Optical techniques for 3D surface reconstruction in computer-assisted laparoscopic surgery

One of the main challenges for computer-assisted surgery (CAS) is to determine the intra-opera- tive morphology and motion of soft-tissues. This information is prerequisite to the registration of multi-modal patient-specific data for enhancing the surgeon’s navigation capabilites by observ- ing beyond exposed tissue surfaces and for providing intelligent control of robotic-assisted in- struments. In minimally invasive surgery (MIS), optical techniques are an increasingly attractive approach for in vivo 3D reconstruction of the soft-tissue surface geometry. This paper reviews the state-of-the-art methods for optical intra-operative 3D reconstruction in laparoscopic surgery and discusses the technical challenges and future perspectives towards clinical translation. With the recent paradigm shift of surgical practice towards MIS and new developments in 3D opti- cal imaging, this is a timely discussion about technologies that could facilitate complex CAS procedures in dynamic and deformable anatomical regions

Vision-based retargeting for endoscopic navigation

Endoscopy is a standard procedure for visualising the human gastrointestinal tract. With the advances in biophotonics, imaging techniques such as narrow band imaging, confocal laser endomicroscopy, and optical coherence tomography can be combined with normal endoscopy for assisting the early diagnosis of diseases, such as cancer. In the past decade, optical biopsy has emerged to be an effective tool for tissue analysis, allowing in vivo and in situ assessment of pathological sites with real-time feature-enhanced microscopic images. However, the non-invasive nature of optical biopsy leads to an intra-examination retargeting problem, which is associated with the difficulty of re-localising a biopsied site consistently throughout the whole examination. In addition to intra-examination retargeting, retargeting of a pathological site is even more challenging across examinations, due to tissue deformation and changing tissue morphologies and appearances. The purpose of this thesis is to address both the intra- and inter-examination retargeting problems associated with optical biopsy. We propose a novel vision-based framework for intra-examination retargeting. The proposed framework is based on combining visual tracking and detection with online learning of the appearance of the biopsied site. Furthermore, a novel cascaded detection approach based on random forests and structured support vector machines is developed to achieve efficient retargeting. To cater for reliable inter-examination retargeting, the solution provided in this thesis is achieved by solving an image retrieval problem, for which an online scene association approach is proposed to summarise an endoscopic video collected in the first examination into distinctive scenes. A hashing-based approach is then used to learn the intrinsic representations of these scenes, such that retargeting can be achieved in subsequent examinations by retrieving the relevant images using the learnt representations. For performance evaluation of the proposed frameworks, extensive phantom, ex vivo and in vivo experiments have been conducted, with results demonstrating the robustness and potential clinical values of the methods proposed.Open Acces

DATA-DRIVEN APPROACH TO IMAGE CLASSIFICATION

Image classification has been a core topic in the computer vision community. Its recent success with convolutional neural network (CNN) algorithm has led to various real world applications such as large scale management of photos/videos on cloud/social-media, image based search for online retailers, self-driving cars, building robots and healthcare. Image classification can be broadly categorized into binary, multi-class and multi-label classification problems. Binary classification involves assigning one of the two class labels to an instance. In multi-class classification problem, an instance should be categorized into one of more than two classes. Multi-label classification is a generalized version of the multi-class classification problem where each image is assigned multiple labels as opposed to a single label. In this work, we first present various methods that take advantage of deep representations (fully connected layer of pre-trained CNN on the ImageNet dataset) and yield better performance on multi-label classification when compared to methods that use over a dozen conventional visual features. Following the success of deep representations, we intend to build a generic end-to-end deep learning framework to address all three problem categories of image classification. However, there are still no well established guidelines (in terms of choosing the number of layers to go deeper, the number of kernels and the size, the type of regularizer, the choice of non-linear function, etc.) to build an efficient deep neural network and often network architecture design is specific to a problem/dataset. Hence, we present some initial efforts in building a computational framework called Deep Decision Network (DDN) which is completely data-driven. DDN is a tree-like structured built stage-wise. During the learning phase, starting from the root network node, DDN automatically builds a network that splits the data into disjoint clusters of classes which would be handled by the subsequent expert networks. This results in a tree-like structured network driven by the data. The proposed approach provides an insight into the data by identifying the group of classes that are hard to classify and require more attention when compared to others. This feature is crucial for people trying to solve the problem with little or no domain knowledge, especially for applications in medical domain. Initially, we evaluate DDN on a binary classification problem and later extend it to more challenging multi-class and multi-label classification problems. The extension of DDN to multi-class and multi-label involves some changes but they still operate under the same underlying principle. In all the three cases, the proposed approach is tested for its recognition performance and scalability on publicly available datasets providing comparison to other methods

A Testbed for Design and Performance Evaluation of Visual Localization Technique inside the Small Intestine

Wireless video capsule endoscopy (VCE) plays an increasingly important role in assisting clinical diagnoses of gastrointestinal (GI) diseases. It provides a non-invasive way to examine the entire small intestine, where other conventional endoscopic instruments can barely reach. Existing examination systems for the VCE cannot track the location of a endoscopic capsule, which prevents the physician from identifying the exact location of the diseases. During the eight hour examination time, the video capsule continuously keeps taking images at a frame rate up to six frame per sec, so it is possible to extract the motion information from the content of the image sequence. Many attempts have been made to develop computer vision algorithms to detect the motion of the capsule based on the small changes in the consecutive video frames and then trace the location of the capsule. However, validation of those algorithms has become a challenging topic because conducting experiments on the human body is extremely difficult due to individual differences and legal issues. In this thesis, two validation approaches for motion tracking of the VCE are presented in detail respectively. One approach is to build a physical testbed with a plastic pipe and an endoscopy camera; the other is to build a virtual testbed by creating a three-dimensional virtual small intestine model and simulating the motion of the capsule. Based on the virtual testbed, a physiological factor, intestinal contraction, has been studied in terms of its influence on visual based localization algorithm and a geometric model for measuring the amount of contraction is proposed and validated via the virtual testbed. Empirical results have made contributions in support of the performance evaluation of other research on the visual based localization algorithm of VCE

Pattern Recognition

Pattern recognition is a very wide research field. It involves factors as diverse as sensors, feature extraction, pattern classification, decision fusion, applications and others. The signals processed are commonly one, two or three dimensional, the processing is done in real- time or takes hours and days, some systems look for one narrow object class, others search huge databases for entries with at least a small amount of similarity. No single person can claim expertise across the whole field, which develops rapidly, updates its paradigms and comprehends several philosophical approaches. This book reflects this diversity by presenting a selection of recent developments within the area of pattern recognition and related fields. It covers theoretical advances in classification and feature extraction as well as application-oriented works. Authors of these 25 works present and advocate recent achievements of their research related to the field of pattern recognition

Image-set, Temporal and Spatiotemporal Representations of Videos for Recognizing, Localizing and Quantifying Actions

This dissertation addresses the problem of learning video representations, which is defined here as transforming the video so that its essential structure is made more visible or accessible for action recognition and quantification. In the literature, a video can be represented by a set of images, by modeling motion or temporal dynamics, and by a 3D graph with pixels as nodes. This dissertation contributes in proposing a set of models to localize, track, segment, recognize and assess actions such as (1) image-set models via aggregating subset features given by regularizing normalized CNNs, (2) image-set models via inter-frame principal recovery and sparsely coding residual actions, (3) temporally local models with spatially global motion estimated by robust feature matching and local motion estimated by action detection with motion model added, (4) spatiotemporal models 3D graph and 3D CNN to model time as a space dimension, (5) supervised hashing by jointly learning embedding and quantization, respectively. State-of-the-art performances are achieved for tasks such as quantifying facial pain and human diving. Primary conclusions of this dissertation are categorized as follows: (i) Image set can capture facial actions that are about collective representation; (ii) Sparse and low-rank representations can have the expression, identity and pose cues untangled and can be learned via an image-set model and also a linear model; (iii) Norm is related with recognizability; similarity metrics and loss functions matter; (v) Combining the MIL based boosting tracker with the Particle Filter motion model induces a good trade-off between the appearance similarity and motion consistence; (iv) Segmenting object locally makes it amenable to assign shape priors; it is feasible to learn knowledge such as shape priors online from Web data with weak supervision; (v) It works locally in both space and time to represent videos as 3D graphs; 3D CNNs work effectively when inputted with temporally meaningful clips; (vi) the rich labeled images or videos help to learn better hash functions after learning binary embedded codes than the random projections. In addition, models proposed for videos can be adapted to other sequential images such as volumetric medical images which are not included in this dissertation

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