Behavioural motifs of larval Drosophila melanogaster and Caenorhabditis elegans

I present a novel method for the unsupervised discovery of behavioural motifs in larval Drosophila melanogaster and Caenorhabditis elegans. Most current approaches to behavioural annotation suffer from the requirement of training data. As a result, automated programs carry the same observational biases as the humans who have annotated the data. The key novel element of my work is that it does not require training data; rather, behavioural motifs are discovered from the data itself. The method is based on an eigenshape representation of posture. Hence, my approach is called the eigenshape annotator (ESA). First, I examine the annotation consistency for a specific behaviour, the Omega turn of C. elegans, and find significant inconsistency in both expert annotation and the various Omega turn detection algorithms. This finding highlights the need for unbiased tools to study behaviour. A behavioural motif is defined as a particular sequence of postures that recurs frequently. In ESA, posture is represented by an eigenshape time series, and motifs are discovered in this representation. To find motifs, the time series is segmented, and the resulting segments are then clustered. The result is a set of self-similar time series segments, i.e. motifs. The advantage of this novel framework over the popular sliding windows approaches is twofold. First, it does not rely on the ‘closest neighbours’ definition of motifs, by which every motif has exactly two instances. Second, it does not require the assumption of exactly equal length for motifs of the same class. Behavioural motifs discovered using the segmentation-clustering framework are used as the basis of the ESA annotator. ESA is fully probabilistic, therefore avoiding rigid threshold values and allowing classification uncertainty to be quantified. I apply eigenshape annotation to both larval Drosophila and C. elegans, and produce a close match to hand annotation of behavioural states. However, many behavioural events cannot be unambiguously classified. By comparing the results to eigenshape annotation of an artificial agent’s behaviour, I argue that the ambiguity is due to greater continuity between behavioural states than is generally assumed for these organisms

Entropy-based particle correspondence for shape populations

Statistical shape analysis of anatomical structures plays an important role in many medical image analysis applications such as understanding the structural changes in anatomy in various stages of growth or disease. Establishing accurate correspondence across object populations is essential for such statistical shape analysis studies

Image databases in medical applications

The number of medical images acquired yearly in hospitals increases all the time. These imaging data contain lots of information on the characteristics of anatomical structures and on their variations. This information can be utilized in numerous medical applications. In deformable model-based segmentation and registration methods, the information in the image databases can be used to give a priori information on the shape of the object studied and the gray-level values in the image, and on their variations. On the other hand, by studying the variations of the object of interest in different populations, the effects of, for example, aging, gender, and diseases on anatomical structures can be detected. In the work described in this Thesis, methods that utilize image databases in medical applications were studied. Methods were developed and compared for deformable model-based segmentation and registration. Model selection procedure, mean models, and combination of classifiers were studied for the construction of a good a priori model. Statistical and probabilistic shape models were generated to constrain the deformations in segmentation and registration so that only the shapes typical to the object studied were accepted. In the shape analysis of the striatum, both volume and local shape changes were studied. The effects of aging and gender, and also the asymmetries were examined. The results proved that the segmentation and registration accuracy of deformable model-based methods can be improved by utilizing the information in image databases. The databases used were relatively small. Therefore, the statistical and probabilistic methods were not able to model all the population-specific variation. On the other hand, the simpler methods, the model selection procedure, mean models, and combination of classifiers, gave good results also with the small image databases. Two main applications were the reconstruction of 3-D geometry from incomplete data and the segmentation of heart ventricles and atria from short- and long-axis magnetic resonance images. In both applications, the methods studied provided promising results. The shape analysis of the striatum showed that the volume of the striatum decreases in aging. Also, the shape of the striatum changes locally. Asymmetries in the shape were found, too, but any gender-related local shape differences were not found.reviewe

Morphometric shape analysis of the human ear

Das Potenzial von menschlichen Außenohren für die persönliche Identifizierung wurde erstmals von Alphonse Bertillon im Jahre 1890 beschrieben (Bertillon 1890, zitiert durch Hurley et al., 2000). In den letzten 120 Jahren untersuchten mehrere Studien biometrische Unterschiede bei menschlichen Ohren um spezifische Identifizierungen festzustellen. Dabei wurden unter anderem Zeichnungen, Photographien und 3D Oberflächenscanner-Daten verwendet. Bezüglich der spezifischen Frage nach einem Geschlechtsunterschied an menschlichen Ohren, wurden von Sforza et al. Im Jahr 2009 vergleichbare geschlechtsspezifische Dimensionen von Ohren analysiert. Die vorliegende Diplomarbeit versucht zu beweisen, dass 3D Oberflächenscans von menschlichen Ohren eine passende Methode für die Analyse von Geschlechtsunterschieden darstellt. Die zu vergleichende Stichrobe (n=29, 14♂, 15♀; durchschnittliches Alter: 25.3 Jahre) besteht aus 3D Oberflächenscans (David Lasercanner 2.4.3) von Gipsmodellen. Nachdem 72 Landmarks inklusive 67 Semilandmarks in Amira 5.2.0 gesetzt wurden, wurden diese Punkte in Edgewarp 3.30 zueinander verschoben (sliding). Anschließend wurden die Daten in Morpheus et al. geladen, gruppiert und mit f (weiblich) und m (männlich) bezeichnet und superimposed (GPA) bevor ein MANOVA P-Test durchgeführt wurde. Außerdem wurde ein PCA in R 1.12.1 berechnet. Die Ergebnisse zeigten, dass es im Bezug auf Geschlechtsunterschiede keine bedeutenden Unterschiede gibt (Versetzungstest / randomized Beispiel 999: p=0.384). Aus den ersten beiden Hauptkomponenten der Analyse ergaben sich eine erklärte Varianz von 44.47% im s.g. shape space und 43.66% im s.g. form space. Von den 29 Proben insgesamt sechs aus der Studie ausgeschlossen, da diese Mängel in den Oberflächendaten aufwiesen. Aufgrund dieser heruntergesetzten Stichprobe ist es leider nicht eindeutig möglich einen klaren Geschlechtsunterschied auszumachen. Die Verwendung der Gipsabdrücke zeigte allerdings eine sehr hohe Genauigkeit im Bezug auf die Morphometrie des Ohres. In Bezugnahme auf den David Laserscanner zeigte sich, dass eine maximaler Fehler von 3mm pro Scan erwartet werden könnte, da dieser von vielen verschiedenen Hardware-Komponenten abhängig ist. Generell lässt sich sagen, dass das Potenzial des David Laserscanner 2.4.3 für die Analyse von komplexen Strukturen wie menschlichen Ohren begrenzt ist

Patterns of subspecies diversity in the giraffe, Giraffa camelopardalis (L. 1758): comparison of systematic methods and their implications for conservation policy

This thesis examines the subspecific taxonomic status of the giraffe and considers the role of formal taxonomy in the formulation of conservation policy. Where species show consistent. geographically structured phenotypic variation such geographic patterns may indicate selective forces (or other population-level effects) acting. upon local populations. These consistent geographic patterns may be recognised formally as subspecies and may be of interest in single or multi-species biodiversity or biogeography studies for delimiting areas of conservation priority. Subspecies may also be used in the formulation of management policies and legislation. Subspecies are, by definition, allopatric. This thesis explicitly uses methodology of systematic biology and phylogenetic reconstruction to investigate patterns of variation between geographic groups. The taxonomic status of the giraffe is apposite for review. The species provides three independent data sets that may be analysed quantitatively for geographic structure; pelage patterns, morphology and genetics. Museum specimens. grouped according to geographic origin, were favoured for study as more than one type of data was often available for an individual. Population aggregation analysis of forty pelage pattern characters maintained six separate subspecies, while agglomerating some neighbouring populations into a subspecies. A 'traditional' morphometric approach, using multivariate statistical analysis of adult skull measurements, was complemented by a geometric morphometric approach; landmarkrestricted eigenshape analysis. Four morphologically distinct groups were recognised by both morphological analyses. Phylogenetic analysis of mitochondrial DNA control region sequences indicates five major cIades. Nested cIade analysis identifies population fragmentation, range expansion and genetic isolation by distance as contributing to the genetic structure of the giraffe. The results of the analyses show remarkable congruence. These results are discussed in terms of the formulation of conservation policy and the differing requirements of'blological and legal classification systems. The value of a formal taxonomic framework to the recognition, and subsequent conservation, of biodiversity is emphasised

The evolution of diversity and life history traits in annual killifish (Austrolebias) and other Cyprinodontiformes

Members of the annual killifish genus Austrolebias live in temporary ponds across South America and possess a remarkable life cycle. These fish live in small ponds that dry out completely; killing the adults but not before they have laid eggs in the substrate of their pond. The desiccation-resistant eggs develop during the dry season, going through multiple stages of diapause until the next wet season rains trigger hatching and the cycle is repeated. There is considerable variation in size in Austrolebias, the largest species can reach up to 150mm in length while the typical size is just 40mm. Phylogenetic trees and species distribution models were built and used together to identify the factors that influence patterns of co-occurrence within this genus. Differences in growth and morphology among Austrolebias species were examined to quantify how differences in growth pattern can lead to the large variation in size and shape seen within the genus. Genomic data was generated for hybrid offspring of two species of Austrolebias using double-digest RAD sequencing. These data were then used to build linkage maps that were in turn used to identify any regions associated with sex determination and potential chromosomal rearrangements. At a broader scale, a generic-level tree for the order Cyprinodontiformes was constructed. Austrolebias is a member of this order, as well as many model fish genera such as Fundulus, Nothobranchius and Poecilia. Two extraordinary reproductive life-history adaptations have evolved in this order; viviparity and annualism. The new tree was used to determine whether the evolution of viviparity or annualism lead to increased rates of diversification. Finally this generic-level tree was used to examine patterns of positive selection in the low-light vision gene, rhodopsin and whether sites under selection were linked to functional changes.Open Acces