Stags of the Sea or Hedgehogs of the Harbor? Inferring the Point of Sculpin Cranial Weaponry

Animal weapons are thought to have evolved to compete for reproductive opportunities within a species. Across the diverse weapon-bearing taxa, several evolutionary trends have emerged: (1) increasing complexity and relative size across ontogeny, (2) sexual dimorphism, and (3) higher levels of random deviations from symmetry (i.e., fluctuating asymmetry) than non-weaponized structures in the same individual. While the evolution of weapons in charismatic animals such as cervids and ceratopsian dinosaurs have received extensive attention, weapon evolution in fishes has received relatively little. In this dissertation, I explore the evolution of cranial weapons in a group of fishes known as sculpins (superfamily Cottoidea), specifically, the subfamily Oligocottinae. I use digital models of evolution built from computed tomography (CT) scans to quantitatively describe the shape of the weaponized preopercle bone and multivariate statistics to compare the shape across species. I examine the assumptions of common macroevolutionary techniques and make recommendations for how to accommodate natural variation in morphology. In the second chapter, coauthors and I contrast 2D vs. 3D landmark-based geometric morphometrics in the fish subfamily Oligocottinae by using 3D landmarks from CT-generated models and comparing the morphospace of the 3D landmarks to one based on 2D landmarks from images. The 2D and 3D shape variables capture common patterns across taxa, such that the pairwise Procrustes distances among taxa correspond and the trends captured by principal component analysis are similar in the xy plane. We use the two sets of landmarks to test several ecomorphological hypotheses from the literature. Both 2D and 3D data reject the hypothesis that head shape correlates significantly with the depth at which a species is commonly found. However, in taxa where shape variation in the z-axis is high, the 2D shape variables show sufficiently strong distortion to influence the outcome of the hypothesis tests regarding the relationship between mouth size and feeding ecology. In the third chapter, coauthors and I address the issue that, while virtually anyone can access the wealth of open access CT data that have been deposited onto repositories such as MorphoSource, relatively few have the training to easily derive a desirable product from them. This chapter fills the gap between the data and the researcher and provides a starting point for interested readers to begin their own analyses of CT data without requiring anything more than a reasonably up to date computer and access to the internet. We outline a set of practices in the production, visualization and analysis of CT data. We focus on those often-tedious nuances of data preparation, formatting, and navigating software that commonly hinder progress in CT-based studies of anatomy, functional morphology, and macroevolution. We also emphasize tools useful for creating pedagogical aides such as 3D prints and images of anatomical structures. In the fourth chapter, I infer the primary function of preopercular spines in oligocottine sculpins. From dissuading predators to gaining an edge on intraspecific rivals, weapons have evolved to meet various needs in both vertebrates and invertebrates. Animals with the most extreme weapons use them to battle conspecifics, but some weapons are used for defense against predation, and others serve as a signal. Many fishes have evolved armaments, but the function of these structures is rarely observed. How, for example, sculpins use the horn-like spines that project from their head remains mysterious. We used previously described trends in the morphology and development of weapons in terrestrial animals to deduce the function of the weaponized preopercle in all sixteen species of sculpins in the subfamily Oligocottinae, which display a diversity of spine shapes, reproductive habits, and degrees of territoriality. We investigated three hallmarks of offensive weapons: ontogenetic change, sexual dimorphism, and fluctuating asymmetry. Geometric morphometrics of microCT scans show no sexual dimorphism in preopercular spine shape, but there is phylogenetically widespread ontogenetic shape change. Fluctuating asymmetry is low to moderate across species. Taken together, these results suggest that despite a form that evokes comparisons to bovid horns, the spines of oligocottine sculpins have evolved primarily as a defense against predators. In the fifth chapter, coauthors and I describe the assumptions made both explicitly and implicitly in many studies of comparative anatomy and macroevolution and test whether these assumptions are robust in a case study of the preopercle shape in oligocottine sculpins. For example, many studies use only one side of one individual to represent the anatomy of a species. We test: (1) the degree to which the shape of the preopercle of one side of an individual matches the shape of the preopercle on its other side, (2) whether trends in ontogenetic shape change of the preopercle are identical on the left and right sides within a species, and (3) the degree to which intraspecific variation affects the outcomes of two common tests of comparative anatomy: allometric growth and morphological character evolution. We find that the left and right side of an individual are more similar in shape to each other than to the preopercle of a different individual only about 52% of the time and that, in fact, a small number of individuals (~2%) actually have a preopercle on one side of their head that is more similar in shape to the preopercle of a member of a different species than it is to the shape of the preopercle on the other side of their own head. We find that 4/17 species show statistically-significant allometric growth of the preopercle on one side of the head but not on the other. Finally, we find that intraspecific variation leads to highly unstable results of common macroevolutionary analyses when species are represented by low (n < 5 - 8) sample sizes. Taken together, these results suggest that trait estimates for species are robust only when based on modest to high sample sizes. They further show that systematic differences in shape and development thereof may be present in left vs. right sides of individuals within a species and careful consideration should be given to whether the left, right, or symmetric component of both is used to represent the shape of each individual

Thirty years of artificial intelligence in medicine (AIME) conferences: A review of research themes

Over the past 30 years, the international conference on Artificial Intelligence in MEdicine (AIME) has been organized at different venues across Europe every 2 years, establishing a forum for scientific exchange and creating an active research community. The Artificial Intelligence in Medicine journal has published theme issues with extended versions of selected AIME papers since 1998

KINE[SIS]TEM'17 From Nature to Architectural Matter

Kine[SiS]tem – From Kinesis + System. Kinesis is a non-linear movement or activity of an organism in response to a stimulus. A system is a set of interacting and interdependent agents forming a complex whole, delineated by its spatial and temporal boundaries, influenced by its environment. How can architectural systems moderate the external environment to enhance comfort conditions in a simple, sustainable and smart way? This is the starting question for the Kine[SiS]tem’17 – From Nature to Architectural Matter International Conference. For decades, architectural design was developed despite (and not with) the climate, based on mechanical heating and cooling. Today, the argument for net zero energy buildings needs very effective strategies to reduce energy requirements. The challenge ahead requires design processes that are built upon consolidated knowledge, make use of advanced technologies and are inspired by nature. These design processes should lead to responsive smart systems that deliver the best performance in each specific design scenario. To control solar radiation is one key factor in low-energy thermal comfort. Computational-controlled sensor-based kinetic surfaces are one of the possible answers to control solar energy in an effective way, within the scope of contradictory objectives throughout the year.FC

Efficient rendering of large 3-D and 4-D scalar fields

Rendering volumetric data, as a compute/communication intensive and highly parallel application, represents the characteristics of future workloads for desktop computers. Interactively rendering volumetric data has been a challenging problem due to its high computational and communication requirements. With the consistent trend toward high resolution data, it has remained a difficult problem despite the continuous increase in processing power, because of the increasing performance gap between computation and communication. On the other hand, the new multi-core architecture trend in computational units in PC, which can be characterized by parallelism and heterogeneity, provides both opportunities and challenges. While the new on-chip parallel architectures offer opportunities for extremely high performance, widespread use of those parallel processors requires extensive changes in previous algorithms to take advantage of the new architectures. In this dissertation, we develop new methods and techniques to support interactive rendering of large volumetric data. In particular, we present a novel method to layout data on disk for efficiently performing an out-of-core axis-aligned slicing of large multidimensional scalar fields. We also present a new method to efficiently build an out-of-core indexing structure for n-dimensional volumetric data. Then, we describe a streaming model for efficiently implementing volume ray casting on a heterogeneous compute resource environment. We describe how we implement the model on SONY/TOSHIBA/IBM Cell Broadband Engine and on NVIDIA CUDA architecture. Our results show that our out-of-core techniques significantly reduce the communication bandwidth requirements and that our streaming model very effectively makes use of the strengths of those heterogeneous parallel compute resource environment for volume rendering. In all cases, we achieve scalability and load balancing, while hiding memory latency

3D reconstruction for plastic surgery simulation based on statistical shape models

This thesis has been accomplished in Crisalix in collaboration with the Universitat Pompeu Fabra within the program of Doctorats Industrials. Crisalix has the mission of enhancing the communication between professionals of plastic surgery and patients by providing a solution to the most common question during the surgery planning process of ``How will I look after the surgery?''. The solution proposed by Crisalix is based in 3D imaging technology. This technology generates the 3D reconstruction that accurately represents the area of the patient that is going to be operated. This is followed by the possibility of creating multiple simulations of the plastic procedure, which results in the representation of the possible outcomes of the surgery. This thesis presents a framework capable to reconstruct 3D shapes of faces and breasts of plastic surgery patients from 2D images and 3D scans. The 3D reconstruction of an object is a challenging problem with many inherent ambiguities. Statistical model based methods are a powerful approach to overcome some of these ambiguities. We follow the intuition of maximizing the use of available prior information by introducing it into statistical model based methods to enhance their properties. First, we explore Active Shape Models (ASM) which are a well known method to perform 2D shapes alignment. However, it is challenging to maintain prior information (e.g. small set of given landmarks) unchanged once the statistical model constraints are applied. We propose a new weighted regularized projection into the parameter space which allows us to obtain shapes that at the same time fulfill the imposed shape constraints and are plausible according to the statistical model. Second, we extend this methodology to be applied to 3D Morphable Models (3DMM), which are a widespread method to perform 3D reconstruction. However, existing methods present some limitations. Some of them are based in non-linear optimizations computationally expensive that can get stuck in local minima. Another limitation is that not all the methods provide enough resolution to represent accurately the anatomy details needed for this application. Given the medical use of the application, the accuracy and robustness of the method, are important factors to take into consideration. We show how 3DMM initialization and 3DMM fitting can be improved using our weighted regularized projection. Finally, we present a framework capable to reconstruct 3D shapes of plastic surgery patients from two possible inputs: 2D images and 3D scans. Our method is used in different stages of the 3D reconstruction pipeline: shape alignment; 3DMM initialization and 3DMM fitting. The developed methods have been integrated in the production environment of Crisalix, proving their validity.Aquesta tesi ha estat realitzada a Crisalix amb la col·laboració de la Universitat Pompeu Fabra sota el pla de Doctorats Industrials. Crisalix té com a objectiu la millora de la comunicació entre els professionals de la cirurgia plàstica i els pacients, proporcionant una solució a la pregunta que sorgeix més freqüentment durant el procés de planificació d'una operació quirúrgica ``Com em veuré després de la cirurgia?''. La solució proposada per Crisalix està basada en la tecnologia d'imatge 3D. Aquesta tecnologia genera la reconstrucció 3D de la zona del pacient operada, seguit de la possibilitat de crear múltiples simulacions obtenint la representació dels possibles resultats de la cirurgia. Aquesta tesi presenta un sistema capaç de reconstruir cares i pits de pacients de cirurgia plàstica a partir de fotos 2D i escanegis. La reconstrucció en 3D d'un objecte és un problema complicat degut a la presència d'ambigüitats. Els mètodes basats en models estadístics son adequats per mitigar-les. En aquest treball, hem seguit la intuïció de maximitzar l'ús d'informació prèvia, introduint-la al model estadístic per millorar les seves propietats. En primer lloc, explorem els Active Shape Models (ASM) que són un conegut mètode fet servir per alinear contorns d'objectes 2D. No obstant, un cop aplicades les correccions de forma del model estadístic, es difícil de mantenir informació de la que es disposava a priori (per exemple, un petit conjunt de punts donat) inalterada. Proposem una nova projecció ponderada amb un terme de regularització, que permet obtenir formes que compleixen les restriccions de forma imposades i alhora són plausibles en concordança amb el model estadístic. En segon lloc, ampliem la metodologia per aplicar-la als anomenats 3D Morphable Models (3DMM) que són un mètode extensivament utilitzat per fer reconstrucció 3D. No obstant, els mètodes de 3DMM existents presenten algunes limitacions. Alguns estan basats en optimitzacions no lineals, computacionalment costoses i que poden quedar atrapades en mínims locals. Una altra limitació, és que no tots el mètodes proporcionen la resolució adequada per representar amb precisió els detalls de l'anatomia. Donat l'ús mèdic de l'aplicació, la precisió i la robustesa són factors molt importants a tenir en compte. Mostrem com la inicialització i l'ajustament de 3DMM poden ser millorats fent servir la projecció ponderada amb regularització proposada. Finalment, es presenta un sistema capaç de reconstruir models 3D de pacients de cirurgia plàstica a partir de dos possibles tipus de dades: imatges 2D i escaneigs en 3D. El nostre mètode es fa servir en diverses etapes del procés de reconstrucció: alineament de formes en imatge, la inicialització i l'ajustament de 3DMM. Els mètodes desenvolupats han estat integrats a l'entorn de producció de Crisalix provant la seva validesa

Feature-Based Correspondences to Infer the Location of Anatomical Landmarks

A methodology has been developed for automatically determining inter-image correspondences between cliques of features extracted from a reference and a query image. Cliques consist of up to threefeatures and correspondences between them are determined via a hierarchy of similarity metrics based on the inherent properties of the features and geometric relationships between those features. As opposed to approaches that determine correspondences solely by voxel intensity, features that also include shape description are used. Specifically, medial-based features areemployed because they are sparse compared to the number of image voxels and can be automatically extracted from the image.The correspondence framework has been extended to automatically estimate the location of anatomical landmarks in the query image by adding landmarks to the cliques. Anatomical landmark locationsare then inferred from the reference image by maximizing landmark correspondences. The ability to infer landmark locations has provided a means to validate the correspondence framework in thepresence of structural variation between images. Moreover, automated landmark estimation imparts the user with anatomical information and can hypothetically be used to initialize andconstrain the search space of segmentation and registration methods.Methods developed in this dissertation were applied to simulated MRI brain images, synthetic images, and images constructed from several variations of a parametric model. Results indicate that the methods are invariant to global translation and rotation and can operate in the presence of structure variation between images.The automated landmark placement method was shown to be accurate as compared to ground-truth that was established both parametrically and manually. It is envisioned that these automated methods could prove useful for alleviating time-consuming and tedious tasks in applications that currently require manual input, and eliminate intra-user subjectivity

Virtuelle endovaskuläre Versorgung von abdominalen Aortenaneurysmen

This thesis is focused on computational methods that predict the outcome of endovascular repair of abdominal aortic aneurysms. Novelties include improvements of the aneurysm model, the stent-graft model as well as the in-silico stent-graft placement methodology. The newly developed methods are applied to patient-specific cases and are validated against real-world postinterventional data. Further, directions for using the in-silico model of endovascular aneurysm repair as personalized preinterventional planning tool in clinical practice are provided.Die vorliegende Arbeit beschäftigt sich mit numerischen Methoden um den Ausgang einer endovaskulären Versorgung von abdominalen Aortenaneurysmen vorherzusagen. Neuheiten umfassen Verbesserungen des Aneurysmenmodells, des Stentgraftmodells sowie der virtuellen Platzierungsmethode des Stentgrafts. Die neu entwickelten Methoden werden auf patientenspezifische Fälle angewandt und werden mit realen postoperativen Daten validiert. Weiterhin werden klinische Anwendungen des Modells der endovaskulären Aneurysmenversorgung als personalisiertes präoperatives Planungswerkzeug präsentiert

Applying image processing techniques to pose estimation and view synthesis.

Fung Yiu-fai Phineas.Thesis (M.Phil.)--Chinese University of Hong Kong, 1999.Includes bibliographical references (leaves 142-148).Abstracts in English and Chinese.Chapter 1 --- Introduction --- p.1Chapter 1.1 --- Model-based Pose Estimation --- p.3Chapter 1.1.1 --- Application - 3D Motion Tracking --- p.4Chapter 1.2 --- Image-based View Synthesis --- p.4Chapter 1.3 --- Thesis Contribution --- p.7Chapter 1.4 --- Thesis Outline --- p.8Chapter 2 --- General Background --- p.9Chapter 2.1 --- Notations --- p.9Chapter 2.2 --- Camera Models --- p.10Chapter 2.2.1 --- Generic Camera Model --- p.10Chapter 2.2.2 --- Full-perspective Camera Model --- p.11Chapter 2.2.3 --- Affine Camera Model --- p.12Chapter 2.2.4 --- Weak-perspective Camera Model --- p.13Chapter 2.2.5 --- Paraperspective Camera Model --- p.14Chapter 2.3 --- Model-based Motion Analysis --- p.15Chapter 2.3.1 --- Point Correspondences --- p.16Chapter 2.3.2 --- Line Correspondences --- p.18Chapter 2.3.3 --- Angle Correspondences --- p.19Chapter 2.4 --- Panoramic Representation --- p.20Chapter 2.4.1 --- Static Mosaic --- p.21Chapter 2.4.2 --- Dynamic Mosaic --- p.22Chapter 2.4.3 --- Temporal Pyramid --- p.23Chapter 2.4.4 --- Spatial Pyramid --- p.23Chapter 2.5 --- Image Pre-processing --- p.24Chapter 2.5.1 --- Feature Extraction --- p.24Chapter 2.5.2 --- Spatial Filtering --- p.27Chapter 2.5.3 --- Local Enhancement --- p.31Chapter 2.5.4 --- Dynamic Range Stretching or Compression --- p.32Chapter 2.5.5 --- YIQ Color Model --- p.33Chapter 3 --- Model-based Pose Estimation --- p.35Chapter 3.1 --- Previous Work --- p.35Chapter 3.1.1 --- Estimation from Established Correspondences --- p.36Chapter 3.1.2 --- Direct Estimation from Image Intensities --- p.49Chapter 3.1.3 --- Perspective-3-Point Problem --- p.51Chapter 3.2 --- Our Iterative P3P Algorithm --- p.58Chapter 3.2.1 --- Gauss-Newton Method --- p.60Chapter 3.2.2 --- Dealing with Ambiguity --- p.61Chapter 3.2.3 --- 3D-to-3D Motion Estimation --- p.66Chapter 3.3 --- Experimental Results --- p.68Chapter 3.3.1 --- Synthetic Data --- p.68Chapter 3.3.2 --- Real Images --- p.72Chapter 3.4 --- Discussions --- p.73Chapter 4 --- Panoramic View Analysis --- p.76Chapter 4.1 --- Advanced Mosaic Representation --- p.76Chapter 4.1.1 --- Frame Alignment Policy --- p.77Chapter 4.1.2 --- Multi-resolution Representation --- p.77Chapter 4.1.3 --- Parallax-based Representation --- p.78Chapter 4.1.4 --- Multiple Moving Objects --- p.79Chapter 4.1.5 --- Layers and Tiles --- p.79Chapter 4.2 --- Panorama Construction --- p.79Chapter 4.2.1 --- Image Acquisition --- p.80Chapter 4.2.2 --- Image Alignment --- p.82Chapter 4.2.3 --- Image Integration --- p.88Chapter 4.2.4 --- Significant Residual Estimation --- p.89Chapter 4.3 --- Advanced Alignment Algorithms --- p.90Chapter 4.3.1 --- Patch-based Alignment --- p.91Chapter 4.3.2 --- Global Alignment (Block Adjustment) --- p.92Chapter 4.3.3 --- Local Alignment (Deghosting) --- p.93Chapter 4.4 --- Mosaic Application --- p.94Chapter 4.4.1 --- Visualization Tool --- p.94Chapter 4.4.2 --- Video Manipulation --- p.95Chapter 4.5 --- Experimental Results --- p.96Chapter 5 --- Panoramic Walkthrough --- p.99Chapter 5.1 --- Problem Statement and Notations --- p.100Chapter 5.2 --- Previous Work --- p.101Chapter 5.2.1 --- 3D Modeling and Rendering --- p.102Chapter 5.2.2 --- Branching Movies --- p.103Chapter 5.2.3 --- Texture Window Scaling --- p.104Chapter 5.2.4 --- Problems with Simple Texture Window Scaling --- p.105Chapter 5.3 --- Our Walkthrough Approach --- p.106Chapter 5.3.1 --- Cylindrical Projection onto Image Plane --- p.106Chapter 5.3.2 --- Generating Intermediate Frames --- p.108Chapter 5.3.3 --- Occlusion Handling --- p.114Chapter 5.4 --- Experimental Results --- p.116Chapter 5.5 --- Discussions --- p.116Chapter 6 --- Conclusion --- p.121Chapter A --- Formulation of Fischler and Bolles' Method for P3P Problems --- p.123Chapter B --- Derivation of z1 and z3 in terms of z2 --- p.127Chapter C --- Derivation of e1 and e2 --- p.129Chapter D --- Derivation of the Update Rule for Gauss-Newton Method --- p.130Chapter E --- Proof of (λ1λ2-λ 4）>〉0 --- p.132Chapter F --- Derivation of φ and hi --- p.133Chapter G --- Derivation of w1j to w4j --- p.134Chapter H --- More Experimental Results on Panoramic Stitching Algorithms --- p.138Bibliography --- p.14