Confocal Laser Endomicroscopy Image Analysis with Deep Convolutional Neural Networks

abstract: Rapid intraoperative diagnosis of brain tumors is of great importance for planning treatment and guiding the surgeon about the extent of resection. Currently, the standard for the preliminary intraoperative tissue analysis is frozen section biopsy that has major limitations such as tissue freezing and cutting artifacts, sampling errors, lack of immediate interaction between the pathologist and the surgeon, and time consuming. Handheld, portable confocal laser endomicroscopy (CLE) is being explored in neurosurgery for its ability to image histopathological features of tissue at cellular resolution in real time during brain tumor surgery. Over the course of examination of the surgical tumor resection, hundreds to thousands of images may be collected. The high number of images requires significant time and storage load for subsequent reviewing, which motivated several research groups to employ deep convolutional neural networks (DCNNs) to improve its utility during surgery. DCNNs have proven to be useful in natural and medical image analysis tasks such as classification, object detection, and image segmentation. This thesis proposes using DCNNs for analyzing CLE images of brain tumors. Particularly, it explores the practicality of DCNNs in three main tasks. First, off-the shelf DCNNs were used to classify images into diagnostic and non-diagnostic. Further experiments showed that both ensemble modeling and transfer learning improved the classifier’s accuracy in evaluating the diagnostic quality of new images at test stage. Second, a weakly-supervised learning pipeline was developed for localizing key features of diagnostic CLE images from gliomas. Third, image style transfer was used to improve the diagnostic quality of CLE images from glioma tumors by transforming the histology patterns in CLE images of fluorescein sodium-stained tissue into the ones in conventional hematoxylin and eosin-stained tissue slides. These studies suggest that DCNNs are opted for analysis of CLE images. They may assist surgeons in sorting out the non-diagnostic images, highlighting the key regions and enhancing their appearance through pattern transformation in real time. With recent advances in deep learning such as generative adversarial networks and semi-supervised learning, new research directions need to be followed to discover more promises of DCNNs in CLE image analysis.Dissertation/ThesisDoctoral Dissertation Neuroscience 201

Intraoperative tissue classification methods in orthopedic and neurological surgeries: A systematic review

Accurate tissue differentiation during orthopedic and neurological surgeries is critical, given that such surgeries involve operations on or in the vicinity of vital neurovascular structures and erroneous surgical maneuvers can lead to surgical complications. By now, the number of emerging technologies tackling the problem of intraoperative tissue classification methods is increasing. Therefore, this systematic review paper intends to give a general overview of existing technologies. The review was done based on the PRISMA principle and two databases: PubMed and IEEE Xplore. The screening process resulted in 60 full-text papers. The general characteristics of the methodology from extracted papers included data processing pipeline, machine learning methods if applicable, types of tissues that can be identified with them, phantom used to conduct the experiment, and evaluation results. This paper can be useful in identifying the problems in the current status of the state-of-the-art intraoperative tissue classification methods and designing new enhanced techniques

Online Super-Resolution For Fibre-Bundle-Based Confocal Laser Endomicroscopy

Probe-based Confocal Laser Endomicroscopy (pCLE) produces microscopic images enabling real-time in vivo optical biopsy. However, the miniaturisation of the optical hardware, specifically the reliance on an optical fibre bundle as an imaging guide, fundamentally limits image quality by producing artefacts, noise, and relatively low contrast and resolution. The reconstruction approaches in clinical pCLE products do not fully alleviate these problems. Consequently, image quality remains a barrier that curbs the full potential of pCLE. Enhancing the image quality of pCLE in real-time remains a challenge. The research in this thesis is a response to this need. I have developed dedicated online super-resolution methods that account for the physics of the image acquisition process. These methods have the potential to replace existing reconstruction algorithms without interfering with the fibre design or the hardware of the device. In this thesis, novel processing pipelines are proposed for enhancing the image quality of pCLE. First, I explored a learning-based super-resolution method that relies on mapping from the low to the high-resolution space. Due to the lack of high-resolution pCLE, I proposed to simulate high-resolution data and use it as a ground truth model that is based on the pCLE acquisition physics. However, pCLE images are reconstructed from irregularly distributed fibre signals, and grid-based Convolutional Neural Networks are not designed to take irregular data as input. To alleviate this problem, I designed a new trainable layer that embeds Nadaraya- Watson regression. Finally, I proposed a novel blind super-resolution approach by deploying unsupervised zero-shot learning accompanied by a down-sampling kernel crafted for pCLE. I evaluated these new methods in two ways: a robust image quality assessment and a perceptual quality test assessed by clinical experts. The results demonstrate that the proposed super-resolution pipelines are superior to the current reconstruction algorithm in terms of image quality and clinician preference

Bayesian image restoration and bacteria detection in optical endomicroscopy

Optical microscopy systems can be used to obtain high-resolution microscopic images of tissue cultures and ex vivo tissue samples. This imaging technique can be translated for in vivo, in situ applications by using optical fibres and miniature optics. Fibred optical endomicroscopy (OEM) can enable optical biopsy in organs inaccessible by any other imaging systems, and hence can provide rapid and accurate diagnosis in a short time. The raw data the system produce is difficult to interpret as it is modulated by a fibre bundle pattern, producing what is called the “honeycomb effect”. Moreover, the data is further degraded due to the fibre core cross coupling problem. On the other hand, there is an unmet clinical need for automatic tools that can help the clinicians to detect fluorescently labelled bacteria in distal lung images. The aim of this thesis is to develop advanced image processing algorithms that can address the above mentioned problems. First, we provide a statistical model for the fibre core cross coupling problem and the sparse sampling by imaging fibre bundles (honeycomb artefact), which are formulated here as a restoration problem for the first time in the literature. We then introduce a non-linear interpolation method, based on Gaussian processes regression, in order to recover an interpretable scene from the deconvolved data. Second, we develop two bacteria detection algorithms, each of which provides different characteristics. The first approach considers joint formulation to the sparse coding and anomaly detection problems. The anomalies here are considered as candidate bacteria, which are annotated with the help of a trained clinician. Although this approach provides good detection performance and outperforms existing methods in the literature, the user has to carefully tune some crucial model parameters. Hence, we propose a more adaptive approach, for which a Bayesian framework is adopted. This approach not only outperforms the proposed supervised approach and existing methods in the literature but also provides computation time that competes with optimization-based methods

Accelerating Surgical Robotics Research: A Review of 10 Years With the da Vinci Research Kit

Robotic-assisted surgery is now well-established in clinical practice and has become the gold standard clinical treatment option for several clinical indications. The field of robotic-assisted surgery is expected to grow substantially in the next decade with a range of new robotic devices emerging to address unmet clinical needs across different specialities. A vibrant surgical robotics research community is pivotal for conceptualizing such new systems as well as for developing and training the engineers and scientists to translate them into practice. The da Vinci Research Kit (dVRK), an academic and industry collaborative effort to re-purpose decommissioned da Vinci surgical systems (Intuitive Surgical Inc, CA, USA) as a research platform for surgical robotics research, has been a key initiative for addressing a barrier to entry for new research groups in surgical robotics. In this paper, we present an extensive review of the publications that have been facilitated by the dVRK over the past decade. We classify research efforts into different categories and outline some of the major challenges and needs for the robotics community to maintain this initiative and build upon it

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

3D Face Modelling, Analysis and Synthesis

Human faces have always been of a special interest to researchers in the computer vision and graphics areas. There has been an explosion in the number of studies around accurately modelling, analysing and synthesising realistic faces for various applications. The importance of human faces emerges from the fact that they are invaluable means of effective communication, recognition, behaviour analysis, conveying emotions, etc. Therefore, addressing the automatic visual perception of human faces efficiently could open up many influential applications in various domains, e.g. virtual/augmented reality, computer-aided surgeries, security and surveillance, entertainment, and many more. However, the vast variability associated with the geometry and appearance of human faces captured in unconstrained videos and images renders their automatic analysis and understanding very challenging even today. The primary objective of this thesis is to develop novel methodologies of 3D computer vision for human faces that go beyond the state of the art and achieve unprecedented quality and robustness. In more detail, this thesis advances the state of the art in 3D facial shape reconstruction and tracking, fine-grained 3D facial motion estimation, expression recognition and facial synthesis with the aid of 3D face modelling. We give a special attention to the case where the input comes from monocular imagery data captured under uncontrolled settings, a.k.a. \textit{in-the-wild} data. This kind of data are available in abundance nowadays on the internet. Analysing these data pushes the boundaries of currently available computer vision algorithms and opens up many new crucial applications in the industry. We define the four targeted vision problems (3D facial reconstruction $\&$ tracking, fine-grained 3D facial motion estimation, expression recognition, facial synthesis) in this thesis as the four 3D-based essential systems for the automatic facial behaviour understanding and show how they rely on each other. Finally, to aid the research conducted in this thesis, we collect and annotate a large-scale videos dataset of monocular facial performances. All of our proposed methods demonstarte very promising quantitative and qualitative results when compared to the state-of-the-art methods

Identifying risk patterns for suicide attempts in individuals with diabetes : a data-driven approach using LASSO regression

Diabetes is a major health concern in the United States, with 34.2 million Americans affected in 2020. Unfortunately, the risk of suicide is also elevated in individuals with diabetes, with around 90,000 people with diabetes committing suicide each year. People with type 1 diabetes are three to four times more likely to attempt suicide, and those with newly diagnosed type 2 diabetes are twice as likely to attempt suicide compared to the general population. However, poor mental health comorbidity is still neglected, and more recommendations are needed to support for people with diabetes. It is widely acknowledged that the comorbidity of depression with diabetes is considered a higher risk factor for suicide attempts Previous studies have used logistic regression to identify risk factors for suicide attempts in individuals with diabetes. However, this technique can be prone to overfitting when the number of variables is high. To address this issue, we used the LASSO (Least Absolute Shrinkage and Selection Operator), a regularization technique, to reduce overfitting in a logistic regression model. It works by adding a penalty term ([lambda]) to the log-likelihood function, which shrinks the estimates of the coefficients. This process allows LASSO to act as a feature selection method, effectively setting coefficients that contribute most to the error to zero. Because few studies have focused on un derstanding the relationship between suicide attempts and diabetes, we used association rule mining ARM an explainable rule based machine learning technique, for knowledge discovery to reveal previously unknown relationships between suicide attempts and diabetes. This approach has already proved useful in the medical field, where it has been applied to electronic health record (EHR) data to discover associations such as disease co-occurrences, drug-disease associations, and symptomatic patterns of disease. However, no previous studies have used ARM to determine risk factors and predict suicide attempts in people with diabetes. The aim of this dissertation is to identify patterns of risk factors for suicide attempts in individuals with diabetes, with the long term goal of developing a clinical decision support system that can be integrated into EHRs. This system would allow healthcare providers to identify patients with diabetes at high risk of suicide attempts and provide appropriate preventive measures during outpatient clinic visits. To achieve this goal, we have three specific aims: (1) to identify potential risk factors for suicide attempts in individuals with diabetes through a literature review; (2) to investigate risk factors for suicide attempts in individuals with diabetes using LASSO regression; (3) to identify risk patterns for suicide attempts in individuals with diabetes using association rule mining. In this dissertation, we have reviewed the literature and compiled a list of data elements for suicide attempts in people with diabetes. We then retrieved data on patients with diabetes from Cerner Real-World Data [trade mark]. LASSO regression was used for feature selection, and ARM was used for investigating the risk patterns. We discovered risk patterns that are understandable and practical for healthcare providers. The findings of this research can inform suicide prevention efforts for people with diabetes and contribute to improved mental health outcomes.Includes bibliographical references

Efficient Decision Support Systems

This series is directed to diverse managerial professionals who are leading the transformation of individual domains by using expert information and domain knowledge to drive decision support systems (DSSs). The series offers a broad range of subjects addressed in specific areas such as health care, business management, banking, agriculture, environmental improvement, natural resource and spatial management, aviation administration, and hybrid applications of information technology aimed to interdisciplinary issues. This book series is composed of three volumes: Volume 1 consists of general concepts and methodology of DSSs; Volume 2 consists of applications of DSSs in the biomedical domain; Volume 3 consists of hybrid applications of DSSs in multidisciplinary domains. The book is shaped decision support strategies in the new infrastructure that assists the readers in full use of the creative technology to manipulate input data and to transform information into useful decisions for decision makers