A New Image Quantitative Method for Diagnosis and Therapeutic Response

abstract: Accurate quantitative information of tumor/lesion volume plays a critical role in diagnosis and treatment assessment. The current clinical practice emphasizes on efficiency, but sacrifices accuracy (bias and precision). In the other hand, many computational algorithms focus on improving the accuracy, but are often time consuming and cumbersome to use. Not to mention that most of them lack validation studies on real clinical data. All of these hinder the translation of these advanced methods from benchside to bedside. In this dissertation, I present a user interactive image application to rapidly extract accurate quantitative information of abnormalities (tumor/lesion) from multi-spectral medical images, such as measuring brain tumor volume from MRI. This is enabled by a GPU level set method, an intelligent algorithm to learn image features from user inputs, and a simple and intuitive graphical user interface with 2D/3D visualization. In addition, a comprehensive workflow is presented to validate image quantitative methods for clinical studies. This application has been evaluated and validated in multiple cases, including quantifying healthy brain white matter volume from MRI and brain lesion volume from CT or MRI. The evaluation studies show that this application has been able to achieve comparable results to the state-of-the-art computer algorithms. More importantly, the retrospective validation study on measuring intracerebral hemorrhage volume from CT scans demonstrates that not only the measurement attributes are superior to the current practice method in terms of bias and precision but also it is achieved without a significant delay in acquisition time. In other words, it could be useful to the clinical trials and clinical practice, especially when intervention and prognostication rely upon accurate baseline lesion volume or upon detecting change in serial lesion volumetric measurements. Obviously, this application is useful to biomedical research areas which desire an accurate quantitative information of anatomies from medical images. In addition, the morphological information is retained also. This is useful to researches which require an accurate delineation of anatomic structures, such as surgery simulation and planning.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

Automatic Segmentation of Mandible from Conventional Methods to Deep Learning-A Review

Medical imaging techniques, such as (cone beam) computed tomography and magnetic resonance imaging, have proven to be a valuable component for oral and maxillofacial surgery (OMFS). Accurate segmentation of the mandible from head and neck (H&N) scans is an important step in order to build a personalized 3D digital mandible model for 3D printing and treatment planning of OMFS. Segmented mandible structures are used to effectively visualize the mandible volumes and to evaluate particular mandible properties quantitatively. However, mandible segmentation is always challenging for both clinicians and researchers, due to complex structures and higher attenuation materials, such as teeth (filling) or metal implants that easily lead to high noise and strong artifacts during scanning. Moreover, the size and shape of the mandible vary to a large extent between individuals. Therefore, mandible segmentation is a tedious and time-consuming task and requires adequate training to be performed properly. With the advancement of computer vision approaches, researchers have developed several algorithms to automatically segment the mandible during the last two decades. The objective of this review was to present the available fully (semi)automatic segmentation methods of the mandible published in different scientific articles. This review provides a vivid description of the scientific advancements to clinicians and researchers in this field to help develop novel automatic methods for clinical applications

Multi-site, Multi-domain Airway Tree Modeling (ATM'22): A Public Benchmark for Pulmonary Airway Segmentation

Open international challenges are becoming the de facto standard for assessing computer vision and image analysis algorithms. In recent years, new methods have extended the reach of pulmonary airway segmentation that is closer to the limit of image resolution. Since EXACT'09 pulmonary airway segmentation, limited effort has been directed to quantitative comparison of newly emerged algorithms driven by the maturity of deep learning based approaches and clinical drive for resolving finer details of distal airways for early intervention of pulmonary diseases. Thus far, public annotated datasets are extremely limited, hindering the development of data-driven methods and detailed performance evaluation of new algorithms. To provide a benchmark for the medical imaging community, we organized the Multi-site, Multi-domain Airway Tree Modeling (ATM'22), which was held as an official challenge event during the MICCAI 2022 conference. ATM'22 provides large-scale CT scans with detailed pulmonary airway annotation, including 500 CT scans (300 for training, 50 for validation, and 150 for testing). The dataset was collected from different sites and it further included a portion of noisy COVID-19 CTs with ground-glass opacity and consolidation. Twenty-three teams participated in the entire phase of the challenge and the algorithms for the top ten teams are reviewed in this paper. Quantitative and qualitative results revealed that deep learning models embedded with the topological continuity enhancement achieved superior performance in general. ATM'22 challenge holds as an open-call design, the training data and the gold standard evaluation are available upon successful registration via its homepage.Comment: 32 pages, 16 figures. Homepage: https://atm22.grand-challenge.org/. Submitte

New Image Processing Methods for Ultrasound Musculoskeletal Applications

In the past few years, ultrasound (US) imaging modalities have received increasing interest as diagnostic tools for orthopedic applications. The goal for many of these novel ultrasonic methods is to be able to create three-dimensional (3D) bone visualization non-invasively, safely and with high accuracy and spatial resolution. Availability of accurate bone segmentation and 3D reconstruction methods would help correctly interpreting complex bone morphology as well as facilitate quantitative analysis. However, in vivo ultrasound images of bones may have poor quality due to uncontrollable motion, high ultrasonic attenuation and the presence of imaging artifacts, which can affect the quality of the bone segmentation and reconstruction results. In this study, we investigate the use of novel ultrasonic processing methods that can significantly improve bone visualization, segmentation and 3D reconstruction in ultrasound volumetric data acquired in applications in vivo. Specifically, in this study, we investigate the use of new elastography-based, Doppler-based and statistical shape model-based methods that can be applied to ultrasound bone imaging applications with the overall major goal of obtaining fast yet accurate 3D bone reconstructions. This study is composed to three projects, which all have the potential to significantly contribute to this major goal. The first project deals with the fast and accurate implementation of correlation-based elastography and poroelastography techniques for real-time assessment of the mechanical properties of musculoskeletal tissues. The rationale behind this project is that, iii in the future, elastography-based features can be used to reduce false positives in ultrasonic bone segmentation methods based on the differences between the mechanical properties of soft tissues and the mechanical properties of hard tissues. In this study, a hybrid computation model is designed, implemented and tested to achieve real time performance without compromise in elastographic image quality . In the second project, a Power Doppler-based signal enhancement method is designed and tested with the intent of increasing the contrast between soft tissue and bone while suppressing the contrast between soft tissue and connective tissue, which is often a cause of false positives in ultrasonic bone segmentation problems. Both in-vitro and in-vivo experiments are performed to statistically analyze the performance of this method. In the third project, a statistical shape model based bone surface segmentation method is proposed and investigated. This method uses statistical models to determine if a curve detected in a segmented ultrasound image belongs to a bone surface or not. Both in-vitro and in-vivo experiments are performed to statistically analyze the performance of this method. I conclude this Dissertation with a discussion on possible future work in the field of ultrasound bone imaging and assessment

Leveraging Supervoxels for Medical Image Volume Segmentation With Limited Supervision

The majority of existing methods for machine learning-based medical image segmentation are supervised models that require large amounts of fully annotated images. These types of datasets are typically not available in the medical domain and are difficult and expensive to generate. A wide-spread use of machine learning based models for medical image segmentation therefore requires the development of data-efficient algorithms that only require limited supervision. To address these challenges, this thesis presents new machine learning methodology for unsupervised lung tumor segmentation and few-shot learning based organ segmentation. When working in the limited supervision paradigm, exploiting the available information in the data is key. The methodology developed in this thesis leverages automatically generated supervoxels in various ways to exploit the structural information in the images. The work on unsupervised tumor segmentation explores the opportunity of performing clustering on a population-level in order to provide the algorithm with as much information as possible. To facilitate this population-level across-patient clustering, supervoxel representations are exploited to reduce the number of samples, and thereby the computational cost. In the work on few-shot learning-based organ segmentation, supervoxels are used to generate pseudo-labels for self-supervised training. Further, to obtain a model that is robust to the typically large and inhomogeneous background class, a novel anomaly detection-inspired classifier is proposed to ease the modelling of the background. To encourage the resulting segmentation maps to respect edges defined in the input space, a supervoxel-informed feature refinement module is proposed to refine the embedded feature vectors during inference. Finally, to improve trustworthiness, an architecture-agnostic mechanism to estimate model uncertainty in few-shot segmentation is developed. Results demonstrate that supervoxels are versatile tools for leveraging structural information in medical data when training segmentation models with limited supervision