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

Predicting Topological Maps for Visual Navigation in Unexplored Environments

We propose a robotic learning system for autonomous exploration and navigation in unexplored environments. We are motivated by the idea that even an unseen environment may be familiar from previous experiences in similar environments. The core of our method, therefore, is a process for building, predicting, and using probabilistic layout graphs for assisting goal-based visual navigation. We describe a navigation system that uses the layout predictions to satisfy high-level goals (e.g. "go to the kitchen") more rapidly and accurately than the prior art. Our proposed navigation framework comprises three stages: (1) Perception and Mapping: building a multi-level 3D scene graph; (2) Prediction: predicting probabilistic 3D scene graph for the unexplored environment; (3) Navigation: assisting navigation with the graphs. We test our framework in Matterport3D and show more success and efficient navigation in unseen environments.Comment: Under revie

Tracking Different Ant Species: An Unsupervised Domain Adaptation Framework and a Dataset for Multi-object Tracking

Tracking individuals is a vital part of many experiments conducted to understand collective behaviour. Ants are the paradigmatic model system for such experiments but their lack of individually distinguishing visual features and their high colony densities make it extremely difficult to perform reliable tracking automatically. Additionally, the wide diversity of their species' appearances makes a generalized approach even harder. In this paper, we propose a data-driven multi-object tracker that, for the first time, employs domain adaptation to achieve the required generalisation. This approach is built upon a joint-detection-and-tracking framework that is extended by a set of domain discriminator modules integrating an adversarial training strategy in addition to the tracking loss. In addition to this novel domain-adaptive tracking framework, we present a new dataset and a benchmark for the ant tracking problem. The dataset contains 57 video sequences with full trajectory annotation, including 30k frames captured from two different ant species moving on different background patterns. It comprises 33 and 24 sequences for source and target domains, respectively. We compare our proposed framework against other domain-adaptive and non-domain-adaptive multi-object tracking baselines using this dataset and show that incorporating domain adaptation at multiple levels of the tracking pipeline yields significant improvements. The code and the dataset are available at https://github.com/chamathabeysinghe/da-tracker

JRDB-Pose: A Large-scale Dataset for Multi-Person Pose Estimation and Tracking

Autonomous robotic systems operating in human environments must understand their surroundings to make accurate and safe decisions. In crowded human scenes with close-up human-robot interaction and robot navigation, a deep understanding requires reasoning about human motion and body dynamics over time with human body pose estimation and tracking. However, existing datasets either do not provide pose annotations or include scene types unrelated to robotic applications. Many datasets also lack the diversity of poses and occlusions found in crowded human scenes. To address this limitation we introduce JRDB-Pose, a large-scale dataset and benchmark for multi-person pose estimation and tracking using videos captured from a social navigation robot. The dataset contains challenge scenes with crowded indoor and outdoor locations and a diverse range of scales and occlusion types. JRDB-Pose provides human pose annotations with per-keypoint occlusion labels and track IDs consistent across the scene. A public evaluation server is made available for fair evaluation on a held-out test set. JRDB-Pose is available at https://jrdb.erc.monash.edu/ .Comment: 13 pages, 11 figure