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

Piecewise-stationary motion modeling and iterative smoothing to track heterogeneous particle motions in dense environments

International audienceOne of the major challenges in multiple particle tracking is the capture of extremely heterogeneous movements of objects in crowded scenes. The presence of numerous assignment candidates in the expected range of particle motion makes the tracking ambiguous and induces false positives. Lowering the ambiguity by reducing the search range, on the other hand, is not an option, as this would increase the rate of false negatives. We propose here a piecewise-stationary motion model (PMM) for the particle transport along an iterative smoother that exploits recursive tracking in multiple rounds in forward and backward temporal directions. By fusing past and future information, our method, termed PMMS, can recover fast transitions from freely or confined diffusive to directed motions with linear time complexity. To avoid false positives we complemented recursive tracking with a robust inline estimator of the search radius for assignment (a.k.a. gating), where past and future information are exploited using only two frames at each optimization step. We demonstrate the improvement of our technique on simulated data – especially the impact of density, variation in frame to frame displacements, and motion switching probability. We evaluated our technique on the 2D particle tracking challenge dataset published by Chenouard et al in 2014. Using high SNR to focus on motion modeling challenges, we show superior performance at high particle density. On biological applications, our algorithm allows us to quantify the extremely small percentage of motor-driven movements of fluorescent particles along microtubules in a dense field of unbound, diffusing particles. We also show with virus imaging that our algorithm can cope with a strong reduction in recording frame rate while keeping the same performance relative to methods relying on fast sampling

Application of the IMM-JPDA filter to multiple target tracking in total internal reflection fluorescence microscopy images

We propose a multi-target tracking method using an Interacting Multiple Model Joint Probabilistic Data Association (IMM-JPDA) filter for tracking vesicles in total internal reflection fluorescence microscopy (TIRFM) sequences. We enhance the accuracy an

Application of the IMM-JPDA filter to multiple target tracking in total internal reflection fluorescence microscopy images

Abstract. We propose a multi-target tracking method using an Interacting Multiple Model Joint Probabilistic Data Association (IMM-JPDA) filter for tracking vesicles in Total Internal Reflection Fluorescence Microscopy (TIRFM) sequences. We enhance the accuracy and reliability of the algorithm by tailoring an appropriate framework to this application. Evaluation of our algorithm is performed on both realistic synthetic data and real TIRFM data. Our results are compared against related methods and a commercial tracking software

Quantitative analysis of microscopy

Particle tracking is an essential tool for the study of dynamics of biological processes. The dynamics of these processes happens in three-dimensional (3D) space as the biological structures themselves are 3D. The focus of this thesis is on the development of single particle tracking methods for analysis of the dynamics of biological processes through the use of image processing techniques. Firstly, introduced is a novel particle tracking method that works with two-dimensional (2D) image data. This method uses the theory of Haar-like features for particle detection and trajectory linking is achieved using a combination of three Kalman filters within an interacting multiple models framework. The trajectory linking process utilises an extended state space variable which better describe the morphology and intensity profiles of the particles under investigation at their current position. This tracking method is validated using both 2D synthetically generated images as well as 2D experimentally collected images. It is shown that this method outperforms 14 other stateof-the-art methods. Next this method is used to analyse the dynamics of fluorescently labelled particles using a live-cell fluorescence microscopy technique, specifically a variant of the super-resolution (SR) method PALM, spt-PALM. From this application, conclusions about the organisation of the proteins under investigation at the cell membrane are drawn. Introduced next is a second particle tracking method which is highly efficient and capable of working with both 2D and 3D image data. This method uses a novel Haar-inspired feature for particle detection, drawing inspiration from the type of particles to be detected which are typically circular in 2D space and spherical in 3D image space. Trajectory linking in this method utilises a global nearest neighbour methodology incorporating both motion models to describe the motion of the particles under investigation and a further extended state space variable describing many more aspects of the particles to be linked. This method is validated using a variety of both 2D and 3D synthetic image data. The methods performance is compared with 14 other state-of-the-art methods showing it to be one of the best overall performing methods. Finally, analysis tools to study a SR image restoration method developed by our research group, referred to as Translation Microscopy (TRAM) are investigated [1]. TRAM can be implemented on any standardised microscope and deliver an improvement in resolution of up to 7-fold. However, the results from TRAM and other SR imaging methods require specialised tools to validate and analyse them. Tools have been developed to validate that TRAM performs correctly using a specially designed ground truth. Furthermore, through analysis of results on a biological sample corroborate other published results based on the size of biological structures, showing again that TRAM performs as expected.EPSC

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

Automatic approach for spot detection in microscopy imaging based on image processing and statistical analysis

Abstract: In biological research, fluorescence microscopy has become one of the vital tools used for observation, allowing researchers to study, visualise and image the details of intracel-lular structures which result in better understanding of biology. However, analysis of large numbers of samples is often required to draw statistically verifiable conclusions. Automated methods for analysis of microscopy image data make it possible to handle large datasets, and at the same time reduce the risk of bias imposed by manual techniques in the image analysis pipeline. This work covers automated methods for extracting quan-titative measurements from microscopy images, enabling the detection of spots resulting from different experimental conditions. The work resulted in four main significant con-tributions developed around the microscopy image analysis pipeline. Firstly, an investiga-tion into the importance of spot detection within the automated image analysis pipeline is conducted. Experimental findings show that poor spot detection adversely affected the remainder of the processing pipeline...D.Ing. (Electrical and Electronic Engineering