Globally Optimal Cell Tracking using Integer Programming

We propose a novel approach to automatically tracking cell populations in time-lapse images. To account for cell occlusions and overlaps, we introduce a robust method that generates an over-complete set of competing detection hypotheses. We then perform detection and tracking simultaneously on these hypotheses by solving to optimality an integer program with only one type of flow variables. This eliminates the need for heuristics to handle missed detections due to occlusions and complex morphology. We demonstrate the effectiveness of our approach on a range of challenging sequences consisting of clumped cells and show that it outperforms state-of-the-art techniques.Comment: Engin T\"uretken and Xinchao Wang contributed equally to this wor

Detecting and Tracking Cells using Network Flow Programming

We propose a novel approach to automatically detecting and tracking cell populations in time-lapse images. Unlike earlier ones that rely on linking a predetermined and potentially under-complete set of detections, we generate an overcomplete set of competing detection hypotheses. We then perform detection and tracking simultaneously by solving an integer program to find an optimal and consistent subset. This eliminates the need for heuristics to handle missed detections due to occlusions and complex morphology. We demonstrate the effectiveness of our approach on a range of challenging image sequences consisting of clumped cells and show that it outperforms state-of-the-art techniques

Network Flow Integer Programming to Track Elliptical Cells in Time-Lapse Sequences

We propose a novel approach to automatically tracking elliptical cell populations in time-lapse image sequences. Given an initial segmentation, we account for partial occlusions and overlaps by generating an over-complete set of competing detection hypotheses. To this end, we fit ellipses to portions of the initial regions and build a hierarchy of ellipses, which are then treated as cell candidates. We then select temporally consistent ones by solving to optimality an integer program with only one type of flow variables. This eliminates the need for heuristics to handle missed detections due to partial occlusions and complex morphology. We demonstrate the effectiveness of our approach on a range of challenging sequences consisting of clumped cells and show that it outperforms state-of-the-art techniques

Tracking Interacting Objects in Image Sequences

Object tracking in image sequences is a key challenge in computer vision. Its goal is to follow objects that move or evolve over time while preserving the identity of each object. However, most existing approaches focus on one class of objects and model only very simple interactions, such as the fact that different objects do not occupy the same spatial location at a given time instance. They ignore that objects may interact in more complex ways. For example, in a parking lot, a person may get in a car and become invisible in the scene. In this thesis, we focus on tracking interacting objects in image sequences. We show that by exploiting the relationship between different objects, we can achieve more reliable tracking results. We explore a wide range of applications, such as tracking players and the ball in team sports, tracking cars and people in a parking lot and tracking dividing cells in biomedical imagery. We start by tracking the ball in team sports, which is a very challenging task because the ball is often occluded by the players. We propose a sequential approach that tracks the players first, and then tracks the ball by deciding which player, if any, is in possession of the ball at any given time. This is very different from standard approaches that first attempt to track the ball and only then to assign possession. We show that our method substantially increases performance when applied to long basketball and soccer sequences. We then focus on simultaneously tracking interacting objects. We achieve this by formulating the tracking problem as a network-flow Mixed Integer Program, and expressing the fact that one object can appear or disappear at locations of another in terms of linear flow constraints. We demonstrate our method on scenes involving cars and passengers, bags being carried and dropped by people, and balls being passed from one player to the next in team sports. In particular, we show that by estimating jointly and globally the trajectories of different types of objects, the presence of the ones which were not initially detected based solely on image evidence can be inferred from the detections of the others. We finally extend our approach to dividing cells in biomedical imagery. In this case, cells interact by overlapping with each other and giving birth to daughter cells. We propose a novel approach to automatically detecting and tracking cell populations in time-lapse images. Unlike earlier approaches that rely on linking a predetermined and potentially incomplete set of detections, we generate an overcomplete set of competing detection hypotheses. We then perform detection and tracking simultaneously by solving an integer program to find the optimal and consistent subset. This eliminates the need for heuristics to handle missed detections due to occlusions and complex morphology. We demonstrate the effectiveness of our approach on a range of challenging image sequences consisting of clumped cells and show that it outperforms the state-of-the-art techniques

Fast parametric snakes for 3D microscopy

We present a new fast active contour for images in 3D microscopy. We introduce a fully parametric design that relies on exponential B-spline bases and allows us to impose a sphere-like topology. The proposed 3D snake can approximate blob-like objects with good accuracy. The optimization process is remarkably fast. Our technique yields successful segmentation results even for a challenging data set where object contours are not well defined. This happens because our parametric approach allows us to favor prior shapes. This work comes with a companion software that allows extensive interactions between the end-user and our snakes through the intuitive manipulation of the few control points that fully characterize them