Advanced Brain Tumour Segmentation from MRI Images

Magnetic resonance imaging (MRI) is widely used medical technology for diagnosis of various tissue abnormalities, detection of tumors. The active development in the computerized medical image segmentation has played a vital role in scientific research. This helps the doctors to take necessary treatment in an easy manner with fast decision making. Brain tumor segmentation is a hot point in the research field of Information technology with biomedical engineering. The brain tumor segmentation is motivated by assessing tumor growth, treatment responses, computer-based surgery, treatment of radiation therapy, and developing tumor growth models. Therefore, computer-aided diagnostic system is meaningful in medical treatments to reducing the workload of doctors and giving the accurate results. This chapter explains the causes, awareness of brain tumor segmentation and its classification, MRI scanning process and its operation, brain tumor classifications, and different segmentation methodologies

Neurosurgery and brain shift: review of the state of the art and main contributions of robotics

Este artículo presenta una revisión acerca de la neurocirugía, los asistentes robóticos en este tipo de procedimiento, y el tratamiento que se le da al problema del desplazamiento que sufre el tejido cerebral, incluyendo las técnicas para la obtención de imágenes médicas. Se abarca de manera especial el fenómeno del desplazamiento cerebral, comúnmente conocido como brain shift, el cual causa pérdida de referencia entre las imágenes preoperatorias y los volúmenes a tratar durante la cirugía guiada por imágenes médicas. Hipotéticamente, con la predicción y corrección del brain shift sobre el sistema de neuronavegación, se podrían planear y seguir trayectorias de mínima invasión, lo que conllevaría a minimizar el daño a los tejidos funcionales y posiblemente a reducir la morbilidad y mortalidad en estos delicados y exigentes procedimientos médicos, como por ejemplo, en la extirpación de un tumor cerebral. Se mencionan también otros inconvenientes asociados a la neurocirugía y se muestra cómo los sistemas robotizados han ayudado a solventar esta problemática. Finalmente se ponen en relieve las perspectivas futuras de esta rama de la medicina, la cual desde muchas disciplinas busca tratar las dolencias del principal órgano del ser humano.This paper presents a review about neurosurgery, robotic assistants in this type of procedure, and the approach to the problem of brain tissue displacement, including techniques for obtaining medical images. It is especially focused on the phenomenon of brain displacement, commonly known as brain shift, which causes a loss of reference between the preoperative images and the volumes to be treated during image-guided surgery. Hypothetically, with brain shift prediction and correction for the neuronavigation system, minimal invasion trajectories could be planned and shortened. This would reduce damage to functional tissues and possibly lower the morbidity and mortality in delicate and demanding medical procedures such as the removal of a brain tumor. This paper also mentions other issues associated with neurosurgery and shows the way robotized systems have helped solve these problems. Finally, it highlights the future perspectives of neurosurgery, a branch of medicine that seeks to treat the ailments of the main organ of the human body from the perspective of many disciplines

Texture Analysis Platform for Imaging Biomarker Research

abstract: The rate of progress in improving survival of patients with solid tumors is slow due to late stage diagnosis and poor tumor characterization processes that fail to effectively reflect the nature of tumor before treatment or the subsequent change in its dynamics because of treatment. Further advancement of targeted therapies relies on advancements in biomarker research. In the context of solid tumors, bio-specimen samples such as biopsies serve as the main source of biomarkers used in the treatment and monitoring of cancer, even though biopsy samples are susceptible to sampling error and more importantly, are local and offer a narrow temporal scope. Because of its established role in cancer care and its non-invasive nature imaging offers the potential to complement the findings of cancer biology. Over the past decade, a compelling body of literature has emerged suggesting a more pivotal role for imaging in the diagnosis, prognosis, and monitoring of diseases. These advances have facilitated the rise of an emerging practice known as Radiomics: the extraction and analysis of large numbers of quantitative features from medical images to improve disease characterization and prediction of outcome. It has been suggested that radiomics can contribute to biomarker discovery by detecting imaging traits that are complementary or interchangeable with other markers. This thesis seeks further advancement of imaging biomarker discovery. This research unfolds over two aims: I) developing a comprehensive methodological pipeline for converting diagnostic imaging data into mineable sources of information, and II) investigating the utility of imaging data in clinical diagnostic applications. Four validation studies were conducted using the radiomics pipeline developed in aim I. These studies had the following goals: (1 distinguishing between benign and malignant head and neck lesions (2) differentiating benign and malignant breast cancers, (3) predicting the status of Human Papillomavirus in head and neck cancers, and (4) predicting neuropsychological performances as they relate to Alzheimer’s disease progression. The long-term objective of this thesis is to improve patient outcome and survival by facilitating incorporation of routine care imaging data into decision making processes.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

SCALING ARTIFICIAL INTELLIGENCE IN ENDOSCOPY: FROM MODEL DEVELOPMENT TO MACHINE LEARNING OPERATIONS FRAMEWORKS

Questa tesi esplora l'integrazione dell'intelligenza artificiale (IA) in Otorinolaringoiatria – Chirurgia di Testa e Collo, concentrandosi sui progressi della computer vision per l’endoscopia e le procedure chirurgiche. La ricerca inizia con una revisione completa dello stato dell’arte dell'IA e della computer vision in questo campo, identificando aree per ulteriori sviluppi. L'obiettivo principale è stato quello di sviluppare un sistema di computer vision per l'analisi di immagini e video endoscopici. La ricerca ha coinvolto la progettazione di strumenti per la rilevazione e segmentazione di neoplasie nelle vie aerodigestive superiori (VADS) e la valutazione della motilità delle corde vocali, cruciale nella stadiazione del carcinoma laringeo. Inoltre, lo studio si è focalizzato sul potenziale dei foundation vision models, vision transformers basati su self-supervised learning, per ridurre la necessità di annotazione da parte di esperti, approccio particolarmente vantaggioso in campi con dati limitati. Inoltre, la ricerca ha incluso lo sviluppo di un'applicazione web per migliorare e velocizzare il processo di annotazione in endoscopia delle VADS, nell’ambito generale delle tecniche di MLOps. La tesi copre varie fasi della ricerca, a partire dalla definizione del quadro concettuale e della metodologia, denominata "Videomics". Include una revisione della letteratura sull'IA in endoscopia clinica, focalizzata sulla Narrow Band Imaging (NBI) e sulle reti neurali convoluzionali (CNN). Lo studio progredisce attraverso diverse fasi, dalla valutazione della qualità delle immagini endoscopiche alla caratterizzazione approfondita delle lesioni neoplastiche. Si affronta anche la necessità di standard nel reporting degli studi di computer vision in ambito medico e si valuta l'applicazione dell'IA in setting dinamici come la motilità delle corde vocali. Una parte significativa della ricerca indaga l'uso di algoritmi di computer vision generalizzati (“foundation models”) e la “commoditization” degli algoritmi di machine learning, utilizzando polipi nasali e il carcinoma orofaringeo come casi studio. Infine, la tesi discute lo sviluppo di ENDO-CLOUD, un sistema basato su cloud per l’analisi della videolaringoscopia, evidenziando le sfide e le soluzioni nella gestione dei dati e l’utilizzo su larga scala di modelli di IA nell'imaging medico.This thesis explores the integration of artificial intelligence (AI) in Otolaryngology – Head and Neck Surgery, focusing on advancements in computer vision for endoscopy and surgical procedures. It begins with a comprehensive review of AI and computer vision advancements in this field, identifying areas for further exploration. The primary aim was to develop a computer vision system for endoscopy analysis. The research involved designing tools for detecting and segmenting neoplasms in the upper aerodigestive tract (UADT) and assessing vocal fold motility, crucial in laryngeal cancer staging. Further, the study delves into the potential of vision foundation models, like vision transformers trained via self-supervision, to reduce the need for expert annotations, particularly beneficial in fields with limited cases. Additionally, the research includes the development of a web application for enhancing and speeding up the annotation process in UADT endoscopy, under the umbrella of Machine Learning Operations (MLOps). The thesis covers various phases of research, starting with defining the conceptual framework and methodology, termed "Videomics". It includes a literature review on AI in clinical endoscopy, focusing on Narrow Band Imaging (NBI) and convolutional neural networks (CNNs). The research progresses through different stages, from quality assessment of endoscopic images to in-depth characterization of neoplastic lesions. It also addresses the need for standards in medical computer vision study reporting and evaluates the application of AI in dynamic vision scenarios like vocal fold motility. A significant part of the research investigates the use of "general purpose" vision algorithms and the commoditization of machine learning algorithms, using nasal polyps and oropharyngeal cancer as case studies. Finally, the thesis discusses the development of ENDO-CLOUD, a cloud-based system for videolaryngoscopy, highlighting the challenges and solutions in data management and the large-scale deployment of AI models in medical imaging

Deep learning assisted MRI guided attenuation correction in PET

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University LondonPositron emission tomography (PET) is a unique imaging modality that provides physiological and functional details of the tissue at the molecular level. However, the acquired PET images have some limitations such as the attenuation. PET attenuation correction is an essential step to obtain the full potential of PET quantification. With the wide use of hybrid PET/MR scanners, magnetic resonance (MR) images are used to address the problem of PET attenuation correction. The MR images segmentation is one simple and robust approach to create pseudo computed tomography (CT) images, which are used to generate attenuation coefficient maps to correct the PET attenuation. Recently, deep learning has been proposed and used as a promising technique to efficiently perform MR and various medical images segmentation. In this research work, deep learning guided segmentation approaches have been proposed to enhance the bone class segmentation of MR brain images in order to generate accurate pseudo-CT images. The first approach has introduced the combination of handcrafted features with deep learning features to enrich the set of features. Multiresolution analysis techniques, which generate multiscale and multidirectional coefficients of an image such as contourlet and shearlet transforms, are applied and combined with deep convolutional neural network (CNN) features. Different experiments have been conducted to investigate the number of selected coefficients and the insertion location of the handcrafted features. The second approach aims at reducing the segmentation algorithm’s complexity while maintaining the segmentation performance. An attention based convolutional encode-decoder network has been proposed to adaptively recalibrate the deep network features. This attention based network consists of two different squeeze and excitation blocks that excite the features spatially and channel wise. The two blocks are combined sequentially to decrease the number of network’s parameters and reduces the model complexity. The third approach has been focuses on the application of transfer learning from different MR sequences such as T1 weighted (T1-w) and T2 weighted (T2-w) images. A pretrained model with T1-w MR sequences is fine tuned to perform the segmentation of T2-w images. Multiple fine tuning approaches and experiments have been conducted to study the best fine tuning mechanism that is able to build an efficient segmentation model for both T1-w and T2-w segmentation. Clinical datasets of fifty patients with different conditions and diagnosis have been used to carry an objective evaluation to measure the segmentation performance of the results obtained by the three proposed methods. The first and second approaches have been validated with other studies in the literature that applied deep network based segmentation technique to perform MR based attenuation correction for PET images. The proposed methods have shown an enhancement in the bone segmentation with an increase of dice similarity coefficient (DSC) from 0.6179 to 0.6567 using an ensemble of CNNs with an improvement percentage of 6.3%. The proposed excitation-based CNN has decreased the model complexity by decreasing the number of trainable parameters by more than 46% where less computing resources are required to train the model. The proposed hybrid transfer learning method has shown its superiority to build a multi-sequences (T1-w and T2-w) segmentation approach compared to other applied transfer learning methods especially with the bone class where the DSC is increased from 0.3841 to 0.5393. Moreover, the hybrid transfer learning approach requires less computing time than transfer learning using open and conservative fine tuning

ChatGPT for Shaping the Future of Dentistry: The Potential of Multi-Modal Large Language Model

The ChatGPT, a lite and conversational variant of Generative Pretrained Transformer 4 (GPT-4) developed by OpenAI, is one of the milestone Large Language Models (LLMs) with billions of parameters. LLMs have stirred up much interest among researchers and practitioners in their impressive skills in natural language processing tasks, which profoundly impact various fields. This paper mainly discusses the future applications of LLMs in dentistry. We introduce two primary LLM deployment methods in dentistry, including automated dental diagnosis and cross-modal dental diagnosis, and examine their potential applications. Especially, equipped with a cross-modal encoder, a single LLM can manage multi-source data and conduct advanced natural language reasoning to perform complex clinical operations. We also present cases to demonstrate the potential of a fully automatic Multi-Modal LLM AI system for dentistry clinical application. While LLMs offer significant potential benefits, the challenges, such as data privacy, data quality, and model bias, need further study. Overall, LLMs have the potential to revolutionize dental diagnosis and treatment, which indicates a promising avenue for clinical application and research in dentistry

Surgical Subtask Automation for Intraluminal Procedures using Deep Reinforcement Learning

Intraluminal procedures have opened up a new sub-field of minimally invasive surgery that use flexible instruments to navigate through complex luminal structures of the body, resulting in reduced invasiveness and improved patient benefits. One of the major challenges in this field is the accurate and precise control of the instrument inside the human body. Robotics has emerged as a promising solution to this problem. However, to achieve successful robotic intraluminal interventions, the control of the instrument needs to be automated to a large extent. The thesis first examines the state-of-the-art in intraluminal surgical robotics and identifies the key challenges in this field, which include the need for safe and effective tool manipulation, and the ability to adapt to unexpected changes in the luminal environment. To address these challenges, the thesis proposes several levels of autonomy that enable the robotic system to perform individual subtasks autonomously, while still allowing the surgeon to retain overall control of the procedure. The approach facilitates the development of specialized algorithms such as Deep Reinforcement Learning (DRL) for subtasks like navigation and tissue manipulation to produce robust surgical gestures. Additionally, the thesis proposes a safety framework that provides formal guarantees to prevent risky actions. The presented approaches are evaluated through a series of experiments using simulation and robotic platforms. The experiments demonstrate that subtask automation can improve the accuracy and efficiency of tool positioning and tissue manipulation, while also reducing the cognitive load on the surgeon. The results of this research have the potential to improve the reliability and safety of intraluminal surgical interventions, ultimately leading to better outcomes for patients and surgeons

Biomedical Image Processing and Classification

Biomedical image processing is an interdisciplinary field involving a variety of disciplines, e.g., electronics, computer science, physics, mathematics, physiology, and medicine. Several imaging techniques have been developed, providing many approaches to the study of the human body. Biomedical image processing is finding an increasing number of important applications in, for example, the study of the internal structure or function of an organ and the diagnosis or treatment of a disease. If associated with classification methods, it can support the development of computer-aided diagnosis (CAD) systems, which could help medical doctors in refining their clinical picture