Foundation and methodologies in computer-aided diagnosis systems for breast cancer detection

Breast cancer is the most prevalent cancer that affects women all over the world. Early detection and treatment of breast cancer could decline the mortality rate. Some issues such as technical reasons, which related to imaging quality and human error, increase misdiagnosis of breast cancer by radiologists. Computer-aided detection systems (CADs) are developed to overcome these restrictions and have been studied in many imaging modalities for breast cancer detection in recent years. The CAD systems improve radiologists’ performance in finding and discriminat- ing between the normal and abnormal tissues. These procedures are performed only as a double reader but the absolute decisions are still made by the radiologist. In this study, the recent CAD systems for breast cancer detec- tion on different modalities such as mammography, ultrasound, MRI, and biopsy histopathological images are introduced. The foundation of CAD systems generally consist of four stages: Pre-processing, Segmentation, Fea- ture extraction, and Classification. The approaches which applied to design different stages of CAD system are summarised. Advantages and disadvantages of different segmentation, feature extraction and classification tech- niques are listed. In addition, the impact of imbalanced datasets in classification outcomes and appropriate methods to solve these issues are discussed. As well as, performance evaluation metrics for various stages of breast cancer detection CAD systems are reviewed

Evaluation of automated organ segmentation for total-body PET-CT

The ability to diagnose rapidly and accurately and treat patients is substantially facilitated by medical images. Radiologists' visual assessment of medical images is crucial to their study. Segmenting images for diagnostic purposes is a crucial step in the medical imaging process. The purpose of medical image segmentation is to locate and isolate ‘Regions of Interest’ (ROI) within a medical image. Several medical uses rely on this procedure, including diagnosis, patient management, and medical study. Medical image segmentation has applications beyond just diagnosis and treatment planning. Quantitative information from medical images can be extracted by image segmentation and employed in the research of new diagnostic and treatment procedures. In addition, image segmentation is a critical procedure in several programs for image processing, including image fusion and registration. In order to construct a single, high-resolution, high-contrast image of an item or organ from several images, a process called "image registration" is used. A more complete picture of the patient's anatomy can be obtained through image fusion, which entails integrating numerous images from different modalities such as computed tomography (CT) and Magnetic resonance imaging (MRI). Once images are obtained using imaging technologies, they go through post-processing procedures before being analyzed. One of the primary and essential steps in post-processing is image segmentation, which involves dividing the images into parts and utilizing only the relevant sections for analysis. This project explores various imaging technologies and tools that can be utilized for image segmentation. Many open-source imaging tools are available for segmenting medical images across various applications. The objective of this study is to use the Jaccard index to evaluate the degree of similarity between the segmentations produced by various medical image visualization and analysis programs

Medical Image Segmentation by Deep Convolutional Neural Networks

Medical image segmentation is a fundamental and critical step for medical image analysis. Due to the complexity and diversity of medical images, the segmentation of medical images continues to be a challenging problem. Recently, deep learning techniques, especially Convolution Neural Networks (CNNs) have received extensive research and achieve great success in many vision tasks. Specifically, with the advent of Fully Convolutional Networks (FCNs), automatic medical image segmentation based on FCNs is a promising research field. This thesis focuses on two medical image segmentation tasks: lung segmentation in chest X-ray images and nuclei segmentation in histopathological images. For the lung segmentation task, we investigate several FCNs that have been successful in semantic and medical image segmentation. We evaluate the performance of these different FCNs on three publicly available chest X-ray image datasets. For the nuclei segmentation task, since the challenges of this task are difficulty in segmenting the small, overlapping and touching nuclei, and limited ability of generalization to nuclei in different organs and tissue types, we propose a novel nuclei segmentation approach based on a two-stage learning framework and Deep Layer Aggregation (DLA). We convert the original binary segmentation task into a two-step task by adding nuclei-boundary prediction (3-classes) as an intermediate step. To solve our two-step task, we design a two-stage learning framework by stacking two U-Nets. The first stage estimates nuclei and their coarse boundaries while the second stage outputs the final fine-grained segmentation map. Furthermore, we also extend the U-Nets with DLA by iteratively merging features across different levels. We evaluate our proposed method on two public diverse nuclei datasets. The experimental results show that our proposed approach outperforms many standard segmentation architectures and recently proposed nuclei segmentation methods, and can be easily generalized across different cell types in various organs

DeepSegNet: An Innovative Framework for Accurate Blood Cell Image Segmentation

Image segmentation plays a crucial and indispensable role in computer vision, as it allows the partitioning of an image into meaningful regions or objects. Among its numerous applications, image segmentation holds particular significance in the domains of medical diagnosis and healthcare. Its vital role in this field stems from its ability to extract and delineate specific anatomical structures, tumors, lesions, and other critical regions from medical images. In medical diagnosis, accurate and precise segmentation of organs and abnormalities is paramount for effective treatment planning, disease monitoring, and surgical interventions. Blood cell image segmentation is highly valuable for medical diagnosis and research, particularly in the domains of hematology and pathology. Precisely segmenting blood cells from microscopic images is essential, as it offers critical insights into various blood-related disorders and diseases. Although deep learning segmentation models have exhibited promising results in blood cell image segmentation, they suffer from several limitations. These drawbacks encompass scarce data availability, inefficient feature extraction, extended computation time, limited generalization to unseen data, challenges with variations, and artifacts. Consequently, these limitations can adversely impact the overall performance of the models. Blood cell image segmentation encounters persistent challenges due to factors like irregular cell shapes, which pose difficulties in boundary delineation, imperfect cell separation in smears, and low cell contrast, leading to visibility issues during segmentation. This research article introduces the innovative DeepSegNet framework, a powerful solution for precise blood cell image segmentation. The performance of widely-used segmentation models like PSPNet, FPN, and DeepLabv3+ is enhanced through the use of sophisticated preprocessing techniques, improving generalization capability, data diversity, and training stability. Additionally, the incorporation of diverse dilated convolutions and feature fusion further contributes to the improvement of these models. The Improved PSPNet, Improved FPN, Deep Lab V3, and Improved Deep Lab V3+ achieved 98.25%, 99.04%, 98.23%, and 99.31% accuracy, respectively, and the Improved Deep Lab V3+ model outperformed well and produced a Dice Coefficient of 99.32% and Precision of 99.38%. The proposed DeepSegNet framework improves overall performance with an increased accuracy of 8.91%, 3.72%, 17.73%, 22.83%, 7.96%, 9.61%, 17.36%, 6.22%, 13.32%, and 14.32% compared to the existing models. This framework, which can be applied to accurately identify and quantify different cell types from blood cell images, is instrumental in diagnosing a variety of hematological disorders and diseases

Frameworks in medical image analysis with deep neural networks

In recent years, deep neural network based medical image analysis has become quite powerful and achieved similar results performance-wise as experts. Consequently, the integration of these tools into the clinical routine as clinical decision support systems is highly desired. The benefits of automatic image analysis for clinicians are massive, ranging from improved diagnostic as well as treatment quality to increased time-efficiency through automated structured reporting. However, implementations in the literature revealed a significant lack of standardization in pipeline building resulting in low reproducibility, high complexity through extensive knowledge requirements for building state-of-the-art pipelines, and difficulties for application in clinical research. The main objective of this work is the standardization of pipeline building in deep neural network based medical image segmentation and classification. This is why the Python frameworks MIScnn for medical image segmentation and AUCMEDI for medical image classification are proposed which simplify the implementation process through intuitive building blocks eliminating the need for time-consuming and error-prone implementation of common components from scratch. The proposed frameworks include state-of-the-art methodology, follow outstanding open-source principles like extensive documentation as well as stability, offer rapid as well as simple application capabilities for deep learning experts as well as clinical researchers, and provide cutting-edge high-performance competitive with the strongest implementations in the literature. As secondary objectives, this work presents more than a dozen in-house studies as well as discusses various external studies utilizing the proposed frameworks in order to prove the capabilities of standardized medical image analysis. The presented studies demonstrate excellent predictive capabilities in applications ranging from COVID-19 detection in computed tomography scans to the integration into a clinical study workflow for Gleason grading of prostate cancer microscopy sections and advance the state-of-the-art in medical image analysis by simplifying experimentation setups for research. Furthermore, studies for increasing reproducibility in performance assessment of medical image segmentation are presented including an open-source metric library for standardized evaluation and a community guideline on proper metric usage. The proposed contributions in this work improve the knowledge representation of the field, enable rapid as well as high-performing applications, facilitate further research, and strengthen the reproducibility of future studies

Advanced Deep Learning for Medical Image Analysis

The application of deep learning is evolving, including in expert systems for healthcare, such as disease classification. Several challenges in the use of deep-learning algorithms in application to disease classification. The study aims to improve classification to address the problem. The thesis proposes a cost-sensitive imbalance training algorithm to address an unequal number of training examples, a two-stage Bayesian optimisation training algorithm and a dual-branch network to train a one-class classification scheme, further improving classification performance

Real-time hand gesture recognition exploiting multiple 2D and 3D cues

The recent introduction of several 3D applications and stereoscopic display technologies has created the necessity of novel human-machine interfaces. The traditional input devices, such as keyboard and mouse, are not able to fully exploit the potential of these interfaces and do not offer a natural interaction. Hand gestures provide, instead, a more natural and sometimes safer way of interacting with computers and other machines without touching them. The use cases for gesture-based interfaces range from gaming to automatic sign language interpretation, health care, robotics, and vehicle automation. Automatic gesture recognition is a challenging problem that has been attaining a growing interest in the research field for several years due to its applications in natural interfaces. The first approaches, based on the recognition from 2D color pictures or video only, suffered of the typical problems characterizing such type of data. Inter occlusions, different skin colors among users even of the same ethnic group and unstable illumination conditions, in facts, often made this problem intractable. Other approaches, instead, solved the previous problems by making the user wear sensorized gloves or hold proper tools designed to help the hand localization in the scene. The recent introduction in the mass market of novel low-cost range cameras, like the Microsoft Kinect, Asus XTION, Creative Senz3D, and the Leap Motion, has opened the way to innovative gesture recognition approaches exploiting the geometry of the framed scene. Most methods share a common gesture recognition pipeline based on firstly identifying the hand in the framed scene, then extracting some relevant features on the hand samples and finally exploiting suitable machine learning techniques in order to recognize the performed gesture from a predefined ``gesture dictionary''. This thesis, based on the previous rationale, proposes a novel gesture recognition framework exploiting both color and geometric cues from low-cost color and range cameras. The dissertation starts by introducing the automatic hand gesture recognition problem, giving an overview of the state-of-art algorithms and the recognition pipeline employed in this work. Then, it briefly describes the major low-cost range cameras and setups used in literature for color and depth data acquisition for hand gesture recognition purposes, highlighting their capabilities and limitations. The methods employed for respectively detecting the hand in the framed scene and segmenting it in its relevant parts are then analyzed with a higher level of detail. The algorithm first exploits skin color information and geometrical considerations for discarding the background samples, then it reliably detects the palm and the finger regions, and removes the forearm. For the palm detection, the method fits the largest circle inscribed in the palm region or, in a more advanced version, an ellipse. A set of robust color and geometric features which can be extracted from the fingers and palm regions, previously segmented, is then illustrated accurately. Geometric features describe properties of the hand contour from its curvature variations, the distances in the 3D space or in the image plane of its points from the hand center or from the palm, or extract relevant information from the palm morphology and from the empty space in the hand convex hull. Color features exploit, instead, the histogram of oriented gradients (HOG), local phase quantization (LPQ) and local ternary patterns (LTP) algorithms to provide further helpful cues from the hand texture and the depth map treated as a grayscale image. Additional features extracted from the Leap Motion data complete the gesture characterization for a more reliable recognition. Moreover, the thesis also reports a novel approach jointly exploiting the geometric data provided by the Leap Motion and the depth data from a range camera for extracting the same depth features with a significantly lower computational effort. This work then addresses the delicate problem of constructing a robust gesture recognition model from the features previously described, using multi-class Support Vector Machines, Random Forests or more powerful ensembles of classifiers. Feature selection techniques, designed to detect the smallest subset of features that allow to train a leaner classification model without a significant accuracy loss, are also considered. The proposed recognition method, tested on subsets of the American Sign Language and experimentally validated, reported very high accuracies. The results showed also how higher accuracies are obtainable by combining proper sets of complementary features and using ensembles of classifiers. Moreover, it is worth noticing that the proposed approach is not sensor dependent, that is, the recognition algorithm is not bound to a specific sensor or technology adopted for the depth data acquisition. Eventually, the gesture recognition algorithm is able to run in real-time even in absence of a thorough optimization, and may be easily extended in a near future with novel descriptors and the support for dynamic gestures