Application of active contours with expert knowledge to heart ventricle segmentation

Automatic heart ventricle segmentation in CT heart images can be an element of system supporting pulmonary embolism diagnosis. To solve that problem in this paper an application of two classical active contour models, snakes and geometric active contours, is proposed. The prepared implementation uses the unified model of those techniques which allows to define forces acting upon a contour only once. The nature of the images causes that the process of force construction requires additional expert knowledge since using only the information visible in the image satisfactory results cannot be obtained

Método de segmentação de objectos em imagens baseado em contornos activos e algoritmo genético

Este trabalho apresenta um método de segmentação de imagem baseado em modelos deformáveis, em particular contornos ativos do tipo balão . O contorno inicial é visto como uma curva elástica que deve ser deformada através da minimização de uma função de energia entre as forças internas da curva relacionadas com a suavidade, elasticidade e rigidez do contorno deformável e as forças externas potencial de atração do contorno em direção ao objeto de interesse geradas a partir da imagem. Este contorno inicial, neste caso inserido no interior do objeto, evolui sob a ação das forças internas e externas. Por este motivo, o modelo deformável de balão considerado equivale a insuflar ou expandir um contorno, isto é a curva inicial definida, até que esta se adapte de maneira ótima à estrutura de interesse presente na imagem a segmentar. A minimização da energia conduz a um equilíbrio entre as forças envolvidas no modelo. O método proposto utiliza o conceito de algoritmos genéticos em conjunto com contornos activos (usualmente conhecidos como snakes) de modo a fornecer uma solução robusta ao problema dos mínimos quadrados que estes tradicionalmente presentam. Os resultados apresentados confirmam o potencial da abordagem proposta e incentivam a continuação de trabalhos de pesquisa de maneira a ampliar sua contribuição em atividades que demandem tarefas de análise de imagem

Spatch based active partitions with linguistically formulated energy

The present paper shows the method of cognitive hierarchical active partitions that can be applied to creation of automatic image understanding systems. The approach, which stems from active contours techniques, allows one to use not only the knowledge contained in an image, but also any additional expert knowledge. Special emphasis is put on the effcient way of knowledge retrieval, which could minimise the necessity to render information expressed in a natural language into a description convenient for recognition algorithms and machine learning

Automatic extraction of bronchus and centerline determination from CT images for three dimensional virtual bronchoscopy.

Law Tsui Ying.Thesis (M.Phil.)--Chinese University of Hong Kong, 2000.Includes bibliographical references (leaves 64-70).Abstracts in English and Chinese.Acknowledgments --- p.iiChapter 1 --- Introduction --- p.1Chapter 1.1 --- Structure of Bronchus --- p.3Chapter 1.2 --- Existing Systems --- p.4Chapter 1.2.1 --- Virtual Endoscope System (VES) --- p.4Chapter 1.2.2 --- Virtual Reality Surgical Simulator --- p.4Chapter 1.2.3 --- Automated Virtual Colonoscopy (AVC) --- p.5Chapter 1.2.4 --- QUICKSEE --- p.5Chapter 1.3 --- Organization of Thesis --- p.6Chapter 2 --- Three Dimensional Visualization in Medicine --- p.7Chapter 2.1 --- Acquisition --- p.8Chapter 2.1.1 --- Computed Tomography --- p.8Chapter 2.2 --- Resampling --- p.9Chapter 2.3 --- Segmentation and Classification --- p.9Chapter 2.3.1 --- Segmentation by Thresholding --- p.10Chapter 2.3.2 --- Segmentation by Texture Analysis --- p.10Chapter 2.3.3 --- Segmentation by Region Growing --- p.10Chapter 2.3.4 --- Segmentation by Edge Detection --- p.11Chapter 2.4 --- Rendering --- p.12Chapter 2.5 --- Display --- p.13Chapter 2.6 --- Hazards of Visualization --- p.13Chapter 2.6.1 --- Adding Visual Richness and Obscuring Important Detail --- p.14Chapter 2.6.2 --- Enhancing Details Incorrectly --- p.14Chapter 2.6.3 --- The Picture is not the Patient --- p.14Chapter 2.6.4 --- Pictures-'R'-Us --- p.14Chapter 3 --- Overview of Advanced Segmentation Methodologies --- p.15Chapter 3.1 --- Mathematical Morphology --- p.15Chapter 3.2 --- Recursive Region Search --- p.16Chapter 3.3 --- Active Region Models --- p.17Chapter 4 --- Overview of Centerline Methodologies --- p.18Chapter 4.1 --- Thinning Approach --- p.18Chapter 4.2 --- Volume Growing Approach --- p.21Chapter 4.3 --- Combination of Mathematical Morphology and Region Growing Schemes --- p.22Chapter 4.4 --- Simultaneous Borders Identification Approach --- p.23Chapter 4.5 --- Tracking Approach --- p.24Chapter 4.6 --- Distance Transform Approach --- p.25Chapter 5 --- Automated Extraction of Bronchus Area --- p.27Chapter 5.1 --- Basic Idea --- p.27Chapter 5.2 --- Outline of the Automated Extraction Algorithm --- p.28Chapter 5.2.1 --- Selection of a Start Point --- p.28Chapter 5.2.2 --- Three Dimensional Region Growing Method --- p.29Chapter 5.2.3 --- Optimization of the Threshold Value --- p.29Chapter 5.3 --- Retrieval of Start Point Algorithm Using Genetic Algorithm --- p.29Chapter 5.3.1 --- Introduction to Genetic Algorithm --- p.30Chapter 5.3.2 --- Problem Modeling --- p.31Chapter 5.3.3 --- Algorithm for Determining a Start Point --- p.33Chapter 5.3.4 --- Genetic Operators --- p.33Chapter 5.4 --- Three Dimensional Painting Algorithm --- p.34Chapter 5.4.1 --- Outline of the Three Dimensional Painting Algorithm --- p.34Chapter 5.5 --- Optimization of the Threshold Value --- p.36Chapter 6 --- Automatic Centerline Determination Algorithm --- p.38Chapter 6.1 --- Distance Transformations --- p.38Chapter 6.2 --- End Points Retrieval --- p.41Chapter 6.3 --- Graph Based Centerline Algorithm --- p.44Chapter 7 --- Experiments and Discussion --- p.48Chapter 7.1 --- Experiment of Automated Determination of Bronchus Algorithm --- p.48Chapter 7.2 --- Experiment of Automatic Centerline Determination Algorithm --- p.54Chapter 8 --- Conclusion --- p.62Bibliography --- p.6

Identificaçao de tumores cerebrais por meio do modelo de contornos ativos e algoritmos genéticos

Orientador: Klaus de GeusDissertaçao (mestrado) - Universidade Federal do Paraná. Setor de Ciencias Exatas. Curso de Pós-graduaçao em Informátic

Dynamical models and machine learning for supervised segmentation

This thesis is concerned with the problem of how to outline regions of interest in medical images, when the boundaries are weak or ambiguous and the region shapes are irregular. The focus on machine learning and interactivity leads to a common theme of the need to balance conflicting requirements. First, any machine learning method must strike a balance between how much it can learn and how well it generalises. Second, interactive methods must balance minimal user demand with maximal user control. To address the problem of weak boundaries,methods of supervised texture classification are investigated that do not use explicit texture features. These methods enable prior knowledge about the image to benefit any segmentation framework. A chosen dynamic contour model, based on probabilistic boundary tracking, combines these image priors with efficient modes of interaction. We show the benefits of the texture classifiers over intensity and gradient-based image models, in both classification and boundary extraction. To address the problem of irregular region shape, we devise a new type of statistical shape model (SSM) that does not use explicit boundary features or assume high-level similarity between region shapes. First, the models are used for shape discrimination, to constrain any segmentation framework by way of regularisation. Second, the SSMs are used for shape generation, allowing probabilistic segmentation frameworks to draw shapes from a prior distribution. The generative models also include novel methods to constrain shape generation according to information from both the image and user interactions. The shape models are first evaluated in terms of discrimination capability, and shown to out-perform other shape descriptors. Experiments also show that the shape models can benefit a standard type of segmentation algorithm by providing shape regularisers. We finally show how to exploit the shape models in supervised segmentation frameworks, and evaluate their benefits in user trials

Prostate Segmentation and Regions of Interest Detection in Transrectal Ultrasound Images

The early detection of prostate cancer plays a significant role in the success of treatment and outcome. To detect prostate cancer, imaging modalities such as TransRectal UltraSound (TRUS) and Magnetic Resonance Imaging (MRI) are relied on. MRI images are more comprehensible than TRUS images which are corrupted by noise such as speckles and shadowing. However, MRI screening is costly, often unavailable in many community hospitals, time consuming, and requires more patient preparation time. Therefore, TRUS is more popular for screening and biopsy guidance for prostate cancer. For these reasons, TRUS images are chosen in this research. Radiologists first segment the prostate image from ultrasound image and then identify the hypoechoic regions which are more likely to exhibit cancer and should be considered for biopsy. In this thesis, the focus is on prostate segmentation and on Regions of Interest (ROI)segmentation. First, the extraneous tissues surrounding the prostate gland are eliminated. Consequently, the process of detecting the cancerous regions is focused on the prostate gland only. Thus, the diagnosing process is significantly shortened. Also, segmentation techniques such as thresholding, region growing, classification, clustering, Markov random field models, artificial neural networks (ANNs), atlas-guided, and deformable models are investigated. In this dissertation, the deformable model technique is selected because it is capable of segmenting difficult images such as ultrasound images. Deformable models are classified as either parametric or geometric deformable models. For the prostate segmentation, one of the parametric deformable models, Gradient Vector Flow (GVF) deformable contour, is adopted because it is capable of segmenting the prostate gland, even if the initial contour is not close to the prostate boundary. The manual segmentation of ultrasound images not only consumes much time and effort, but also leads to operator-dependent results. Therefore, a fully automatic prostate segmentation algorithm is proposed based on knowledge-based rules. The new algorithm results are evaluated with respect to their manual outlining by using distance-based and area-based metrics. Also, the novel technique is compared with two well-known semi-automatic algorithms to illustrate its superiority. With hypothesis testing, the proposed algorithm is statistically superior to the other two algorithms. The newly developed algorithm is operator-independent and capable of accurately segmenting a prostate gland with any shape and orientation from the ultrasound image. The focus of the second part of the research is to locate the regions which are more prone to cancer. Although the parametric dynamic contour technique can readily segment a single region, it is not conducive for segmenting multiple regions, as required in the regions of interest (ROI) segmentation part. Since the number of regions is not known beforehand, the problem is stated as 3D one by using level set approach to handle the topology changes such as splitting and merging the contours. For the proposed ROI segmentation algorithm, one of the geometric deformable models, active contours without edges, is used. This technique is capable of segmenting the regions with either weak edges, or even, no edges at all. The results of the proposed ROI segmentation algorithm are compared with those of the two experts' manual marking. The results are also compared with the common regions manually marked by both experts and with the total regions marked by either expert. The proposed ROI segmentation algorithm is also evaluated by using region-based and pixel-based strategies. The evaluation results indicate that the proposed algorithm produces similar results to those of the experts' manual markings, but with the added advantages of being fast and reliable. This novel algorithm also detects some regions that have been missed by one expert but confirmed by the other. In conclusion, the two newly devised algorithms can assist experts in segmenting the prostate image and detecting the suspicious abnormal regions that should be considered for biopsy. This leads to the reduction the number of biopsies, early detection of the diseased regions, proper management, and possible reduction of death related to prostate cancer

Micropallet Arrays as an Integrated Platform for the Characterization and Manipulation of Single Cells

Cell isolations remain a critical bottleneck in cell biology. Fluorescence activated cell sorting (FACS) revolutionized the field by enabling rapid sorting of samples based on cell surface markers and bulk optical properties. Despite these advances, it remains impossible or prohibitively difficult to sort cells based on dynamic and morphological characteristics or to sort cells from extremely small samples such as are typically acquired from patient biopsies and small animal models. The work described in this dissertation is focused on the development of an integrated platform that can surmount the limitations of existing sorting technologies through the integration of a microfabricated platform and image cytometry. The integration of simple microdevices such as microwell arrays with image-based cytometry has enabled temporally and spatially resolved single-cell measurements to be performed with high-throughput yet such instruments remain incapable of sorting cells based on this expanded feature-space. Micropallet arrays are a simple, scalable platform for performing high-throughput single-cell assays with spatial and temporal resolution. Individual elements from the array can also be released using low-energy laser pulses, enabling single-cell isolations to be performed with high purity and yield from extremely small samples. A transparent, biocompatible and superparamagnetic composite photoresist was developed to enable the fabrication of micropallet arrays which could be manipulated by external magnetic fields after release. This enabled the collection of released micropallets against gravity to improve the purity of sorts. An imaging cytometer was developed which combined high-throughput automated image acquisition and analysis of micropallet arrays with automated laser-based miropallet release for single-cell isolation. As a demonstration of the capability of micropallet arrays to sort exceedingly small and diverse samples as well as to characterize the performance of the automated platform, patient-derived xenograft tumor samples were sorted to yield pure populations of tumor cells from a mixture of tumor and host stromal tissue. This platform was subsequently applied to the study of the heterogeneity exhibited by monoclonal melanoma cell populations in their dynamic response to stimulation by Wnt-3a.Doctor of Philosoph