Novel Approaches to the Representation and Analysis of 3D Segmented Anatomical Districts

Nowadays, image processing and 3D shape analysis are an integral part of clinical practice and have the potentiality to support clinicians with advanced analysis and visualization techniques. Both approaches provide visual and quantitative information to medical practitioners, even if from different points of view. Indeed, shape analysis is aimed at studying the morphology of anatomical structures, while image processing is focused more on the tissue or functional information provided by the pixels/voxels intensities levels. Despite the progress obtained by research in both fields, a junction between these two complementary worlds is missing. When working with 3D models analyzing shape features, the information of the volume surrounding the structure is lost, since a segmentation process is needed to obtain the 3D shape model; however, the 3D nature of the anatomical structure is represented explicitly. With volume images, instead, the tissue information related to the imaged volume is the core of the analysis, while the shape and morphology of the structure are just implicitly represented, thus not clear enough. The aim of this Thesis work is the integration of these two approaches in order to increase the amount of information available for physicians, allowing a more accurate analysis of each patient. An augmented visualization tool able to provide information on both the anatomical structure shape and the surrounding volume through a hybrid representation, could reduce the gap between the two approaches and provide a more complete anatomical rendering of the subject. To this end, given a segmented anatomical district, we propose a novel mapping of volumetric data onto the segmented surface. The grey-levels of the image voxels are mapped through a volume-surface correspondence map, which defines a grey-level texture on the segmented surface. The resulting texture mapping is coherent to the local morphology of the segmented anatomical structure and provides an enhanced visual representation of the anatomical district. The integration of volume-based and surface-based information in a unique 3D representation also supports the identification and characterization of morphological landmarks and pathology evaluations. The main research contributions of the Ph.D. activities and Thesis are: \u2022 the development of a novel integration algorithm that combines surface-based (segmented 3D anatomical structure meshes) and volume-based (MRI volumes) information. The integration supports different criteria for the grey-levels mapping onto the segmented surface; \u2022 the development of methodological approaches for using the grey-levels mapping together with morphological analysis. The final goal is to solve problems in real clinical tasks, such as the identification of (patient-specific) ligament insertion sites on bones from segmented MR images, the characterization of the local morphology of bones/tissues, the early diagnosis, classification, and monitoring of muscle-skeletal pathologies; \u2022 the analysis of segmentation procedures, with a focus on the tissue classification process, in order to reduce operator dependency and to overcome the absence of a real gold standard for the evaluation of automatic segmentations; \u2022 the evaluation and comparison of (unsupervised) segmentation methods, finalized to define a novel segmentation method for low-field MR images, and for the local correction/improvement of a given segmentation. The proposed method is simple but effectively integrates information derived from medical image analysis and 3D shape analysis. Moreover, the algorithm is general enough to be applied to different anatomical districts independently of the segmentation method, imaging techniques (such as CT), or image resolution. The volume information can be integrated easily in different shape analysis applications, taking into consideration not only the morphology of the input shape but also the real context in which it is inserted, to solve clinical tasks. The results obtained by this combined analysis have been evaluated through statistical analysis

Quantitative analysis with machine learning models for multi-parametric brain imaging data

Gliomas are considered to be the most common primary adult malignant brain tumor. With the dramatic increases in computational power and improvements in image analysis algorithms, computer-aided medical image analysis has been introduced into clinical applications. Precision tumor grading and genotyping play an indispensable role in clinical diagnosis, treatment and prognosis. Gliomas diagnostic procedures include histopathological imaging tests, molecular imaging scans and tumor grading. Pathologic review of tumor morphology in histologic sections is the traditional method for cancer classification and grading, yet human study has limitations that can result in low reproducibility and inter-observer agreement. Compared with histopathological images, Magnetic resonance (MR) imaging present the different structure and functional features, which might serve as noninvasive surrogates for tumor genotypes. Therefore, computer-aided image analysis has been adopted in clinical application, which might partially overcome these shortcomings due to its capacity to quantitatively and reproducibly measure multilevel features on multi-parametric medical information. Imaging features obtained from a single modal image do not fully represent the disease, so quantitative imaging features, including morphological, structural, cellular and molecular level features, derived from multi-modality medical images should be integrated into computer-aided medical image analysis. The image quality differentiation between multi-modality images is a challenge in the field of computer-aided medical image analysis. In this thesis, we aim to integrate the quantitative imaging data obtained from multiple modalities into mathematical models of tumor prediction response to achieve additional insights into practical predictive value. Our major contributions in this thesis are: 1. Firstly, to resolve the imaging quality difference and observer-dependent in histological image diagnosis, we proposed an automated machine-learning brain tumor-grading platform to investigate contributions of multi-parameters from multimodal data including imaging parameters or features from Whole Slide Images (WSI) and the proliferation marker KI-67. For each WSI, we extract both visual parameters such as morphology parameters and sub-visual parameters including first-order and second-order features. A quantitative interpretable machine learning approach (Local Interpretable Model-Agnostic Explanations) was followed to measure the contribution of features for single case. Most grading systems based on machine learning models are considered “black boxes,” whereas with this system the clinically trusted reasoning could be revealed. The quantitative analysis and explanation may assist clinicians to better understand the disease and accordingly to choose optimal treatments for improving clinical outcomes. 2. Based on the automated brain tumor-grading platform we propose, multimodal Magnetic Resonance Images (MRIs) have been introduced in our research. A new imaging–tissue correlation based approach called RA-PA-Thomics was proposed to predict the IDH genotype. Inspired by the concept of image fusion, we integrate multimodal MRIs and the scans of histopathological images for indirect, fast, and cost saving IDH genotyping. The proposed model has been verified by multiple evaluation criteria for the integrated data set and compared to the results in the prior art. The experimental data set includes public data sets and image information from two hospitals. Experimental results indicate that the model provided improves the accuracy of glioma grading and genotyping

Unsupervised brain anomaly detection in MR images

Brain disorders are characterized by morphological deformations in shape and size of (sub)cortical structures in one or both hemispheres. These deformations cause deviations from the normal pattern of brain asymmetries, resulting in asymmetric lesions that directly affect the patient’s condition. Unsupervised methods aim to learn a model from unlabeled healthy images, so that an unseen image that breaks priors of this model, i.e., an outlier, is considered an anomaly. Consequently, they are generic in detecting any lesions, e.g., coming from multiple diseases, as long as these notably differ from healthy training images. This thesis addresses the development of solutions to leverage unsupervised machine learning for the detection/analysis of abnormal brain asymmetries related to anomalies in magnetic resonance (MR) images. First, we propose an automatic probabilistic-atlas-based approach for anomalous brain image segmentation. Second, we explore an automatic method for the detection of abnormal hippocampi from abnormal asymmetries based on deep generative networks and a one-class classifier. Third, we present a more generic framework to detect abnormal asymmetries in the entire brain hemispheres. Our approach extracts pairs of symmetric regions — called supervoxels — in both hemispheres of a test image under study. One-class classifiers then analyze the asymmetries present in each pair. Experimental results on 3D MR-T1 images from healthy subjects and patients with a variety of lesions show the effectiveness and robustness of the proposed unsupervised approaches for brain anomaly detection

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

Liver segmentation using marker controlled watershed transform

The largest organ in the body is the liver and primarily helps in metabolism and detoxification. Liver segmentation is a crucial step in liver cancer detection in computer vision-based biomedical image analysis. Liver segmentation is a critical task and results in under-segmentation and over-segmentation due to the complex structure of abdominal computed tomography (CT) images, noise, and textural variations over the image. This paper presents liver segmentation in abdominal CT images using marker-based watershed transforms. In the pre-processing stage, a modified double stage gaussian filter (MDSGF) is used to enhance the contrast, and preserve the edge and texture information of liver CT images. Further, marker controlled watershed transform is utilized for the segmentation of liver images from the abdominal CT images. Liver segmentation using suggested MDSGF and marker-based watershed transform help to diminish the under-segmentation and over-segmentation of the liver object. The performance of the proposed system is evaluated on the LiTS dataset based on Dice score (DS), relative volume difference (RVD), volumetric overlapping error (VOE), and Jaccard index (JI). The proposed method gives (Dice score of 0.959, RVD of 0.09, VOE of 0.089, and JI of 0.921)