MIA - a free and open source software for gray scale medical image analysis

Background Gray scale images make the bulk of data in bio-medical image analysis, and hence, the main focus of many image processing tasks lies in the processing of these monochrome images. With ever improving acquisition devices, spatial and temporal image resolution increases, and data sets become very large. Various image processing frameworks exists that make the development of new algorithms easy by using high level programming languages or visual programming. These frameworks are also accessable to researchers that have no background or little in software development because they take care of otherwise complex tasks. Specifically, the management of working memory is taken care of automatically, usually at the price of requiring more it. As a result, processing large data sets with these tools becomes increasingly difficult on work station class computers. One alternative to using these high level processing tools is the development of new algorithms in a languages like C++, that gives the developer full control over how memory is handled, but the resulting workflow for the prototyping of new algorithms is rather time intensive, and also not appropriate for a researcher with little or no knowledge in software development. Another alternative is in using command line tools that run image processing tasks, use the hard disk to store intermediate results, and provide automation by using shell scripts. Although not as convenient as, e.g. visual programming, this approach is still accessable to researchers without a background in computer science. However, only few tools exist that provide this kind of processing interface, they are usually quite task specific, and don’t provide an clear approach when one wants to shape a new command line tool from a prototype shell script. Results The proposed framework, MIA, provides a combination of command line tools, plug-ins, and libraries that make it possible to run image processing tasks interactively in a command shell and to prototype by using the according shell scripting language. Since the hard disk becomes the temporal storage memory management is usually a non-issue in the prototyping phase. By using string-based descriptions for filters, optimizers, and the likes, the transition from shell scripts to full fledged programs implemented in C++ is also made easy. In addition, its design based on atomic plug-ins and single tasks command line tools makes it easy to extend MIA, usually without the requirement to touch or recompile existing code. Conclusion In this article, we describe the general design of MIA, a general purpouse framework for gray scale image processing. We demonstrated the applicability of the software with example applications from three different research scenarios, namely motion compensation in myocardial perfusion imaging, the processing of high resolution image data that arises in virtual anthropology, and retrospective analysis of treatment outcome in orthognathic surgery. With MIA prototyping algorithms by using shell scripts that combine small, single-task command line tools is a viable alternative to the use of high level languages, an approach that is especially useful when large data sets need to be processed.

Efficient numerical methods for global linear instability. Analysis and modeling of non-orthogonal swept attachment-line boundary layer flow

The aim of this thesis is to study the mechanisms of instability that occur in swept wings when the angle of attack increases. For this, a simplified model for the a simplified model for the non-orthogonal swept leading edge boundary layer has been used as well as different numerical techniques in order to solve the linear stability problem that describes the behavior of perturbations superposed upon this base flow. Two different approaches, matrix-free and matrix forming methods, have been validated using direct numerical simulations with spectral resolution. In this way, flow instability in the non-orthogonal swept attachment-line boundary layer is addressed in a linear analysis framework via the solution of the pertinent global (Bi-Global) PDE-based eigenvalue problem. Subsequently, a simple extension of the extended G¨ortler-H¨ammerlin ODEbased polynomial model proposed by Theofilis, Fedorov, Obrist & Dallmann (2003) for orthogonal flow, which includes previous models as particular cases and recovers global instability analysis results, is presented for non-orthogonal flow. Direct numerical simulations have been used to verify the stability results and unravel the limits of validity of the basic flow model analyzed. The effect of the angle of attack, AoA, on the critical conditions of the non-orthogonal problem has been documented; an increase of the angle of attack, from AoA = 0 (orthogonal flow) up to values close to _/2 which make the assumptions under which the basic flow is derived questionable, is found to systematically destabilize the flow. The critical conditions of non-orthogonal flows at 0 _ AoA _ _/2 are shown to be recoverable from those of orthogonal flow, via a simple analytical transformation involving AoA. These results can help to understand the mechanisms of destabilization that occurs in the attachment line of wings at finite angles of attack. Studies taking into account variations of the pressure field in the basic flow or the extension to compressible flows are issues that remain open. El objetivo de esta tesis es estudiar los mecanismos de la inestabilidad que se producen en ciertos dispositivos aerodinámicos cuando se aumenta el ángulo de ataque. Para ello se ha utilizado un modelo simplificado del flujo de base, así como diferentes técnicas numéricas, con el fin de resolver el problema de estabilidad lineal asociado que describe el comportamiento de las perturbaciones. Estos métodos; sin y con formación de matriz, se han validado utilizando simulaciones numéricas directas con resolución espectral. De esta manera, la inestabilidad del flujo de capa límite laminar oblicuo entorno a la línea de estancamiento se aborda en un marco de análisis lineal por medio del método Bi-Global de resolución del problema de valores propios en derivadas parciales. Posteriormente se propone una extensión simple para el flujo no-ortogonal del modelo polinomial de ecuaciones diferenciales ordinarias, G¨ortler-H¨ammerlin extendido, propuesto por Theofilis et al. (2003) para el flujo ortogonal, que incluye los modelos previos como casos particulares y recupera los resultados del analisis global de estabilidad lineal. Se han realizado simulaciones directas con el fin de verificar los resultados del análisis de estabilidad así como para investigar los límites de validez del modelo de flujo base utilizado. En este trabajo se ha documentado el efecto del ángulo de ataque AoA en las condiciones críticas del problema no ortogonal obteniendo que el incremento del ángulo de ataque, de AoA = 0 (flujo ortogonal) hasta valores próximos a _/2, en el cual las hipótesis sobre las que se basa el flujo base dejan de ser válidas, tiende sistemáticamente a desestabilizar el flujo. Las condiciones críticas del caso no ortogonal 0 _ AoA _ _/2 pueden recuperarse a partir del caso ortogonal mediante el uso de una transformación analítica simple que implica el ángulo de ataque AoA. Estos resultados pueden ayudar a comprender los mecanismos de desestabilización que se producen en el borde de ataque de las alas de los aviones a ángulos de ataque finitos. Como tareas pendientes quedaría realizar estudios que tengan en cuenta variaciones del campo de presión en el flujo base así como la extensión de éste al caso de flujos compresibles.

Computational Study of the Fe(CN)(2)CO Cofactor and Its Binding to HypC Protein.

In the intricate maturation process of [NiFe]-hydrogenases, the Fe(CN)2CO cofactor is first assembled in a HypCD complex with iron coordinated by cysteines from both proteins and CO is added after ligation of cyanides. The small accessory protein HypC is known to play a role in delivering the cofactor needed for assembling the hydrogenase active site. However, the chemical nature of the Fe(CN)2CO moiety and the stability of the cofactor–HypC complex are open questions. In this work, we address geometries, properties, and the nature of bonding of all chemical species involved in formation and binding of the cofactor by means of quantum calculations. We also study the influence of environmental effects and binding to cysteines on vibrational frequencies of stretching modes of CO and CN used to detect the presence of Fe(CN)2CO. Carbon monoxide is found to be much more sensitive to sulfur binding and the polarity of the medium than cyanides. The stability of the HypC–cofactor complex is analyzed by means of molecular dynamics simulation of cofactor-free and cofactor-bound forms of HypC. The results show that HypC is stable enough to carry the cofactor, but since its binding cysteine is located at the N-terminal unstructured tail, it presents large motions in solution, which suggests the need for a guiding interaction to achieve delivery of the cofactor.

Evolution of microstructure, macrotexture and mechanical properties of commercially pure Ti during ECAP-conform processing and drawing

Long-length ultrafine-grained (UFG) Ti rods are produced by equal-channel angular pressing via the conform scheme (ECAP-C) at 200 °C, which is followed by drawing at 200 °C. The evolution of microstructure, macrotexture, and mechanical properties (yield strength, ultimate tensile strength, failure stress, uniform elongation, elongation to failure) of pure Ti during this thermo-mechanical processing is studied. Special attention is also paid to the effect of microstructure on the mechanical behavior of the material after macrolocalization of plastic flow. The number of ECAP-C passes varies in the range of 1–10. The microstructure is more refined with increasing number of ECAP-C passes. Formation of homogeneous microstructure with a grain/subgrain size of 200 nm and its saturation after 6 ECAP-C passes are observed. Strength properties increase with increasing number of ECAP passes and saturate after 6 ECAP-C passes to a yield strength of 973 MPa, an ultimate tensile strength of 1035 MPa, and a true failure stress of 1400 MPa (from 625, 750, and 1150 MPa in the as-received condition). The true strain at failure failure decreases after ECAP-C processing. The reduction of area and true strain to failure values do not decrease after ECAP-C processing. The sample after 6 ECAP-C passes is subjected to drawing at 200¯C resulting in reduction of a grain/subgrain size to 150 nm, formation of (10 1¯0) fiber texture with respect to the rod axis, and further increase of the yield strength up to 1190 MPa, the ultimate tensile strength up to 1230 MPa and the true failure stress up to 1600 MPa. It is demonstrated that UFG CP Ti has low resistance to macrolocalization of plastic deformation and high resistance to crack formation after necking.

Extension of Euskalduna Conference Centre and Concert Hall: A Contemporary Application of Irregular Reciprocal Frames

Reciprocal frame structures, formed by a set of self-supported elements in a closed circuit, have long been used since antiquity to cover large spans with small elements. The roof structure of the Euskalduna conference centre and concert hall extension in Bilbao, covering an irregu- lar geometry of 3000 m2 with a maximum span of 45 m, presented an interesting opportunity to revisit the concept and to apply these classical systems. Furthermore, its analysis and develop- ment led to an interesting discussion on reciprocal frames. They showed great sensitivity of these systems to the local modification of a particular element, establishment of irregular load paths, mobilisation of almost the entire sys- tem when locally applying a punctual load and, finally, its large deformability. Besides, reciprocal frames present particular construction complexities and possibilities due to the moderate length of the structural elements, the predominance of shear-only connec- tions and the necessity of the entire system to be completely erected to guarantee its stability. Euskalduna extension, completed in 2012, is one of the largest and a very par- ticular case of irregular reciprocal frame structures built in the world. It shows the formal possibilities and potentiality of reciprocal frames to respond to free and irregular geometries.

A free real-time hourly tilted solar irradiation data Website for Europe

The engineering of solar power applications, such as photovoltaic energy (PV) or thermal solar energy requires the knowledge of the solar resource available for the solar energy system. This solar resource is generally obtained from datasets, and is either measured by ground-stations, through the use of pyranometers, or by satellites. The solar irradiation data are generally not free, and their cost can be high, in particular if high temporal resolution is required, such as hourly data. In this work, we present an alternative method to provide free hourly global solar tilted irradiation data for the whole European territory through a web platform. The method that we have developed generates solar irradiation data from a combination of clear-sky simulations and weather conditions data. The results are publicly available for free through Soweda, a Web interface. To our knowledge, this is the first time that hourly solar irradiation data are made available online, in real-time, and for free, to the public. The accuracy of these data is not suitable for applications that require high data accuracy, but can be very useful for other applications that only require a rough estimate of solar irradiation.

Arquifanía: la arquitectura como manifestación

Arquifanía: arquitectura y epifanía. La revelación que se da en el proyectar, en el construir y en el habitar. Desentrañar los protagonistas y el escenario de ese encuentro es el objetivo de esta tesis. Nace de una doble inquietud: la relación entre literatura y arquitectura y la constatación de algo inconmensurable en la arquitectura. A lo largo de los siglos la teoría de la arquitectura ha hecho un gran esfuerzo por racionalizar todos los aspectos de la disciplina. La sistematización del orden y jerarquía de los espacios, el uso de parámetros más rigurosos en los cálculos estructurales, el desarrollo de la técnica y el estudio de los esquemas funcionales han supuesto una fuente inagotable de manifestaciones arquitectónicas. Los paradigmas científicos, incluso, han resultado fundamentales en la creación de nuevos lenguajes. Sin embargo, en este camino de racionalización se han orillado aspectos de difícil cuantificación. Pese a que en la experiencia diaria del arquitecto se constata la presencia de parámetros inconmensurables, la teoría de la arquitectura no ha integrado de forma sistemática este conocimiento. De aquí nace la presente tesis doctoral. En ella se estudia, por analogía con el resto de artes, el concepto de manifestación. Se analiza de qué manera la obra arquitectónica se manifiesta, haciendo uso de su autonomía, y se convierte en la que dirige al arquitecto en todos los tiempos de la existencia de la obra: desde su génesis en el tiempo del proyecto hasta la experiencia de la obra terminada en el tiempo de la historia. Se considera que reflexionar en el concepto de manifestación puede aportar luces sobre la disciplina arquitectónica en un doble momento. Se estudia por una parte la actitud y el proceder del arquitecto ante la génesis del proyecto y por otra su posicionamiento ante la obra ya existente, sometida a su análisis (para la posterior síntesis) generando una espiral de conocimiento siempre abierta y en continuo enriquecimiento. Se analiza la obra de María Zambrano, filósofa, y José Ángel Valente, poeta, en busca de la definición del concepto de manifestación. El momento creativo, la naturaleza de la palabra poética, la actitud del poeta ante su obra, el conocimiento y la revelación de la belleza son temas recurrentes en sus obras y crean un corpus teórico que permite elaborar una teoría poética sólida y abierta, llena de sugerencias que se dirige con precisión al momento de la generación de la forma: su epifanía. A continuación se repasa el concepto de manifestación en la actividad de algunos artistas de la modernidad que, de manera implícita o explícita, han hablado del concepto de epifanía. A menudo de forma intuitiva, los artistas han detectado en su actividad la condición de ser depositarios de un don que se renueva en cada obra ejecutada. Entrelazado con su trabajo y con la disciplina diaria los artistas experimentan un diálogo con la obra, que se revela libre y con voluntad de manifestarse. Enunciado el problema y hecho el repaso por el mundo de la creación artística, nos enfrentamos con el núcleo de la tesis: ¿hasta qué punto y de qué manera el concepto de manifestación es válido en arquitectura? El discurso busca en la actividad de múltiples arquitectos la validez del concepto de manifestación. Se rastrean testimonios, textos, obras y análisis de obras. De esta investigación surge una topografía, un atlas de revelaciones de manifestaciones arquitectónicas: constataciones explícitas, testimonios implícitos o intuiciones. A través de este periplo entre el concepto de manifestación que la razón poética ofrece y la experiencia de muchos arquitectos se intenta responder, aunque sea parcialmente, a las preguntas que surgen al llevar a las últimas consecuencias la arquifanía: ¿En qué momento existe una voluntad de forma? ¿De qué manera encuentra el arquitecto la forma? ¿Cómo se le presenta? ¿Es el arquitecto el verdadero artífice de la obra? ¿O es en cambio un ser a la espera de la aparición? ABSTRACT Archiphany: architecture and epiphany. The revelation taking place in designing, building and living. The objective of the present dissertation is to unravel the protagonists and the scenario of this encounter. It stems from a double interest: the relationship between literature and architecture and the discovery of something incommensurable in architecture. Over the centuries, architectural theory has made a great effort in order to rationalise all aspects of this discipline. Thus, the systematization of the order and hierarchy of space, the use of more rigorous parameters on the structural analysis, the development of technical capacities and the study of functional schemes have been an inexhaustible source of architectural manifestations. Even scientific paradigms have been essential in the creation of new languages. However, aspects of difficult quantification have been relegated in this path of rationalisation. Whereas the presence of immeasurable parameters are encountered in the daily experience of the architect, architectural theory has failed to systematically integrate this knowledge. This is the driving force of this thesis. It explores, by analogy with the other arts, the concept of manifestation. It discusses how the architectural work manifests itself, making use of its autonomy, becoming the one leading the architect during the whole existence of the work: from its genesis in the designing time until the experience of the completed work in the historical time. In the present dissertation, it is assumed that reflecting on the concept of manifestation might shed light on two different moments on the way to project architecture. The architect approach to the project genesis is studied on the one hand, while in the other hand it is considered his positioning in front of the existing work, as well as his analysis (for a following synthesis) that generates an ever-open and ever-enriching spiral of knowledge. In the search for a definition of the concept of manifestation, the work of the philosopher María Zambrano and the poet José Ángel Valente are analysed. The creative moment, the nature of the poetic word, the attitude of the poet in front of his work, the knowledge and the revelation of beauty are persistent issues in their works. They create a theoretical corpus allowing to develop a sound and open poetical theory full of suggestions, accurately directed to the time of the form generation: its epiphany. The concept of manifestation is then reviewed in the activity of some modern artists that talked about the concept of epiphany –either implicitly or explicitly. Often in an intuitive way, artists have come to realize in their activity to be the depositories of a gift that is renewed in each work. Intertwined with their work and with their daily discipline, artists experience a dialogue with the work, which proves to be free and willing to manifest itself. Having stated the problem and having reviewed the world of artistic creation, we are confronted with the core of the thesis: Up to which extent and in which way is the concept of manifestation valid for architecture? Validity and evidence of this concept is sought in the activity of multiple architects. Texts, works, analysis, reviews and testimonies are investigated. From this research, a topography, an atlas of revelations of architectural manifestations arises: explicit findings, implicit witnesses or intuitions. By means of this journey going from the concept of manifestation hinted by the poetic reason to the experience of many architects, the ultimate questions risen by archiphany are meant to be answered (though partially): When does a will of form emerge? How does the architect find the form? How does it appear? Is the architect the true creator of the work? Or is he instead a being waiting for the vision?

Modeling and Simulation of Upper Brachial Plexus Injury

This article presents the first musculoskeletal model and simulation of upper plexus brachial injury. From this model is possible to analyse forces and movement ranges in order to develop a robotic exoskeleton to improve rehabilitation. The software that currently exists for musculoskeletal modeling is varied and most have advanced features for proper analysis and study of motion simulations. Whilst more powerful computer packages are usually expensive, there are other free and open source packages available which offer different tools to perform animations and simulations and which obtain forces and moments of inertia. Among them, Musculoskeletal Modeling Software was selected to construct a model of the upper limb, which has 7 degrees of freedom and 10 muscles. These muscles are important for two of the movements simulated in this article that are part of the post-surgery rehabilitation protocol. We performed different movement animations which are made using the inertial measurement unit to capture real data from movements made by a human being. We also performed the simulation of forces produced in elbow flexion-extension and arm abduction-adduction of a healthy subject and one with upper brachial plexus injury in a postoperative state to compare the force that is capable of being produced in both cases.