Learning-based depth and pose prediction for 3D scene reconstruction in endoscopy

Colorectal cancer is the third most common cancer worldwide. Early detection and treatment of pre-cancerous tissue during colonoscopy is critical to improving prognosis. However, navigating within the colon and inspecting the endoluminal tissue comprehensively are challenging, and success in both varies based on the endoscopist's skill and experience. Computer-assisted interventions in colonoscopy show much promise in improving navigation and inspection. For instance, 3D reconstruction of the colon during colonoscopy could promote more thorough examinations and increase adenoma detection rates which are associated with improved survival rates. Given the stakes, this thesis seeks to advance the state of research from feature-based traditional methods closer to a data-driven 3D reconstruction pipeline for colonoscopy. More specifically, this thesis explores different methods that improve subtasks of learning-based 3D reconstruction. The main tasks are depth prediction and camera pose estimation. As training data is unavailable, the author, together with her co-authors, proposes and publishes several synthetic datasets and promotes domain adaptation models to improve applicability to real data. We show, through extensive experiments, that our depth prediction methods produce more robust results than previous work. Our pose estimation network trained on our new synthetic data outperforms self-supervised methods on real sequences. Our box embeddings allow us to interpret the geometric relationship and scale difference between two images of the same surface without the need for feature matches that are often unobtainable in surgical scenes. Together, the methods introduced in this thesis help work towards a complete, data-driven 3D reconstruction pipeline for endoscopy

Enhancing endoscopic navigation and polyp detection using artificial intelligence

Colorectal cancer (CRC) is one most common and deadly forms of cancer. It has a very high mortality rate if the disease advances to late stages however early diagnosis and treatment can be curative is hence essential to enhancing disease management. Colonoscopy is considered the gold standard for CRC screening and early therapeutic treatment. The effectiveness of colonoscopy is highly dependent on the operator’s skill, as a high level of hand-eye coordination is required to control the endoscope and fully examine the colon wall. Because of this, detection rates can vary between different gastroenterologists and technology have been proposed as solutions to assist disease detection and standardise detection rates. This thesis focuses on developing artificial intelligence algorithms to assist gastroenterologists during colonoscopy with the potential to ensure a baseline standard of quality in CRC screening. To achieve such assistance, the technical contributions develop deep learning methods and architectures for automated endoscopic image analysis to address both the detection of lesions in the endoscopic image and the 3D mapping of the endoluminal environment. The proposed detection models can run in real-time and assist visualization of different polyp types. Meanwhile the 3D reconstruction and mapping models developed are the basis for ensuring that the entire colon has been examined appropriately and to support quantitative measurement of polyp sizes using the image during a procedure. Results and validation studies presented within the thesis demonstrate how the developed algorithms perform on both general scenes and on clinical data. The feasibility of clinical translation is demonstrated for all of the models on endoscopic data from human participants during CRC screening examinations

A review on model-based and model-free approaches to control soft actuators and their potentials in colonoscopy

Colorectal cancer (CRC) is the third most common cancer worldwide and responsible for approximately 1 million deaths annually. Early screening is essential to increase the chances of survival, and it can also reduce the cost of treatments for healthcare centres. Colonoscopy is the gold standard for CRC screening and treatment, but it has several drawbacks, including difficulty in manoeuvring the device, patient discomfort, and high cost. Soft endorobots, small and compliant devices thatcan reduce the force exerted on the colonic wall, offer a potential solution to these issues. However, controlling these soft robots is challenging due to their deformable materials and the limitations of mathematical models. In this Review, we discuss model-free and model-based approaches for controlling soft robots that can potentially be applied to endorobots for colonoscopy. We highlight the importance of selecting appropriate control methods based on various parameters, such as sensor and actuator solutions. This review aims to contribute to the development of smart control strategies for soft endorobots that can enhance the effectiveness and safety of robotics in colonoscopy. These strategies can be defined based on the available information about the robot and surrounding environment, control demands, mechanical design impact and characterization data based on calibration.<br/

Computer-aided Visualization of Colonoscopy

Colonoscopy is the most widely used medical technique to examine the human large intestine (colon) and eliminate precancerous or malignant lesions, i.e., polyps. It uses a high-definition camera to examine the inner surface of the colon. Very often, a portion of the colon surface is not visualized during the procedure. Unsurveyed portions of the colon can harbor polyps that then progress to colorectal cancer. Unfortunately, it is hard for the endoscopist to realize there is unsurveyed surface from the video as it is formed. A system to alert endoscopists to missed surface area could thus more fully protect patients from colorectal cancer following colonoscopy. In this dissertation computer-aided visualization techniques were developed in order to solve this problem:1. A novel Simultaneous Localization and Mapping (SLAM) algorithm called RNNSLAM was proposed to address the difficulties of applying a traditional SLAM system on colonic images. I improved a standard SLAM system with a previously proposed Recurrent Neural Network for Depth and Pose Estimation (RNN-DP). The combination of SLAM’s optimization mechanism and RNN-DP’s prior knowledge achieved state-of-the-art performance on colonoscopy, especially addressing the drift problem in both SLAM and RNN-DP. A fusion module was added to this system to generate a dense 3D surface.2. I conducted exploration research on recognizing colonic places that have been visited based on video frames. This technique called image relocalization or retrieval is needed for helping the endoscopist to fully survey the previously unsurveyed regions. A benchmark testing dataset was created for colon image retrieval. Deep neural networks were successfully trained using Structure from Motion results on colonoscopy and achieved promising results.3. To visualize highly-curved portions of a colon or the whole colon, a generalized cylinder deformation algorithm was proposed to semi-flatten the geometry of the colon model for more succinct and global visualization.Doctor of Philosoph

Supervised cnn strategies for optical image segmentation and classification in interventional medicine

The analysis of interventional images is a topic of high interest for the medical-image analysis community. Such an analysis may provide interventional-medicine professionals with both decision support and context awareness, with the final goal of improving patient safety. The aim of this chapter is to give an overview of some of the most recent approaches (up&nbsp;to 2018) in the field, with a focus on Convolutional Neural Networks (CNNs) for both segmentation and classification tasks. For each approach, summary tables are presented reporting the used dataset, involved anatomical region and achieved performance. Benefits and disadvantages of each approach are highlighted and discussed. Available datasets for algorithm training and testing and commonly used performance metrics are summarized to offer a source of information for researchers that are approaching the field of interventional-image analysis. The advancements in deep learning for medical-image analysis are involving more and more the interventional-medicine field. However, these advancements are undeniably slower than in other fields (e.g. preoperative-image analysis) and considerable work still needs to be done in order to provide clinicians with all possible support during interventional-medicine procedures

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