Computational Methods for Segmentation of Multi-Modal Multi-Dimensional Cardiac Images

Segmentation of the heart structures helps compute the cardiac contractile function quantified via the systolic and diastolic volumes, ejection fraction, and myocardial mass, representing a reliable diagnostic value. Similarly, quantification of the myocardial mechanics throughout the cardiac cycle, analysis of the activation patterns in the heart via electrocardiography (ECG) signals, serve as good cardiac diagnosis indicators. Furthermore, high quality anatomical models of the heart can be used in planning and guidance of minimally invasive interventions under the assistance of image guidance. The most crucial step for the above mentioned applications is to segment the ventricles and myocardium from the acquired cardiac image data. Although the manual delineation of the heart structures is deemed as the gold-standard approach, it requires significant time and effort, and is highly susceptible to inter- and intra-observer variability. These limitations suggest a need for fast, robust, and accurate semi- or fully-automatic segmentation algorithms. However, the complex motion and anatomy of the heart, indistinct borders due to blood flow, the presence of trabeculations, intensity inhomogeneity, and various other imaging artifacts, makes the segmentation task challenging. In this work, we present and evaluate segmentation algorithms for multi-modal, multi-dimensional cardiac image datasets. Firstly, we segment the left ventricle (LV) blood-pool from a tri-plane 2D+time trans-esophageal (TEE) ultrasound acquisition using local phase based filtering and graph-cut technique, propagate the segmentation throughout the cardiac cycle using non-rigid registration-based motion extraction, and reconstruct the 3D LV geometry. Secondly, we segment the LV blood-pool and myocardium from an open-source 4D cardiac cine Magnetic Resonance Imaging (MRI) dataset by incorporating average atlas based shape constraint into the graph-cut framework and iterative segmentation refinement. The developed fast and robust framework is further extended to perform right ventricle (RV) blood-pool segmentation from a different open-source 4D cardiac cine MRI dataset. Next, we employ convolutional neural network based multi-task learning framework to segment the myocardium and regress its area, simultaneously, and show that segmentation based computation of the myocardial area is significantly better than that regressed directly from the network, while also being more interpretable. Finally, we impose a weak shape constraint via multi-task learning framework in a fully convolutional network and show improved segmentation performance for LV, RV and myocardium across healthy and pathological cases, as well as, in the challenging apical and basal slices in two open-source 4D cardiac cine MRI datasets. We demonstrate the accuracy and robustness of the proposed segmentation methods by comparing the obtained results against the provided gold-standard manual segmentations, as well as with other competing segmentation methods

Exploiting Structural Regularities and Beyond: Vision-based Localization and Mapping in Man-Made Environments

Image-based estimation of camera motion, known as visual odometry (VO), plays a very important role in many robotic applications such as control and navigation of unmanned mobile robots, especially when no external navigation reference signal is available. The core problem of VO is the estimation of the camera’s ego-motion (i.e. tracking) either between successive frames, namely relative pose estimation, or with respect to a global map, namely absolute pose estimation. This thesis aims to develop efficient, accurate and robust VO solutions by taking advantage of structural regularities in man-made environments, such as piece-wise planar structures, Manhattan World and more generally, contours and edges. Furthermore, to handle challenging scenarios that are beyond the limits of classical sensor based VO solutions, we investigate a recently emerging sensor — the event camera and study on event-based mapping — one of the key problems in the event-based VO/SLAM. The main achievements are summarized as follows. First, we revisit an old topic on relative pose estimation: accurately and robustly estimating the fundamental matrix given a collection of independently estimated homograhies. Three classical methods are reviewed and then we show a simple but nontrivial two-step normalization within the direct linear method that achieves similar performance to the less attractive and more computationally intensive hallucinated points based method. Second, an efficient 3D rotation estimation algorithm for depth cameras in piece-wise planar environments is presented. It shows that by using surface normal vectors as an input, planar modes in the corresponding density distribution function can be discovered and continuously tracked using efficient non-parametric estimation techniques. The relative rotation can be estimated by registering entire bundles of planar modes by using robust L1-norm minimization. Third, an efficient alternative to the iterative closest point algorithm for real-time tracking of modern depth cameras in ManhattanWorlds is developed. We exploit the common orthogonal structure of man-made environments in order to decouple the estimation of the rotation and the three degrees of freedom of the translation. The derived camera orientation is absolute and thus free of long-term drift, which in turn benefits the accuracy of the translation estimation as well. Fourth, we look into a more general structural regularity—edges. A real-time VO system that uses Canny edges is proposed for RGB-D cameras. Two novel alternatives to classical distance transforms are developed with great properties that significantly improve the classical Euclidean distance field based methods in terms of efficiency, accuracy and robustness. Finally, to deal with challenging scenarios that go beyond what standard RGB/RGB-D cameras can handle, we investigate the recently emerging event camera and focus on the problem of 3D reconstruction from data captured by a stereo event-camera rig moving in a static scene, such as in the context of stereo Simultaneous Localization and Mapping

Filter-Based Probabilistic Markov Random Field Image Priors: Learning, Evaluation, and Image Analysis

Markov random fields (MRF) based on linear filter responses are one of the most popular forms for modeling image priors due to their rigorous probabilistic interpretations and versatility in various applications. In this dissertation, we propose an application-independent method to quantitatively evaluate MRF image priors using model samples. To this end, we developed an efficient auxiliary-variable Gibbs samplers for a general class of MRFs with flexible potentials. We found that the popular pairwise and high-order MRF priors capture image statistics quite roughly and exhibit poor generative properties. We further developed new learning strategies and obtained high-order MRFs that well capture the statistics of the inbuilt features, thus being real maximum-entropy models, and other important statistical properties of natural images, outlining the capabilities of MRFs. We suggest a multi-modal extension of MRF potentials which not only allows to train more expressive priors, but also helps to reveal more insights of MRF variants, based on which we are able to train compact, fully-convolutional restricted Boltzmann machines (RBM) that can model visual repetitive textures even better than more complex and deep models. The learned high-order MRFs allow us to develop new methods for various real-world image analysis problems. For denoising of natural images and deconvolution of microscopy images, the MRF priors are employed in a pure generative setting. We propose efficient sampling-based methods to infer Bayesian minimum mean squared error (MMSE) estimates, which substantially outperform maximum a-posteriori (MAP) estimates and can compete with state-of-the-art discriminative methods. For non-rigid registration of live cell nuclei in time-lapse microscopy images, we propose a global optical flow-based method. The statistics of noise in fluorescence microscopy images are studied to derive an adaptive weighting scheme for increasing model robustness. High-order MRFs are also employed to train image filters for extracting important features of cell nuclei and the deformation of nuclei are then estimated in the learned feature spaces. The developed method outperforms previous approaches in terms of both registration accuracy and computational efficiency

Exploiting Points and Lines in Regression Forests for RGB-D Camera Relocalization

Camera relocalization plays a vital role in many robotics and computer vision tasks, such as global localization, recovery from tracking failure and loop closure detection. Recent random forests based methods exploit randomly sampled pixel comparison features to predict 3D world locations for 2D image locations to guide the camera pose optimization. However, these image features are only sampled randomly in the images, without considering the spatial structures or geometric information, leading to large errors or failure cases with the existence of poorly textured areas or in motion blur. Line segment features are more robust in these environments. In this work, we propose to jointly exploit points and lines within the framework of uncertainty driven regression forests. The proposed approach is thoroughly evaluated on three publicly available datasets against several strong state-of-the-art baselines in terms of several different error metrics. Experimental results prove the efficacy of our method, showing superior or on-par state-of-the-art performance.Comment: published as a conference paper at 2018 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS

A Comprehensive Survey of Deep Learning in Remote Sensing: Theories, Tools and Challenges for the Community

In recent years, deep learning (DL), a re-branding of neural networks (NNs), has risen to the top in numerous areas, namely computer vision (CV), speech recognition, natural language processing, etc. Whereas remote sensing (RS) possesses a number of unique challenges, primarily related to sensors and applications, inevitably RS draws from many of the same theories as CV; e.g., statistics, fusion, and machine learning, to name a few. This means that the RS community should be aware of, if not at the leading edge of, of advancements like DL. Herein, we provide the most comprehensive survey of state-of-the-art RS DL research. We also review recent new developments in the DL field that can be used in DL for RS. Namely, we focus on theories, tools and challenges for the RS community. Specifically, we focus on unsolved challenges and opportunities as it relates to (i) inadequate data sets, (ii) human-understandable solutions for modelling physical phenomena, (iii) Big Data, (iv) non-traditional heterogeneous data sources, (v) DL architectures and learning algorithms for spectral, spatial and temporal data, (vi) transfer learning, (vii) an improved theoretical understanding of DL systems, (viii) high barriers to entry, and (ix) training and optimizing the DL.Comment: 64 pages, 411 references. To appear in Journal of Applied Remote Sensin

Fast Monte-Carlo Localization on Aerial Vehicles using Approximate Continuous Belief Representations

Size, weight, and power constrained platforms impose constraints on computational resources that introduce unique challenges in implementing localization algorithms. We present a framework to perform fast localization on such platforms enabled by the compressive capabilities of Gaussian Mixture Model representations of point cloud data. Given raw structural data from a depth sensor and pitch and roll estimates from an on-board attitude reference system, a multi-hypothesis particle filter localizes the vehicle by exploiting the likelihood of the data originating from the mixture model. We demonstrate analysis of this likelihood in the vicinity of the ground truth pose and detail its utilization in a particle filter-based vehicle localization strategy, and later present results of real-time implementations on a desktop system and an off-the-shelf embedded platform that outperform localization results from running a state-of-the-art algorithm on the same environment