Deep learning for digitized histology image analysis

“Cervical cancer is the fourth most frequent cancer that affects women worldwide. Assessment of cervical intraepithelial neoplasia (CIN) through histopathology remains as the standard for absolute determination of cancer. The examination of tissue samples under a microscope requires considerable time and effort from expert pathologists. There is a need to design an automated tool to assist pathologists for digitized histology slide analysis. Pre-cervical cancer is generally determined by examining the CIN which is the growth of atypical cells from the basement membrane (bottom) to the top of the epithelium. It has four grades, including: Normal, CIN1, CIN2, and CIN3. In this research, different facets of an automated digitized histology epithelium assessment pipeline have been explored to mimic the pathologist diagnostic approach. The entire pipeline from slide to epithelium CIN grade has been designed and developed using deep learning models and imaging techniques to analyze the whole slide image (WSI). The process is as follows: 1) identification of epithelium by filtering the regions extracted from a low-resolution image with a binary classifier network; 2) epithelium segmentation; 3) deep regression for pixel-wise segmentation of epithelium by patch-based image analysis; 4) attention-based CIN classification with localized sequential feature modeling. Deep learning-based nuclei detection by superpixels was performed as an extension of our research. Results from this research indicate an improved performance of CIN assessment over state-of-the-art methods for nuclei segmentation, epithelium segmentation, and CIN classification, as well as the development of a prototype WSI-level tool”--Abstract, page iv

Towards Secure and Intelligent Diagnosis: Deep Learning and Blockchain Technology for Computer-Aided Diagnosis Systems

Cancer is the second leading cause of death across the world after cardiovascular disease. The survival rate of patients with cancerous tissue can significantly decrease due to late-stage diagnosis. Nowadays, advancements of whole slide imaging scanners have resulted in a dramatic increase of patient data in the domain of digital pathology. Large-scale histopathology images need to be analyzed promptly for early cancer detection which is critical for improving patient's survival rate and treatment planning. Advances of medical image processing and deep learning methods have facilitated the extraction and analysis of high-level features from histopathological data that could assist in life-critical diagnosis and reduce the considerable healthcare cost associated with cancer. In clinical trials, due to the complexity and large variance of collected image data, developing computer-aided diagnosis systems to support quantitative medical image analysis is an area of active research. The first goal of this research is to automate the classification and segmentation process of cancerous regions in histopathology images of different cancer tissues by developing models using deep learning-based architectures. In this research, a framework with different modules is proposed, including (1) data pre-processing, (2) data augmentation, (3) feature extraction, and (4) deep learning architectures. Four validation studies were designed to conduct this research. (1) differentiating benign and malignant lesions in breast cancer (2) differentiating between immature leukemic blasts and normal cells in leukemia cancer (3) differentiating benign and malignant regions in lung cancer, and (4) differentiating benign and malignant regions in colorectal cancer. Training machine learning models, disease diagnosis, and treatment often requires collecting patients' medical data. Privacy and trusted authenticity concerns make data owners reluctant to share their personal and medical data. Motivated by the advantages of Blockchain technology in healthcare data sharing frameworks, the focus of the second part of this research is to integrate Blockchain technology in computer-aided diagnosis systems to address the problems of managing access control, authentication, provenance, and confidentiality of sensitive medical data. To do so, a hierarchical identity and attribute-based access control mechanism using smart contract and Ethereum Blockchain is proposed to securely process healthcare data without revealing sensitive information to an unauthorized party leveraging the trustworthiness of transactions in a collaborative healthcare environment. The proposed access control mechanism provides a solution to the challenges associated with centralized access control systems and ensures data transparency and traceability for secure data sharing, and data ownership