Simplified multitarget tracking using the PHD filter for microscopic video data

The probability hypothesis density (PHD) filter from the theory of random finite sets is a well-known method for multitarget tracking. We present the Gaussian mixture (GM) and improved sequential Monte Carlo implementations of the PHD filter for visual tracking. These implementations are shown to provide advantages over previous PHD filter implementations on visual data by removing complications such as clustering and data association and also having beneficial computational characteristics. The GM-PHD filter is deployed on microscopic visual data to extract trajectories of free-swimming bacteria in order to analyze their motion. Using this method, a significantly larger number of tracks are obtained than was previously possible. This permits calculation of reliable distributions for parameters of bacterial motion. The PHD filter output was tested by checking agreement with a careful manual analysis. A comparison between the PHD filter and alternative tracking methods was carried out using simulated data, demonstrating superior performance by the PHD filter in a range of realistic scenarios

A multiple model probability hypothesis density tracker for time-lapse cell microscopy sequences

Abstract. Quantitative analysis of the dynamics of tiny cellular and subcellular structures in time-lapse cell microscopy sequences requires the development of a reliable multi-target tracking method capable of tracking numerous similar targets in the presence of high levels of noise, high target density, maneuvering motion patterns and intricate interactions. The linear Gaussian jump Markov system probability hypothesis density (LGJMS-PHD) filter is a recent Bayesian tracking filter that is well-suited for this task. However, the existing recursion equations for this filter do not consider a state-dependent transition probability matrix. As required in many biological applications, we propose a new closed-form recursion that incorporates this assumption and introduce a general framework for particle tracking using the proposed filter. We apply our scheme to multi-target tracking in total internal reflection fluorescence microscopy (TIRFM) sequences and evaluate the performance of our filter against the existing LGJMS-PHD and IMM-JPDA filters

Blending of Learning-based Tracking and Object Detection for Monocular Camera-based Target Following

Deep learning has recently started being applied to visual tracking of generic objects in video streams. For the purposes of robotics applications, it is very important for a target tracker to recover its track if it is lost due to heavy or prolonged occlusions or motion blur of the target. We present a real-time approach which fuses a generic target tracker and object detection module with a target re-identification module. Our work focuses on improving the performance of Convolutional Recurrent Neural Network-based object trackers in cases where the object of interest belongs to the category of \emph{familiar} objects. Our proposed approach is sufficiently lightweight to track objects at 85-90 FPS while attaining competitive results on challenging benchmarks.Comment: Accepted in 24th International Symposium on Mathematical Theory of Networks and Systems (MTNS 2020): Cambridge, UK (updated conference date: 23-27 August 2021

Bayesian multi-target tracking: application to total internal reflection fluorescence microscopy

This thesis focuses on the problem of automated tracking of tiny cellular and sub-cellular structures, known as particles, in the sequences acquired from total internal reflection fluorescence microscopy (TIRFM) imaging technique. Our primary biological motivation is to develop an automated system for tracking the sub-cellular structures involving exocytosis (an intracellular mechanism) which is helpful for studying the possible causes of the defects in diseases such as diabetes and obesity. However, all methods proposed in this thesis are generalized to be applicable for a wide range of particle tracking applications. A reliable multi-particle tracking method should be capable of tracking numerous similar objects in the presence of high levels of noise, high target density and complex motions and interactions. In this thesis, we choose the Bayesian filtering framework as our main approach to deal with this problem. We focus on the approaches that work based on detections. Therefore, in this thesis, we first propose a method that robustly detects the particles in the noisy TIRFM sequences with inhomogeneous and time-varying background. In order to evaluate our detection and tracking methods on the sequences with known and reliable ground truth, we also present a framework for generating realistic synthetic TIRFM data. To propose a reliable multi-particle tracking method for TIRFM sequences, we suggest a framework by combining two robust Bayesian filters, the interacting multiple model and joint probabilistic data association (IMM-JPDA) filters. The performance of our particle tracking method is compared against those of several popular and state-of-the art particle tracking approaches on both synthetic and real sequences. Although our approach performs well in tracking particles, it can be very computationally demanding for the applications with dense targets with poor detections. To propose a computationally cheap, but reliable, multi-particle tracking method, we investigate the performance of a recent multi-target Bayesian filter based on random finite theory, the probability hypothesis density (PHD) filter, on our application. To this end, we propose a general framework for tracking particles using this filter. Moreover, we assess the performance of our proposed PHD filter on both synthetic and real sequences with high level of noise and particle density. We compare its results from both aspects of accuracy and processing time against our IMM-JPDA filter. Finally, we suggest a framework for tracking particles in a challenging problem where the noise characteristic and the background intensity of sequences change during the acquisition process which make detection profile and clutter rate time-variant. To deal with this, we propose a bootstrap filter using another type of the random finite set based Bayesian filters, the cardinalized PHD (CPHD) filter, composed of an estimator and a tracker. The estimator adaptively estimates the required meta parameters for the tracker such as clutter rate and the detection probability while the tracker estimates the state of the targets. We evaluate the performance of our bootstrap on both synthetic and real sequences under these time-varying conditions. Moreover, its performance is compared against those of our other particle trackers as well as the state-of-the art particle tracking approaches

Methods for Automated Neuron Image Analysis

Knowledge of neuronal cell morphology is essential for performing specialized analyses in the endeavor to understand neuron behavior and unravel the underlying principles of brain function. Neurons can be captured with a high level of detail using modern microscopes, but many neuroscientific studies require a more explicit and accessible representation than offered by the resulting images, underscoring the need for digital reconstruction of neuronal morphology from the images into a tree-like graph structure. This thesis proposes new computational methods for automated detection and reconstruction of neurons from fluorescence microscopy images. Specifically, the successive chapters describe and evaluate original solutions to problems such as the detection of landmarks (critical points) of the neuronal tree, complete tracing and reconstruction of the tree, and the detection of regions containing neurons in high-content screens

Contextual information aided target tracking and path planning for autonomous ground vehicles

Recently, autonomous vehicles have received worldwide attentions from academic research, automotive industry and the general public. In order to achieve a higher level of automation, one of the most fundamental requirements of autonomous vehicles is the capability to respond to internal and external changes in a safe, timely and appropriate manner. Situational awareness and decision making are two crucial enabling technologies for safe operation of autonomous vehicles. This thesis presents a solution for improving the automation level of autonomous vehicles in both situational awareness and decision making aspects by utilising additional domain knowledge such as constraints and influence on a moving object caused by environment and interaction between different moving objects. This includes two specific sub-systems, model based target tracking in environmental perception module and motion planning in path planning module. In the first part, a rigorous Bayesian framework is developed for pooling road constraint information and sensor measurement data of a ground vehicle to provide better situational awareness. Consequently, a new multiple targets tracking (MTT) strategy is proposed for solving target tracking problems with nonlinear dynamic systems and additional state constraints. Besides road constraint information, a vehicle movement is generally affected by its surrounding environment known as interaction information. A novel dynamic modelling approach is then proposed by considering the interaction information as virtual force which is constructed by involving the target state, desired dynamics and interaction information. The proposed modelling approach is then accommodated in the proposed MTT strategy for incorporating different types of domain knowledge in a comprehensive manner. In the second part, a new path planning strategy for autonomous vehicles operating in partially known dynamic environment is suggested. The proposed MTT technique is utilized to provide accurate on-board tracking information with associated level of uncertainty. Based on the tracking information, a path planning strategy is developed to generate collision free paths by not only predicting the future states of the moving objects but also taking into account the propagation of the associated estimation uncertainty within a given horizon. To cope with a dynamic and uncertain road environment, the strategy is implemented in a receding horizon fashion

Robust Automatic Multi-Sperm Tracking in Time-Lapse Images

Human sperm cell counting, tracking and motility analysis is of significant interest to biologists studying sperm function and to medical practitioners evaluating male infertility. Today, the prevailing method for analyzing sperm at fertility clinics and research laboratories is laborious and subjective. Namely, the number and quality of sperm are often visually appraised by technicians using a microscope. Although total sperm count and sperm concentration can be reasonably estimated when standard protocols are applied, they have little diagnostic value except in identifying pathologically extreme abnormalities. More dynamic sperm swimming parameters such as curvilinear velocity (VCL), straight-line velocity (VSL), linearity of forward progression (LIN) and amplitude of lateral head displacement (ALH) are increasingly believed to have clinical significance in predicting infertility but are impossible for a human observer to visually discern. Expensive computer-assisted semen analysis (CASA) instruments are also sometimes used but are severely encumbered by crude ad-hoc tracking algorithms which cannot track sperm in close proximity or whose paths intersect and are typically limited to analyzing video clips of < 1 sec duration.In this thesis, we present a robust automatic multi-sperm tracking algorithm that can measure dynamic sperm motility parameters over time in pre-recorded time-lapse images. This effort is informed by progress in signal processing and target tracking technologies over the last three decades. Multi-target tracking algorithms originally developed for radar, sonar and video processing have addressed similar problems in other domains. In this thesis, we demonstrate that their methodologies can be used for sperm tracking and motility analysis. To resolve sperm measurement-to-track association conflicts, we applied and evaluated three multi-target tracking algorithms: the probabilistic data association filter (PDAF), the joint probabilistic data association filter (JPDAF) and the exact nearest neighbor extension to the JPDAF (ENN-JPDAF). We validated the accuracy of our tracking and motility analysis by using simulated sperm trajectories whose ground truth tracks were perfectly known. Using samples collected from five patients at a fertility clinic, we demonstrated automatic sperm detection and tracking even during challenging multi-sperm collision events. Combined analysis, testing and simulation support the use of probabilistic data association techniques robust automatic multi-sperm tracking. This method could provide fertility specialists with new data visualizations and interpretations previously impossible with existing laboratory protocols