Active skeleton for bacteria modeling

The investigation of spatio-temporal dynamics of bacterial cells and their molecular components requires automated image analysis tools to track cell shape properties and molecular component locations inside the cells. In the study of bacteria aging, the molecular components of interest are protein aggregates accumulated near bacteria boundaries. This particular location makes very ambiguous the correspondence between aggregates and cells, since computing accurately bacteria boundaries in phase-contrast time-lapse imaging is a challenging task. This paper proposes an active skeleton formulation for bacteria modeling which provides several advantages: an easy computation of shape properties (perimeter, length, thickness, orientation), an improved boundary accuracy in noisy images, and a natural bacteria-centered coordinate system that permits the intrinsic location of molecular components inside the cell. Starting from an initial skeleton estimate, the medial axis of the bacterium is obtained by minimizing an energy function which incorporates bacteria shape constraints. Experimental results on biological images and comparative evaluation of the performances validate the proposed approach for modeling cigar-shaped bacteria like Escherichia coli. The Image-J plugin of the proposed method can be found online at http://fluobactracker.inrialpes.fr.Comment: Published in Computer Methods in Biomechanics and Biomedical Engineering: Imaging and Visualizationto appear i

Shape-based invariant features extraction for object recognition

International audienceThe emergence of new technologies enables generating large quantity of digital information including images; this leads to an increasing number of generated digital images. Therefore it appears a necessity for automatic systems for image retrieval. These systems consist of techniques used for query specification and re-trieval of images from an image collection. The most frequent and the most com-mon means for image retrieval is the indexing using textual keywords. But for some special application domains and face to the huge quantity of images, key-words are no more sufficient or unpractical. Moreover, images are rich in content; so in order to overcome these mentioned difficulties, some approaches are pro-posed based on visual features derived directly from the content of the image: these are the content-based image retrieval (CBIR) approaches. They allow users to search the desired image by specifying image queries: a query can be an exam-ple, a sketch or visual features (e.g., colour, texture and shape). Once the features have been defined and extracted, the retrieval becomes a task of measuring simi-larity between image features. An important property of these features is to be in-variant under various deformations that the observed image could undergo. In this chapter, we will present a number of existing methods for CBIR applica-tions. We will also describe some measures that are usually used for similarity measurement. At the end, and as an application example, we present a specific ap-proach, that we are developing, to illustrate the topic by providing experimental results

A Stochastic Grammar of Images

This exploratory paper quests for a stochastic and context sensitive grammar of images. The grammar should achieve the following four objectives and thus serves as a unified framework of representation, learning, and recognition for a large number of object categories. (i) The grammar represents both the hierarchical decompositions from scenes, to objects, parts, primitives and pixels by terminal and non-terminal nodes and the contexts for spatial and functional relations by horizontal links between the nodes. It formulates each object category as the set of all possible valid configurations produced by the grammar. (ii) The grammar is embodied in a simple And-Or graph representation where each Or-node points to alternative sub-configurations and an And-node is decomposed into a number of components. This representation supports recursive top-down/bottom-up procedures for image parsing under the Bayesian framework and make it convenient to scale up in complexity. Given an input image, the image parsing task constructs a most probable parse graph on-the-fly as the output interpretation and this parse graph is a subgraph of the And-Or graph after making choice on the Or-nodes. (iii) A probabilistic model is defined on this And-Or graph representation to account for the natural occurrence frequency of objects and parts as well as their relations. This model is learned from a relatively small training set per category and then sampled to synthesize a large number of configurations to cover novel object instances in the test set. This generalization capability is mostly missing in discriminative machine learning methods and can largely improve recognition performance in experiments. (iv) To fill the well-known semantic gap between symbols and raw signals, the grammar includes a series of visual dictionaries and organizes them through graph composition. At the bottom-level the dictionary is a set of image primitives each having a number of anchor points with open bonds to link with other primitives. These primitives can be combined to form larger and larger graph structures for parts and objects. The ambiguities in inferring local primitives shall be resolved through top-down computation using larger structures. Finally these primitives forms a primal sketch representation which will generate the input image with every pixels explained. The proposal grammar integrates three prominent representations in the literature: stochastic grammars for composition, Markov (or graphical) models for contexts, and sparse coding with primitives (wavelets). It also combines the structure-based and appearance based methods in the vision literature. Finally the paper presents three case studies to illustrate the proposed grammar.Mathematic

Représentations de niveau intermédiaire pour la modélisation d'objets

In this thesis we propose the use of mid-level representations, and in particular i) medial axes, ii) object parts, and iii)convolutional features, for modelling objects.The first part of the thesis deals with detecting medial axes in natural RGB images. We adopt a learning approach, utilizing colour, texture and spectral clustering features, to build a classifier that produces a dense probability map for symmetry. Multiple Instance Learning (MIL) allows us to treat scale and orientation as latent variables during training, while a variation based on random forests offers significant gains in terms of running time.In the second part of the thesis we focus on object part modeling using both hand-crafted and learned feature representations. We develop a coarse-to-fine, hierarchical approach that uses probabilistic bounds for part scores to decrease the computational cost of mixture models with a large number of HOG-based templates. These efficiently computed probabilistic bounds allow us to quickly discard large parts of the image, and evaluate the exact convolution scores only at promising locations. Our approach achieves a "4times-5times" speedup over the naive approach with minimal loss in performance.We also employ convolutional features to improve object detection. We use a popular CNN architecture to extract responses from an intermediate convolutional layer. We integrate these responses in the classic DPM pipeline, replacing hand-crafted HOG features, and observe a significant boost in detection performance (~14.5% increase in mAP).In the last part of the thesis we experiment with fully convolutional neural networks for the segmentation of object parts.We re-purpose a state-of-the-art CNN to perform fine-grained semantic segmentation of object parts and use a fully-connected CRF as a post-processing step to obtain sharp boundaries.We also inject prior shape information in our model through a Restricted Boltzmann Machine, trained on ground-truth segmentations.Finally, we train a new fully-convolutional architecture from a random initialization, to segment different parts of the human brain in magnetic resonance image data.Our methods achieve state-of-the-art results on both types of data.Dans cette thèse, nous proposons l'utilisation de représentations de niveau intermédiaire, et en particulier i) d'axes médians, ii) de parties d'objets, et iii) des caractéristiques convolutionnels, pour modéliser des objets.La première partie de la thèse traite de détecter les axes médians dans des images naturelles en couleur. Nous adoptons une approche d'apprentissage, en utilisant la couleur, la texture et les caractéristiques de regroupement spectral pour construire un classificateur qui produit une carte de probabilité dense pour la symétrie. Le Multiple Instance Learning (MIL) nous permet de traiter l'échelle et l'orientation comme des variables latentes pendant l'entraînement, tandis qu'une variante fondée sur les forêts aléatoires offre des gains significatifs en termes de temps de calcul.Dans la deuxième partie de la thèse, nous traitons de la modélisation des objets, utilisant des modèles de parties déformables (DPM). Nous développons une approche « coarse-to-fine » hiérarchique, qui utilise des bornes probabilistes pour diminuer le coût de calcul dans les modèles à grand nombre de composants basés sur HOGs. Ces bornes probabilistes, calculés de manière efficace, nous permettent d'écarter rapidement de grandes parties de l'image, et d'évaluer précisément les filtres convolutionnels seulement à des endroits prometteurs. Notre approche permet d'obtenir une accélération de 4-5 fois sur l'approche naïve, avec une perte minimale en performance.Nous employons aussi des réseaux de neurones convolutionnels (CNN) pour améliorer la détection d'objets. Nous utilisons une architecture CNN communément utilisée pour extraire les réponses de la dernière couche de convolution. Nous intégrons ces réponses dans l'architecture DPM classique, remplaçant les descripteurs HOG fabriqués à la main, et nous observons une augmentation significative de la performance de détection (~14.5% de mAP).Dans la dernière partie de la thèse nous expérimentons avec des réseaux de neurones entièrement convolutionnels pous la segmentation de parties d'objets.Nous réadaptons un CNN utilisé à l'état de l'art pour effectuer une segmentation sémantique fine de parties d'objets et nous utilisons un CRF entièrement connecté comme étape de post-traitement pour obtenir des bords fins.Nous introduirons aussi un à priori sur les formes à l'aide d'une Restricted Boltzmann Machine (RBM), à partir des segmentations de vérité terrain.Enfin, nous concevons une nouvelle architecture entièrement convolutionnel, et l'entraînons sur des données d'image à résonance magnétique du cerveau, afin de segmenter les différentes parties du cerveau humain.Notre approche permet d'atteindre des résultats à l'état de l'art sur les deux types de données

Combining shape and color. A bottom-up approach to evaluate object similarities

The objective of the present work is to develop a bottom-up approach to estimate the similarity between two unknown objects. Given a set of digital images, we want to identify the main objects and to determine whether they are similar or not. In the last decades many object recognition and classification strategies, driven by higher-level activities, have been successfully developed. The peculiarity of this work, instead, is the attempt to work without any training phase nor a priori knowledge about the objects or their context. Indeed, if we suppose to be in an unstructured and completely unknown environment, usually we have to deal with novel objects never seen before; under these hypothesis, it would be very useful to define some kind of similarity among the instances under analysis (even if we do not know which category they belong to). To obtain this result, we start observing that human beings use a lot of information and analyze very different aspects to achieve object recognition: shape, position, color and so on. Hence we try to reproduce part of this process, combining different methodologies (each working on a specific characteristic) to obtain a more meaningful idea of similarity. Mainly inspired by the human conception of representation, we identify two main characteristics and we called them the implicit and explicit models. The term "explicit" is used to account for the main traits of what, in the human representation, connotes a principal source of information regarding a category, a sort of a visual synecdoche (corresponding to the shape); the term "implicit", on the other hand, accounts for the object rendered by shadows and lights, colors and volumetric impression, a sort of a visual metonymy (corresponding to the chromatic characteristics). During the work, we had to face several problems and we tried to define specific solutions. In particular, our contributions are about: - defining a bottom-up approach for image segmentation (which does not rely on any a priori knowledge); - combining different features to evaluate objects similarity (particularly focusiing on shape and color); - defining a generic distance (similarity) measure between objects (without any attempt to identify the possible category they belong to); - analyzing the consequences of using the number of modes as an estimation of the number of mixture’s components (in the Expectation-Maximization algorithm)

Multi-Dimensional Medial Geometry: Formulation, Computation, and Applications

Medial axis is a classical shape descriptor. It is a piece of geometry that lies in the middle of the original shape. Compared to the original shape representation, the medial axis is always one dimension lower and it carries many intrinsic shape properties explicitly. Therefore, it is widely used in a large amount of applications in various fields. However, medial axis is unstable to the boundary noise, often referred to as its instability. A small amount of change on the object boundary can cause a dramatic change in the medial axis. To tackle this problem, a significance measure is often associated with the medial axis, so that medial points with small significance are removed and only the stable part remains. In addition to this problem, many applications prefer even lower dimensional medial forms, e.g., shape centers of 2D shapes, and medial curves of 3D shapes. Unfortunately, good significance measures and good definitions of lower dimensional medial forms are still lacking. In this dissertation, we extended Blum\u27s grassfire burning to the medial axis in both 2D and 3D to define a significance measure as a distance function on the medial axis. We show that this distance function is well behaved and it has nice properties. In 2D, we also define a shape center based on this distance function. We then devise an iterative algorithm to compute the distance function and the shape center. We demonstrate usefulness of this distance function and shape center in various applications. Finally we point out the direction for future research based on this dissertation

Exploring 3D Shapes through Real Functions

This thesis lays in the context of research on representation, modelling and coding knowledge related to digital shapes, where by shape it is meant any individual object having a visual appareance which exists in some two-, three- or higher dimensional space. Digital shapes are digital representations of either physically existing or virtual objects that can be processed by computer applications. While the technological advances in terms of hardware and software have made available plenty of tools for using and interacting with the geometry of shapes, to manipulate and retrieve huge amount of data it is necessary to define methods able to effectively code them. In this thesis a conceptual model is proposed which represents a given 3D object through the coding of its salient features and defines an abstraction of the object, discarding irrelevant details. The approach is based on the shape descriptors defined with respect to real functions, which provide a very useful shape abstraction method for the analysis and structuring of the information contained in the discrete shape model. A distinctive feature of these shape descriptors is their capability of combining topological and geometrical information properties of the shape, giving an abstraction of the main shape features. To fully develop this conceptual model, both theoretical and computational aspects have been considered, related to the definition and the extension of the different shape descriptors to the computational domain. Main emphasis is devoted to the application of these shape descriptors in computational settings; to this aim we display a number of application domains that span from shape retrieval, to shape classification and to best view selection.Questa tesi si colloca nell\u27ambito di ricerca riguardante la rappresentazione, la modellazione e la codifica della conoscenza connessa a forme digitali, dove per forma si intende l\u27aspetto visuale di ogni oggetto che esiste in due, tre o pi? dimensioni. Le forme digitali sono rappresentazioni di oggetti sia reali che virtuali, che possono essere manipolate da un calcolatore. Lo sviluppo tecnologico degli ultimi anni in materia di hardware e software ha messo a disposizione una grande quantit? di strumenti per acquisire, rappresentare e processare la geometria degli oggetti; tuttavia per gestire questa grande mole di dati ? necessario sviluppare metodi in grado di fornirne una codifica efficiente. In questa tesi si propone un modello concettuale che descrive un oggetto 3D attraverso la codifica delle caratteristiche salienti e ne definisce una bozza ad alto livello, tralasciando dettagli irrilevanti. Alla base di questo approccio ? l\u27utilizzo di descrittori basati su funzioni reali in quanto forniscono un\u27astrazione della forma molto utile per analizzare e strutturare l\u27informazione contenuta nel modello discreto della forma. Una peculiarit? di tali descrittori di forma ? la capacit? di combinare propriet? topologiche e geometriche consentendo di astrarne le principali caratteristiche. Per sviluppare questo modello concettuale, ? stato necessario considerare gli aspetti sia teorici che computazionali relativi alla definizione e all\u27estensione in ambito discreto di vari descrittori di forma. Particolare attenzione ? stata rivolta all\u27applicazione dei descrittori studiati in ambito computazionale; a questo scopo sono stati considerati numerosi contesti applicativi, che variano dal riconoscimento alla classificazione di forme, all\u27individuazione della posizione pi? significativa di un oggetto