Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis

Super-resolution microscopy provides direct insight into fundamental biological processes occurring at length scales smaller than light’s diffraction limit. The analysis of data at such scales has brought statistical and machine learning methods into the mainstream. Here we provide a survey of data analysis methods starting from an overview of basic statistical techniques underlying the analysis of super-resolution and, more broadly, imaging data. We subsequently break down the analysis of super-resolution data into four problems: the localization problem, the counting problem, the linking problem, and what we’ve termed the interpretation problem

Multi-camera Realtime 3D Tracking of Multiple Flying Animals

Automated tracking of animal movement allows analyses that would not otherwise be possible by providing great quantities of data. The additional capability of tracking in realtime - with minimal latency - opens up the experimental possibility of manipulating sensory feedback, thus allowing detailed explorations of the neural basis for control of behavior. Here we describe a new system capable of tracking the position and body orientation of animals such as flies and birds. The system operates with less than 40 msec latency and can track multiple animals simultaneously. To achieve these results, a multi target tracking algorithm was developed based on the Extended Kalman Filter and the Nearest Neighbor Standard Filter data association algorithm. In one implementation, an eleven camera system is capable of tracking three flies simultaneously at 60 frames per second using a gigabit network of nine standard Intel Pentium 4 and Core 2 Duo computers. This manuscript presents the rationale and details of the algorithms employed and shows three implementations of the system. An experiment was performed using the tracking system to measure the effect of visual contrast on the flight speed of Drosophila melanogaster. At low contrasts, speed is more variable and faster on average than at high contrasts. Thus, the system is already a useful tool to study the neurobiology and behavior of freely flying animals. If combined with other techniques, such as `virtual reality'-type computer graphics or genetic manipulation, the tracking system would offer a powerful new way to investigate the biology of flying animals.Comment: pdfTeX using libpoppler 3.141592-1.40.3-2.2 (Web2C 7.5.6), 18 pages with 9 figure

Multiple cue integration for robust tracking in dynamic environments: application to video relighting

L'anàlisi de moviment i seguiment d'objectes ha estat un dels pricipals focus d'atenció en la comunitat de visió per computador durant les dues darreres dècades. L'interès per aquesta àrea de recerca resideix en el seu ample ventall d'aplicabilitat, que s'extén des de tasques de navegació de vehicles autònoms i robots, fins a aplications en la indústria de l'entreteniment i realitat virtual.Tot i que s'han aconseguit resultats espectaculars en problemes específics, el seguiment d'objectes continua essent un problema obert, ja que els mètodes disponibles són propensos a ser sensibles a diversos factors i condicions no estacionàries de l'entorn, com ara moviments impredictibles de l'objecte a seguir, canvis suaus o abruptes de la il·luminació, proximitat d'objectes similars o fons confusos. Enfront aquests factors de confusió la integració de múltiples característiques ha demostrat que permet millorar la robustesa dels algoritmes de seguiment. En els darrers anys, degut a la creixent capacitat de càlcul dels ordinadors, hi ha hagut un significatiu increment en el disseny de complexes sistemes de seguiment que consideren simultàniament múltiples característiques de l'objecte. No obstant, la majoria d'aquests algoritmes estan basats enheurístiques i regles ad-hoc formulades per aplications específiques, fent-ne impossible l'extrapolació a noves condicions de l'entorn.En aquesta tesi proposem un marc probabilístic general per integrar el nombre de característiques de l'objecte que siguin necessàries, permetent que interactuin mútuament per tal d'estimar-ne el seu estat amb precisió, i per tant, estimar amb precisió la posició de l'objecte que s'està seguint. Aquest marc, s'utilitza posteriorment per dissenyar un algoritme de seguiment, que es valida en diverses seqüències de vídeo que contenen canvis abruptes de posició i il·luminació, camuflament de l'objecte i deformacions no rígides. Entre les característiques que s'han utilitzat per representar l'objecte, cal destacar la paramatrització robusta del color en un espai de color dependent de l'objecte, que permet distingir-lo del fons més clarament que altres espais de color típicament ulitzats al llarg de la literatura.En la darrera part de la tesi dissenyem una tècnica per re-il·luminar tant escenes estàtiques com en moviment, de les que s'en desconeix la geometria. La re-il·luminació es realitza amb un mètode 'basat en imatges', on la generació de les images de l'escena sota noves condicions d'il·luminació s'aconsegueix a partir de combinacions lineals d'un conjunt d'imatges de referència pre-capturades, i que han estat generades il·luminant l'escena amb patrons de llum coneguts. Com que la posició i intensitat de les fonts d'il.luminació que formen aquests patrons de llum es pot controlar, és natural preguntar-nos: quina és la manera més òptima d'il·luminar una escena per tal de reduir el nombre d'imatges de referència? Demostrem que la millor manera d'il·luminar l'escena (és a dir, la que minimitza el nombre d'imatges de referència) no és utilitzant una seqüència de fonts d'il·luminació puntuals, com es fa generalment, sinó a través d'una seqüència de patrons de llum d'una base d'il·luminació depenent de l'objecte. És important destacar que quan es re-il·luminen seqüències de vídeo, les imatges successives s'han d'alinear respecte a un sistema de coordenades comú. Com que cada imatge ha estat generada per un patró de llum diferent il·uminant l'escena, es produiran canvis d'il·luminació bruscos entre imatges de referència consecutives. Sota aquestes circumstàncies, el mètode de seguiment proposat en aquesta tesi juga un paper fonamental. Finalment, presentem diversos resultats on re-il·luminem seqüències de vídeo reals d'objectes i cares d'actors en moviment. En cada cas, tot i que s'adquireix un únic vídeo, som capaços de re-il·luminar una i altra vegada, controlant la direcció de la llum, la seva intensitat, i el color.Motion analysis and object tracking has been one of the principal focus of attention over the past two decades within the computer vision community. The interest of this research area lies in its wide range of applicability, extending from autonomous vehicle and robot navigation tasks, to entertainment and virtual reality applications.Even though impressive results have been obtained in specific problems, object tracking is still an open problem, since available methods are prone to be sensitive to several artifacts and non-stationary environment conditions, such as unpredictable target movements, gradual or abrupt changes of illumination, proximity of similar objects or cluttered backgrounds. Multiple cue integration has been proved to enhance the robustness of the tracking algorithms in front of such disturbances. In recent years, due to the increasing power of the computers, there has been a significant interest in building complex tracking systems which simultaneously consider multiple cues. However, most of these algorithms are based on heuristics and ad-hoc rules formulated for specific applications, making impossible to extrapolate them to new environment conditions.In this dissertation we propose a general probabilistic framework to integrate as many object features as necessary, permitting them to mutually interact in order to obtain a precise estimation of its state, and thus, a precise estimate of the target position. This framework is utilized to design a tracking algorithm, which is validated on several video sequences involving abrupt position and illumination changes, target camouflaging and non-rigid deformations. Among the utilized features to represent the target, it is important to point out the use of a robust parameterization of the target color in an object dependent colorspace which allows to distinguish the object from the background more clearly than other colorspaces commonly used in the literature.In the last part of the dissertation, we design an approach for relighting static and moving scenes with unknown geometry. The relighting is performed through an -image-based' methodology, where the rendering under new lighting conditions is achieved by linear combinations of a set of pre-acquired reference images of the scene illuminated by known light patterns. Since the placement and brightness of the light sources composing such light patterns can be controlled, it is natural to ask: what is the optimal way to illuminate the scene to reduce the number of reference images that are needed? We show that the best way to light the scene (i.e., the way that minimizes the number of reference images) is not using a sequence of single, compact light sources as is most commonly done, but rather to use a sequence of lighting patterns as given by an object-dependent lighting basis. It is important to note that when relighting video sequences, consecutive images need to be aligned with respect to a common coordinate frame. However, since each frame is generated by a different light pattern illuminating the scene, abrupt illumination changes between consecutive reference images are produced. Under these circumstances, the tracking framework designed in this dissertation plays a central role. Finally, we present several relighting results on real video sequences of moving objects, moving faces, and scenes containing both. In each case, although a single video clip was captured, we are able to relight again and again, controlling the lighting direction, extent, and color.Postprint (published version

Stereo Vision Tracking of Multiple Objects in Complex Indoor Environments

This paper presents a novel system capable of solving the problem of tracking multiple targets in a crowded, complex and dynamic indoor environment, like those typical of mobile robot applications. The proposed solution is based on a stereo vision set in the acquisition step and a probabilistic algorithm in the obstacles position estimation process. The system obtains 3D position and speed information related to each object in the robot’s environment; then it achieves a classification between building elements (ceiling, walls, columns and so on) and the rest of items in robot surroundings. All objects in robot surroundings, both dynamic and static, are considered to be obstacles but the structure of the environment itself. A combination of a Bayesian algorithm and a deterministic clustering process is used in order to obtain a multimodal representation of speed and position of detected obstacles. Performance of the final system has been tested against state of the art proposals; test results validate the authors’ proposal. The designed algorithms and procedures provide a solution to those applications where similar multimodal data structures are found