Point tracking: an a-contrario approach

In this work, we propose a new approach to recover trajectories from points previously detected in a sequence of images. In presence of spurious and missing detections, actual trajectories can be characterized by an a-contrario model, that estimates the probability of observing a similar trajectory in random data. This results in a single criterion combining trajectory characteristics (duration, number of points, smoothness) and data statistics (number of images and detected points), which can then be used to drive a dynamic programming algorithm able to extract sequentially the most meaningful trajectories. The performances obtained on synthetic and real-world data are studied in detail, and shown to compare favorably to the state-of-the-art ROADS algorithm

Localization of protein aggregation in Escherichia coli is governed by diffusion and nucleoid macromolecular crowding effect

Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian). Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3d individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids) are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion- aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of "soft" intracellular structuring (based on macromolecular crowding) in diffusion-based protein localization in E. coli.Comment: PLoS Computational Biology (2013

Méthodes probabiliste pour le suivi de points et l'analyse d'images biologiques

The subject of this thesis is the problem of object tracking, that we approached using statistical methods. The first contribution of this work is the conception of a tracking algorithm of bacterial cells in a sequence of image, to recover their lineage; this work has led to the implementation of a software suite that is currently in use in a research laboratory. The second contribution is a theoretical study of the detection of trajectories in a cloud of points. We define a trajectory detector using the a-contrario statistical framework, which requires essentially no parameter to run. This detector yields remarkable results, and is in particular able to detect trajectories in sequences containing a large number of noise points, while keeping a very low number of false detections. We then study more specifically the correspondence problem between two point clouds, a problem often encountered for the detection of trajectories or the matching of stereographic images. We first introduce a theoretically optimal model for the point correspondence problem that makes it possible to study the performances of several classical algorithms in a variety of conditions. We then formulate a parameterless point correspondence algorithm using the a-contrario framework, that enables us to define a new trajectory tracking algorithm.Nous nous intéressons dans cette thèse au problème du suivi d'objets, que nous abordons par des méthodes statistiques. La première contribution de cette thèse est la conception d'un algorithme de suivi de bactéries dans une séquence d'image et de reconstruction de leur lignage, travail ayant donné lieu à la réalisation d'une suite logicielle aujourd'hui utilisée dans un laboratoire de recherche en biologie. La deuxième contribution est une étude théorique du problème de la détection de trajectoires dans un nuage de points. Nous définissons un détecteur de trajectoires utilisant le cadre statistique des méthodes a contrario, qui ne requiert essentiellement aucun paramètre pour fonctionner. Ce détecteur fournit des résultats remarquables, et permet notamment de retrouver des trajectoires dans des séquences contenant un grand nombre de points de bruit, tout en conservant un taux de fausses détections de trajectoires très faible. Nous étudions ensuite plus spécifiquement le problème de l'affectation de nuages de points entre deux images, problème rencontré notamment pour la détection de trajectoires ou l'appariement d'images stéréographiques. Nous proposons d'abord un modèle théoriquement optimal pour l'affectation de points qui nous permet d'étudier les performances de plusieurs algorithmes classiques dans différentes conditions. Nous formulons ensuite un algorithme sans paramètre en utilisant le cadre a contrario, ce qui nous permet ensuite d'obtenir un nouvel algorithme de suivi de trajectoires