Hypothesis-based image segmentation for object learning and recognition

Denecke A. Hypothesis-based image segmentation for object learning and recognition. Bielefeld: Universität Bielefeld; 2010.This thesis addresses the figure-ground segmentation problem in the context of complex systems for automatic object recognition as well as for the online and interactive acquisition of visual representations. First the problem of image segmentation in general terms and next its importance for object learning in current state-of-the-art systems is introduced. Secondly a method using artificial neural networks is presented. This approach on the basis of Generalized Learning Vector Quantization is investigated in challenging scenarios such as the real-time figure-ground segmentation of complex shaped objects under continuously changing environment conditions. The ability to fulfill these requirements characterizes the novelty of the approach compared to state-of-the-art methods. Finally our technique is extended towards online adaption of model complexity and the integration of several segmentation cues. This yields a framework for object segmentation that is applicable to improve current systems for visual object learning and recognition

Reconstruction of neuronal activity and connectivity patterns in the zebrafish olfactory bulb

In the olfactory bulb (OB), odors evoke distributed patterns of activity across glomeruli that are reorganized by networks of interneurons (INs). This reorganization results in multiple computations including a decorrelation of activity patterns across the output neurons, the mitral cells (MCs). To understand the mechanistic basis of these computations it is essential to analyze the relationship between function and structure of the underlying circuit. I combined in vivo twophoton calcium imaging with dense circuit reconstruction from complete serial block-face electron microscopy (SBEM) stacks of the larval zebrafish OB (4.5 dpf) with a voxel size of 9x9x25nm. To address bottlenecks in the workflow of SBEM, I developed a novel embedding and staining procedure that effectively reduces surface charging in SBEM and enables to acquire SBEM stacks with at least a ten-fold increase in both, signal-to-noise as well as acquisition speed. I set up a high throughput neuron reconstruction pipeline with >30 professional tracers that is available for the scientific community (ariadne-service.com). To assure efficient and accurate circuit reconstruction, I developed PyKNOSSOS, a Python software for skeleton tracing and synapse annotation, and CORE, a skeleton consolidation procedure that combines redundant reconstruction with targeted expert input. Using these procedures I reconstructed all neurons (>1000) in the larval OB. Unlike in the adult OB, INs were rare and appeared to represent specific subtypes, indicating that different sub-circuits develop sequentially. MCs were uniglomerular whereas inter-glomerular projections of INs were complex and biased towards groups of glomeruli that receive input from common types of sensory neurons. Hence, the IN network in the OB exhibits a topological organization that is governed by glomerular identity. Calcium imaging revealed that the larval OB circuitry already decorrelates activity patterns evoked by similar odors. The comparison of inter-glomerular connectivity to the functional interactions between glomeruli indicates that pattern decorrelation depends on specific, non-random inter-glomerular IN projections. Hence, the topology of IN networks in the OB appears to be an important determinant of circuit function

Short-term memory of temporal aspects of noxious and innocuous thermal sensation : psychophysical and fMRI studies

La douleur peut être considérée comme un système de protection qui signale une menace et qui nous avertit des dégâts imminents aux tissus. En tant que mécanisme de défense, il nécessite l'apprentissage et la mémoire des expériences du passé pour la survie et les comportements liés à la douleur. Par conséquent, notre expérience de la douleur actuelle est fortement influencée par les expériences antérieures et l'apprentissage. Cependant, malgré son importance, notre compréhension actuelle de l'interaction entre le système de la douleur et le système de mémoire est très limitée. La mémoire de la douleur est un sujet de recherche très vaste. Il nécessite une compréhension des mécanismes impliqués à chaque étape du système de mémoire (mémoire immédiate, à court terme et à long terme) et l'interaction entre eux. Parmi les étapes multiples de la mémoire, la mémoire à court terme de la douleur est une zone qui est moins recherchée, alors qu'il existe une énorme quantité de recherche neuroscientifique dans la mémoire à court terme sur d'autres modalités, en particulier la vision. L'étude de la mémoire à court terme de la douleur est particulièrement importante car cette trace de la mémoire à court terme de la douleur est ensuite convertie en mémoire à long terme et affecte ensuite les expériences futures de la douleur. Cette thèse est largement axée sur la mémoire à court terme de la douleur. La complexité et la multi dimensionnalité de la douleur ajoutent encore un autre élément à la recherche sur la mémoire de la douleur. Par exemple, la trace de la mémoire de la douleur peut contenir des traces de mémoire de diverses composantes de la douleur telles que la réponse sensorielle affective, cognitive et motrice et l'interaction entre elles. Par conséquent, une première étape dans l'exploration neuroscientifique de la mémoire de la douleur nécessite la réduction de l'expérience de la douleur tout en englobant tous ces différents composants à un seul composant. Dans la recherche présentée ici, nous avons généralement examiné cela par des instructions d'attention ‘ top-down’ pour assister à la dimension sensorielle de la douleur. La recherche précédente sur la mémoire à court terme de la douleur a également porté principalement sur la dimension sensorielle de la douleur. Cependant, parmi les dimensions sensorielles de la douleur, la mémoire à court terme de l'intensité et de la dimension spatiale de la douleur a fait l'objet de recherches antérieures. Malgré son importance, la dimension temporelle de la douleur est restée complètement inexplorée dans la recherche sur la mémoire de la douleur. La recherche menée dans cette thèse est consacrée à l'exploration de la mémoire à court terme de la durée de la douleur. La durée de la douleur peut être suivie de manière indépendante, mais peut également être suivie conjointement avec la dimension d'intensité telle que le suivi dynamique de l'intensité de la douleur dans le temps. Les études menées dans cette thèse traitent spécifiquement du traitement isolé de la durée de la douleur ainsi que du traitement conjoint de la dimension durée / intensité de la douleur. La première étude psychophysique a exploré la nature de la représentation mentale du modèle de mémoire de la douleur thermique dynamique et a également été conçue pour aborder les différences de la dimension sensorielle et affective de la douleur thermique dans la mémoire à court terme. La deuxième étude psychophysique portait sur les propriétés de la mémoire à court terme de la sensation thermique non douloureux en comparant le suivi dynamique de la sensation et le suivi isolé de la durée d'un événement thermique non douloureux. La troisième étude poursuit l'exploration du traitement dynamique de la durée conjointement avec l'intensité par rapport au traitement isolé de la durée dans la mémoire à court terme en utilisant des stimuli thermiques douloureuse une résonance magnétique fonctionnelle (IRMF). Dans l'ensemble, les résultats des études psychophysiques ont montré une transformation significative de la durée et de la dynamique de la sensation thermique douloureux et non-douloureux dans la mémoire à court terme; comme la perte d'informations somatosensorielles temporelles en mémoire. Nous avons en outre montré une amélioration du rappel de la durée dans le suivi dynamique de la durée, en comparaison avec le suivi de la durée isolée. Nous avons également montré des différences dans les corrélats neuronaux de la mémoire à court terme de la durée de douleur par rapport à la dynamique de douleur. L'étude de l'IRMF a montré des similitudes frappantes dans les corrélats neuronaux sous-jacents à la mémoire à court terme de douleur et d'autres modalités telles que la contribution des coticés fronto-pariétales ainsi que les corticaux sensoriels impliqués dans le traitement perceptuel.Pain can be viewed as a protective system that signals threat and alerts us to impending tissue damage. As a defense mechanism, it necessitates the learning and memory of past painful experiences for survival and pain-related behavior. Therefore our current pain experience is heavily influenced by previous experiences and learning. However, despite its importance, our current understanding of the interaction between the pain system and the memory system is very limited. Pain memory is a very broad topic of research on its own. It requires an understanding of the mechanisms involved at each stage of the memory system (immediate, short-term, and long-term memory), and the interaction among them. Among the multiple stages of memory, the short-term memory of pain is an area that is less researched, while there are enormous amount of neuroscientific research in short-term memory of other modalities, particularly vision. Investigation of the short-term memory of pain is especially important as the short-term memory trace of pain is converted to long-term memory and subsequently affects future pain experiences. This thesis is broadly focused on the short-term memory of pain. The complexity and multi-dimensionality of pain adds yet another element to the research on pain memory. For example, the memory trace of pain may contain memory traces of various components of pain such as sensory, affective, cognitive, and motoric responses, and the interactions among them. Therefore, an initial step in the neuroscientific exploration of pain memory requires narrowing down the pain experience, which encompasses all of these various components, to one single component. In the research presented here, we achieved this using top-down attentional instructions to attend to the sensory component of pain. The previous research on short-term memory of pain also focused mainly on the sensory component of pain. However, within the sensory component of pain the short-term memory of intensity and spatial dimension of pain has been the focus of previous research. Despite its importance, the temporal dimension of pain remained completely unexplored in pain memory research. Thus, the research conducted in this thesis is devoted to the exploration of short-term memory of the duration of pain. Pain duration can be tracked independently, but it can also be tracked conjointly with intensity, such as in dynamic tracking of pain intensity over time. The studies addressed in this thesis examined the isolated processing of pain duration as well as conjoint processing of the duration and intensity of pain. The first psychophysical study explored the nature of the mental representation of the memory template of dynamic thermal pain sensation and, additionally, addressed the differences between the sensory versus affective dimensions of thermal pain sensation in short-term memory. The second psychophysical study focused on properties of the short-term memory of innocuous thermal sensation by comparing dynamic tracking of sensation versus isolated tracking of duration of an innocuous thermal event. The third study explored the dynamic processing of duration conjointly with intensity, versus the isolated processing of duration in short-term memory, using noxious thermal stimuli and functional magnetic resonance imaging (fMRI). Overall, the results of the psychophysical studies showed significant transformation of duration and dynamics information of noxious and innocuous thermal sensation in short-term memory, such as loss of temporal somatosensory information. Additionally, we showed improvement in duration recall during dynamic tracking versus isolated tracking of duration. The fMRI study revealed differences in neural correlates of short-term memory of pain duration versus pain dynamics. Importantly, it also showed striking similarities between neural correlates underlying the short-term memory of pain and those underlying other modalities, such as a contribution of fronto-parietal cortices as well as sensory cortices involved in perceptual processing

Sox10 regulates enteric neural crest cell migration in the developing gut

Concurrent Sessions 1: 1.3 - Organs to organisms: Models of Human Diseases: abstract no. 1417th ISDB 2013 cum 72nd Annual Meeting of the Society for Developmental Biology, VII Latin American Society of Developmental Biology Meeting and XI Congreso de la Sociedad Mexicana de Biologia del Desarrollo. The Conference's web site is located at http://www.inb.unam.mx/isdb/Sox10 is a HMG-domain containing transcription factor which plays important roles in neural crest cell survival and differentiation. Mutations of Sox10 have been identified in patients with Waardenburg-Hirschsprung syndrome, who suffer from deafness, pigmentation defects and intestinal aganglionosis. Enteric neural crest cells (ENCCs) with Sox10 mutation undergo premature differentiation and fail to colonize the distal hindgut. It is unclear, however, whether Sox10 plays a role in the migration of ENCCs. To visualize the migration behaviour of mutant ENCCs, we generated a Sox10NGFP mouse model where EGFP is fused to the N-terminal domain of Sox10. Using time-lapse imaging, we found that ENCCs in Sox10NGFP/+ mutants displays lower migration speed and altered trajectories compared to normal controls. This behaviour was cell-autonomous, as shown by organotypic grafting of Sox10NGFP/+ gut segments onto control guts and vice versa. ENCCs encounter different extracellular matrix (ECM) molecules along the developing gut. We performed gut explant culture on various ECM and found that Sox10NGFP/+ ENCCs tend to form aggregates, particularly on fibronectin. Time-lapse imaging of single cells in gut explant culture indicated that the tightly-packed Sox10 mutant cells failed to exhibit contact inhibition of locomotion. We determined the expression of adhesion molecule families by qPCR analysis, and found integrin expression unaffected while L1-cam and selected cadherins were altered, suggesting that Sox10 mutation affects cell adhesion properties of ENCCs. Our findings identify a de novo role of Sox10 in regulating the migration behaviour of ENCCs, which has important implications for the treatment of Hirschsprung disease.postprin

Analysis of craniofacial defects in Six1/Eya1-associated Branchio-Oto-Renal Syndrome

Poster Session I - Morphogenesis: 205/B10117th ISDB 2013 cum 72nd Annual Meeting of the Society for Developmental Biology, 7th Latin American Society of Developmental Biology Meeting and 11th Congreso de la Sociedad Mexicana de Biologia del Desarrollo.Branchio-Oto-Renal (BOR) syndrome patients exhibit craniofacial and renal anomalies as well as deafness. BOR syndrome is caused by mutations in Six1 or Eya1, both of which regulate cell proliferation and differentiation. The molecular mechanism underlying the craniofacial and branchial arch (BA) defects in BOR syndrome is unclear. We have found that Hoxb3 is up-regulated in the second branchial arch (BA2) of Six1-/- mutants. Moreover, Hoxb3 over-expression in transgenic mice leads to BA abnormalities which are similar to the BA defects in Six1-/- or Eya1-/- mutants, suggesting a regulatory relationship among Six1, Eya1 and Hoxb3 genes. The aim of this study is to investigate the molecular mechanism underlying abnormal BA development in BOR syndrome using Six1 and Eya1 mutant mice. Two potential Six1 binding sites were identified on the Hoxb3 gene. In vitro and in vivo Chromatin IP assays showed that Six1 could directly bind to one of the sites specifically. Furthermore, using a chick in ovo luciferase assay we showed that Six1 could suppress gene expression through one of the specific binding sites. On the other hand, in Six1-/- mutants, we found that the Notch ligand Jag1 was up-regulated in BA2. Similarly, in Hoxb3 transgenic mice, ectopic expression of Jag1 could be also detected in BA2. To investigate the activation of Notch signaling pathway, we found that Notch intracellular domain (NICD), a direct indicator of Notch pathway activation, was up-regulated in BAs of Six1-/-; Eya1-/- double mutants. Our results indicate that Hoxb3 and Notch signaling pathway are involved in mediating the craniofacial defects of Six1/Eya1-associated Branchio-Oto-Renal Syndrome.postprin

Structured manifolds for motion production and segmentation : a structured Kernel Regression approach

Steffen JF. Structured manifolds for motion production and segmentation : a structured Kernel Regression approach. Bielefeld (Germany): Bielefeld University; 2010

Affective Computing

This book provides an overview of state of the art research in Affective Computing. It presents new ideas, original results and practical experiences in this increasingly important research field. The book consists of 23 chapters categorized into four sections. Since one of the most important means of human communication is facial expression, the first section of this book (Chapters 1 to 7) presents a research on synthesis and recognition of facial expressions. Given that we not only use the face but also body movements to express ourselves, in the second section (Chapters 8 to 11) we present a research on perception and generation of emotional expressions by using full-body motions. The third section of the book (Chapters 12 to 16) presents computational models on emotion, as well as findings from neuroscience research. In the last section of the book (Chapters 17 to 22) we present applications related to affective computing

Unbiased Multidimensional Analysis Reveals Novel Principles of Cortical Interneuron Synaptic Organization

Neurons display exquisite specificity in synaptic connectivity, but we lack a complete under-standing of neuronal connectivity and the rules that govern it. A major impediment to addressing this question lies in the vast diversity of neurons, the small size and large number of synapses formed by any given neuron over a wide territory, and the need to study these connections in intact tissue. We therefore developed an image-based tool to assess synaptic specificity in tissue sections and dissociated culture. We focused on three interneuron subpopulations that target distinct subcellular regions of the post-synaptic cell: soma-targeting basket cells (BCs), axon initial segment (AlS)-targeting chandelier cells (ChCs), and distal dendrite-targeting somatostatin cells (SstCs). Using mouse dissociated cortical culture as a starting point, we built a machine learning (ML) based image processing and analysis pipeline to classify individual presynaptic boutons at scale. Supervised ML classification revealed similar subcellular targeting profiles for these interneuron populations in slice and culture, indicating that targeting is primarily regulated by cell intrinsic programs. We also observed a remarkable target-dependent laminar organization in vivo. An unsupervised ML analysis using the same input data not only identified the same three canonical targeting classes, but also revealed that these classes are comprised of multiple subpopulations. In slice, these synaptic subpopulations displayed distinct laminar or-ganization. In dissociated culture, two soma-targeting synaptic subpopulations mapped to target cells with different cellular profiles. The six dendrite-targeting synaptic subpopulations were found at increasing distances from target soma, suggesting molecularly distinct proximal, medial, and distal dendritic compartments in culture. Tracking subtype targeting across axonal branches of individual neurons indicated that SstCs and BCs utilize distinct targeting strategies in culture that accord with established findings in vivo. In sum, our synaptic analysis pipeline revealed novel synaptic subpopulations in interneurons. Further analysis uncovered novel aspects of interneuron synaptic biology that, remarkably, are retained in culture