed approach is achieved by applying the algorithm to all slices with a constant number of iteration and performing the contour evolution without any user defined initial contour. The obtained results are evaluated with four different similarity measures and they show that the automatic segmentation approach gives successful results

Active contours for intensity inhomogeneous image segmentation

La “inhomogeneidad” (falta d'homogeneïtat) d'intensitat és un problema ben conegut en la segmentació d'imatges, la qual cosa afecta la precisió dels mètodes de segmentació basats en la intensitat. En aquesta tesi, es proposen mètodes de contorn actiu basat en fronteres i regions per segmentar imatges inhomogènies. En primer lloc, s'ha proposat un mètode de contorn actiu basat en fronteres mitjançant Diferència de Gaussianes (DoG), que ajuda a segmentar l'estructura global de la imatge. En segon lloc, hem proposat un mètode de contorn actiu basat en regions per corregir i segmentar imatges inhomogènies. S'ha utilitzat un nucli de transformació de fase (phase stretch transform - PST) per calcular noves intensitats mitjanes i camps de polarització, que s'empren per definir una imatge ajustada de polarització. En tercer lloc, s'ha proposat un altre mètode de contorn actiu basat en regions utilitzant un funcional d'energia basat en imatges ajustades locals i globals. El camp de polarització s'aproxima amb una distribució Gaussiana i el biaix de les regions no homogènies es corregeix dividint la imatge original pel camp aproximat de polarització. Finalment, s'ha proposat un mètode híbrid de contorns actius multifàsic (quatre fases) per dividir una imatge de RM cerebral en tres regions diferents: matèria blanca (WM), matèria grisa (GM) i líquid cefaloraquidi (CSF). En aquest treball, també s'ha dissenyat un mètode de post-processat (correcció de píxels) per millorar la precisió de les regions WM, GM i CSF segmentades. S'han utilitzat resultats experimentals tant amb imatges sintètiques com amb imatges reals de RM del cervell per a una comparació quantitativa i qualitativa amb mètodes de contorns actius de l'estat de l'art per mostrar els avantatges de les tècniques de segmentació proposades.La “inhomogeneidad” (falta de homogeneidad) de intensidad es un problema bien conocido en la segmentación de imágenes, lo que afecta la precisión de los métodos de segmentación basados en la intensidad. En esta tesis, se proponen métodos de contorno activo basado en bordes y regiones para segmentar imágenes inhomogéneas. En primer lugar, se ha propuesto un método de contorno activo basado en fronteras mediante Diferencia de Gaussianas (DoG), que ayuda a segmentar la estructura global de la imagen. En segundo lugar, hemos propuesto un método de contorno activo basado en regiones para corregir y segmentar imágenes inhomogéneas. Se ha utilizado un núcleo de transformación de fase (phase stretch transform - PST) para calcular nuevas intensidades medias y campos de polarización, que se emplean para definir una imagen ajustada de polarización. En tercer lugar, se ha propuesto otro método de contorno activo basado en regiones utilizando un funcional de energía basado en imágenes ajustadas locales y globales. El campo de polarización se aproxima con una distribución Gaussiana y el sesgo de las regiones no homogéneas se corrige dividiendo la imagen original por el campo aproximado de polarización. Finalmente, se ha propuesto un método híbrido de contornos activos multifásico (cuatro fases) para dividir una imagen de RM cerebral en tres regiones distintas: materia blanca (WM), materia gris (GM) y líquido cefalorraquídeo (CSF). En este trabajo, también se ha diseñado un método de post-procesado (corrección de píxeles) para mejorar la precisión de las regiones WM, GM y CSF segmentadas. Se han utilizado resultados experimentales tanto con imágenes sintéticas como con imágenes reales de RM del cerebro para una comparación cuantitativa y cualitativa con métodos de contornos activos del estado del arte para mostrar las ventajas de las técnicas de segmentación propuestas.Intensity inhomogeneity is a well-known problem in image segmentation, which affects the accuracy of intensity-based segmentation methods. In this thesis, edge-based and region-based active contour methods are proposed to segment intensity inhomogeneous images. Firstly, we have proposed an edge-based active contour method based on the Difference of Gaussians (DoG), which helps to segment the global structure of the image. Secondly, we have proposed a region-based active contour method to both correct and segment intensity inhomogeneous images. A phase stretch transform (PST) kernel has been used to compute new intensity means and bias field, which are employed to define a bias fitted image. Thirdly, another region-based active contour method has been proposed using an energy functional based on local and global fitted images. Bias field is approximated with a Gaussian distribution and the bias of intensity inhomogeneous regions is corrected by dividing the original image by the approximated bias field. Finally, a hybrid region-based multiphase (four-phase) active contours method has been proposed to partition a brain MR image into three distinct regions: white matter (WM), gray matter (GM) and cerebrospinal fluid (CSF). In this work, a post-processing (pixel correction) method has also been devised to improve the accuracy of the segmented WM, GM and CSF regions. Experimental results with both synthetic and real brain MR images have been used for a quantitative and qualitative comparison with state-of-the-art active contour methods to show the advantages of the proposed segmentation techniques

Segmentation of Intensity Inhomogeneous Brain MR Images Using Active Contours

Segmentation of intensity inhomogeneous regions is a well-known problem in image analysis applications. This paper presents a region-based active contour method for image segmentation, which properly works in the context of intensity inhomogeneity problem. The proposed region-based active contour method embeds both region and gradient information unlike traditional methods. It contains mainly two terms, area and length, in which the area term practices a new region-based signed pressure force (SPF) function, which utilizes mean values from a certain neighborhood using the local binary fitted (LBF) energy model. In turn, the length term uses gradient information. The novelty of our method is to locally compute new SPF function, which uses local mean values and is able to detect boundaries of the homogenous regions. Finally, a truncated Gaussian kernel is used to regularize the level set function, which not only regularizes it but also removes the need of computationally expensive reinitialization. The proposed method targets the segmentation problem of intensity inhomogeneous images and reduces the time complexity among locally computed active contour methods. The experimental results show that the proposed method yields better segmentation result as well as less time complexity compared with the state-of-the-art active contour methods

Segmentation of Intensity-Corrupted Medical Images Using Adaptive Weight-Based Hybrid Active Contours

6Segmentation accuracy is an important criterion for evaluating the performance of segmentation techniques used to extract objects of interest from images, such as the active contour model. However, segmentation accuracy can be affected by image artifacts such as intensity inhomogeneity, which makes it difficult to extract objects with inhomogeneous intensities. To address this issue, this paper proposes a hybrid region-based active contour model for the segmentation of inhomogeneous images. The proposed hybrid energy functional combines local and global intensity functions; an incorporated weight function is parameterized based on local image contrast. The inclusion of this weight function smoothens the contours at different intensity level boundaries, thereby yielding improved segmentation. The weight function suppresses false contour evolution and also regularizes object boundaries. Compared with other state-of-the-art methods, the proposed approach achieves superior results over synthetic and real images. Based on a quantitative analysis over the mini-MIAS and PH2 databases, the superiority of the proposed model in terms of segmentation accuracy, as compared with the ground truths, was confirmed. Furthermore, when using the proposed model, the processing time for image segmentation is lower than those when using other methods.openopenMemon A.A.; Soomro S.; Shahid M.T.; Munir A.; Niaz A.; Choi K.N.Memon, A. A.; Soomro, S.; Shahid, M. T.; Munir, A.; Niaz, A.; Choi, K. N

Brain MR Image Segmentation Based on an Adaptive Combination of Global and Local Fuzzy Energy

This paper presents a novel fuzzy algorithm for segmentation of brain MR images and simultaneous estimation of intensity inhomogeneity. The proposed algorithm defines an objective function including a local fuzzy energy and a global fuzzy energy. Based on the assumption that the local image intensities belonging to each different tissue satisfy Gaussian distributions with different means, we derive the local fuzzy energy by utilizing maximum a posterior probability (MAP) and Bayes rule. The global fuzzy energy is defined by measuring the distance between the original image and the corresponding inhomogeneity-free image. We combine the global fuzzy energy with the local fuzzy energy using an adaptive weight function whose value varies with the local contrast of the image. This combination enables the proposed algorithm to address intensity inhomogeneity and to improve the accuracy of segmentation and its robustness to initialization. Besides, the proposed algorithm incorporates neighborhood spatial information into the membership function to reduce the impact of noise. Experimental results for synthetic and real images validate the desirable performances of the proposed algorithm

Active skeleton for bacteria modeling

The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualizationto appear i