Breast Ultrasound Image Segmentation Based on Uncertainty Reduction and Context Information

Breast cancer frequently occurs in women over the world. It was one of the most serious diseases and the second common cancer among women in 2019. The survival rate of stages 0 and 1 of breast cancer is closed to 100%. It is urgent to develop an approach that can detect breast cancer in the early stages. Breast ultrasound (BUS) imaging is low-cost, portable, and effective; therefore, it becomes the most crucial approach for breast cancer diagnosis. However, BUS images are of poor quality, low contrast, and uncertain. The computer-aided diagnosis (CAD) system is developed for breast cancer to prevent misdiagnosis. There have been many types of research for BUS image segmentation based on classic machine learning and computer vision methods, e.g., clustering methods, thresholding methods, level set, active contour, and graph cut. Since deep neural networks have been widely utilized in nature image semantic segmentation and achieved good results, deep learning approaches are also applied to BUS image segmentation. However, the previous methods still suffer some shortcomings. Firstly, the previous non-deep learning approaches highly depend on the manually selected features, such as texture, frequency, and intensity. Secondly, the previous deep learning approaches do not solve the uncertainty and noise in BUS images and deep learning architectures. Meanwhile, the previous methods also do not involve context information such as medical knowledge about breast cancer. In this work, three approaches are proposed to measure and reduce uncertainty and noise in deep neural networks. Also, three approaches are designed to involve medical knowledge and long-range distance context information in machine learning algorithms. The proposed methods are applied to breast ultrasound image segmentation. In the first part, three fuzzy uncertainty reduction architectures are designed to measure the uncertainty degree for pixels and channels in the convolutional feature maps. Then, medical knowledge constrained conditional random fields are proposed to reflect the breast layer structure and refine the segmentation results. A novel shape-adaptive convolutional operator is proposed to provide long-distance context information in the convolutional layer. Finally, a fuzzy generative adversarial network is proposed to reduce uncertainty. The new approaches are applied to 4 breast ultrasound image datasets: one multi-category dataset and three public datasets with pixel-wise ground truths for tumor and background. The proposed methods achieve the best performance among 15 BUS image segmentation methods on the four datasets

Semi-Automatic Segmentation of Normal Female Pelvic Floor Structures from Magnetic Resonance Images

Stress urinary incontinence (SUI) and pelvic organ prolapse (POP) are important health issues affecting millions of American women. Investigation of the cause of SUI and POP requires a better understand of the anatomy of female pelvic floor. In addition, pre-surgical planning and individualized treatment plans require development of patient-specific three-dimensional or virtual reality models. The biggest challenge in building those models is to segment pelvic floor structures from magnetic resonance images because of their complex shapes, which make manual segmentation labor-intensive and inaccurate. In this dissertation, a quick and reliable semi-automatic segmentation method based on a shape model is proposed. The model is built on statistical analysis of the shapes of structures in a training set. A local feature map of the target image is obtained by applying a filtering pipeline, including contrast enhancement, noise reduction, smoothing, and edge extraction. With the shape model and feature map, automatic segmentation is performed by matching the model to the border of the structure using an optimization technique called evolution strategy. Segmentation performance is evaluated by calculating a similarity coefficient between semi-automatic and manual segmentation results. Taguchi analysis is performed to investigate the significance of segmentation parameters and provide tuning trends for better performance. The proposed method was successfully tested on both two-dimensional and three-dimensional image segmentation using the levator ani and obturator muscles as examples. Although the method is designed for segmentation of female pelvic floor structures, it can also be applied to other structures or organs without large shape variatio

Semi-Automatic Segmentation of Normal Female Pelvic Floor Structures from Magnetic Resonance Images

Stress urinary incontinence (SUI) and pelvic organ prolapse (POP) are important health issues affecting millions of American women. Investigation of the cause of SUI and POP requires a better understand of the anatomy of female pelvic floor. In addition, pre-surgical planning and individualized treatment plans require development of patient-specific three-dimensional or virtual reality models. The biggest challenge in building those models is to segment pelvic floor structures from magnetic resonance images because of their complex shapes, which make manual segmentation labor-intensive and inaccurate. In this dissertation, a quick and reliable semi-automatic segmentation method based on a shape model is proposed. The model is built on statistical analysis of the shapes of structures in a training set. A local feature map of the target image is obtained by applying a filtering pipeline, including contrast enhancement, noise reduction, smoothing, and edge extraction. With the shape model and feature map, automatic segmentation is performed by matching the model to the border of the structure using an optimization technique called evolution strategy. Segmentation performance is evaluated by calculating a similarity coefficient between semi-automatic and manual segmentation results. Taguchi analysis is performed to investigate the significance of segmentation parameters and provide tuning trends for better performance. The proposed method was successfully tested on both two-dimensional and three-dimensional image segmentation using the levator ani and obturator muscles as examples. Although the method is designed for segmentation of female pelvic floor structures, it can also be applied to other structures or organs without large shape variatio

Semi-Automatic Segmentation of Normal Female Pelvic Floor Structures from Magnetic Resonance Images

Stress urinary incontinence (SUI) and pelvic organ prolapse (POP) are important health issues affecting millions of American women. Investigation of the cause of SUI and POP requires a better understand of the anatomy of female pelvic floor. In addition, pre-surgical planning and individualized treatment plans require development of patient-specific three-dimensional or virtual reality models. The biggest challenge in building those models is to segment pelvic floor structures from magnetic resonance images because of their complex shapes, which make manual segmentation labor-intensive and inaccurate. In this dissertation, a quick and reliable semi-automatic segmentation method based on a shape model is proposed. The model is built on statistical analysis of the shapes of structures in a training set. A local feature map of the target image is obtained by applying a filtering pipeline, including contrast enhancement, noise reduction, smoothing, and edge extraction. With the shape model and feature map, automatic segmentation is performed by matching the model to the border of the structure using an optimization technique called evolution strategy. Segmentation performance is evaluated by calculating a similarity coefficient between semi-automatic and manual segmentation results. Taguchi analysis is performed to investigate the significance of segmentation parameters and provide tuning trends for better performance. The proposed method was successfully tested on both two-dimensional and three-dimensional image segmentation using the levator ani and obturator muscles as examples. Although the method is designed for segmentation of female pelvic floor structures, it can also be applied to other structures or organs without large shape variatio

Biomedical Signal and Image Processing

Written for senior-level and first year graduate students in biomedical signal and image processing, this book describes fundamental signal and image processing techniques that are used to process biomedical information. The book also discusses application of these techniques in the processing of some of the main biomedical signals and images, such as EEG, ECG, MRI, and CT. New features of this edition include the technical updating of each chapter along with the addition of many more examples, the majority of which are MATLAB based

Deep Learning Models for Classification of COVID-19 Cases by Medical Images

In recent times, the use of chest Computed Tomography (CT) images for detecting coronavirus infections has gained significant attention, owing to their ability to reveal bilateral changes in affected individuals. However, classifying patients from medical images presents a formidable challenge, particularly in identifying such bilateral changes. To tackle this challenge, our study harnesses the power of deep learning models for the precise classification of infected patients. Our research involves a comparative analysis of deep transfer learning-based classification models, including DenseNet201, GoogleNet, and AlexNet, against carefully chosen supervised learning models. Additionally, our work encompasses Covid-19 classification, which involves the identification and differentiation of medical images, such as X-rays and electrocardiograms, that exhibit telltale signs of Covid-19 infection. This comprehensive approach ensures that our models can handle a wide range of medical image types and effectively identify characteristic patterns indicative of Covid-19. By conducting meticulous research and employing advanced deep learning techniques, we have made significant strides in enhancing the accuracy and speed of Covid-19 diagnosis. Our results demonstrate the effectiveness of these models and their potential to make substantial contributions to the global effort to combat COVID-19.Comment: Master's thesi

Deep Learning in Cardiology

The medical field is creating large amount of data that physicians are unable to decipher and use efficiently. Moreover, rule-based expert systems are inefficient in solving complicated medical tasks or for creating insights using big data. Deep learning has emerged as a more accurate and effective technology in a wide range of medical problems such as diagnosis, prediction and intervention. Deep learning is a representation learning method that consists of layers that transform the data non-linearly, thus, revealing hierarchical relationships and structures. In this review we survey deep learning application papers that use structured data, signal and imaging modalities from cardiology. We discuss the advantages and limitations of applying deep learning in cardiology that also apply in medicine in general, while proposing certain directions as the most viable for clinical use.Comment: 27 pages, 2 figures, 10 table