Image Processing Algorithms for Electron Microscopy

The development of the electron microscopy (EM) has led to new algorithms devoted to the analysis of the images obtained by the EM know as micrographs. These images are characterized for being noisy, making the extraction of information a difficult task. To that end, several reconstruction packages are being developed that provide with powerful tools to denoise, extract and analyze the micrographs to obtain the 3D model (volume) of the sample. Since there is no a gold standard that can be followed to process all micrographs in a single way, researches rely on the combination of algorithms of several packages to get the optimal result. However, the lack of consensus between the packages makes difficult to combine different programs. Also, the algorithms should be made as simple and automatic as possible to facilitate the task of the researchers without degrading the quality of the results. The purpose of this bachelor thesis is to introduce required algorithms that can be used to reconstruct the 3D model of a sample out of the micrographs acquired by the electron microscope. The analysis will be focused on two individual and complementary tasks: the development of a mathematical basis aimed at the automatization and simplification of the deformation calculations carried out to optimize the 3D templates used to reconstruct new 3D models, and the protocolization of a package that uses ab initio methods to avoid the requirements of a 3D template to reconstruct a model. The algorithms will be tested in order to validate and analyze their performance, so they can be used in real problems and applications.Ingeniería Biomédic

Chiral symmetry breaking and entropy production in Dean vortices

In toroidal pipes, the secondary flow in cross section is a mirror symmetric pair of counter-rotating axially oriented Dean vortices. This mirror symmetry is broken in helical pipes. We investigate in detail the mirror symmetry breaking in these secondary flows in going from toroidal to helical geometries. We quantify the degree of mirror symmetry breaking in helical flows by calculating both an (i) order-parameter − 1 ≤ χ ≤ 1 that measures the net integrated chirality of vortices in section and (ii) the entropy production due to both viscous shear forces and convection for Dean vortices as the Dean number and pitch of the helix are varied. We prove that the entropy production due to convective processes is always greater than that due to viscous shear, for stationary incompressible flows in the absence of body forces. For the same pipe radius and pipe curvature, fluid density, viscosity, and entrance flows, the vortex entropy production in the stationary state is minimized for helical conduits (for a given Dean number) with respect to that of toroidal pipes (zero pitch). The dissipation in the fluid flow due to Dean vortices decreases in going from a toroidal to a helical geometry, while the chiral order parameter tends to χ = ± 1 for finite values of the pitch as the Dean number is decreased.This research has been funded by Grant No. PID2020-116846GB-C22 by the Spanish Ministry of Science and Innovation/State Agency of Research Grant No. MCIN/AEI/10.13039/501100011033 and by "ERDF A way of making Europe." We are grateful to Josep M. Ribo for many useful discussions

Development of a swift “Go-Fast” execution mode for the !UCDebug ARM debugger

RESUMEN: Las asignaturas del área de Estructura y Organización de Computadores en la Universidad de Cantabria utilizan la arquitectura ARM de referencia para sus lecciones tanto teóricas como prácticas. Durante los laboratorios de algunas de estas asignaturas los alumnos utilizan el depurador !UCDebug para ejecutar y depurar su código. Parte de estas prácticas se realizan empleando periféricos, de los cuales algunos tienen requerimientos temporales estrictos para su correcto funcionamiento. El depurador no contaba con una forma de ejecutar códigos que utilizasen estos dispositivos debido a que sus modos de ejecución introducían un gran overhead, haciendo que no se pudiera interactuar con los dispositivos correctamente. En este proyecto se busca implementar un nuevo modo de ejecución para !UCDebug que proporcione tiempos de ejecución similares a los de la ejecución en el sistema nativo. Esto permitiría poder utilizar una mayor variedad de periféricos en los laboratorios de las asignaturas. Antes de comenzar con el desarrollo de este nuevo modo, se desarrolló una suite de tests por la falta de un mecanismo que verificase el funcionamiento del depurador. Esta suite de tests tiene como propósito el poder comprobar que las funcionalidades del depurador se ajusten a lo esperado. El nuevo modo, denominado modo Go-Fast, emplea una estrategia basada en el desarrollo de un handler de las SWIs. Como desarrollo adicional, se buscó una forma de que el usuario pueda interactuar con el depurador mientras ejecuta en este modo, para lo que se optó por un mecanismo de interrupciones periódicas. Con el desarrollo realizado en este proyecto el depurador ha demostrado que puede llegar a ejecutar correctamente los mismos códigos de ensamblador ARM que el sistema nativo, hasta el punto que se ha comprobado el depurador.ABSTRACT: Computer Structure and Organization courses at the University of Cantabria follow the ARM architecture as a reference for their lectures and practical sessions. In some of these courses, students use the !UCDebug ARM debugger at the computer lab to run and debug their codes. Part of these practical lessons are conducted using peripheral devices, some of which have strict time requirements for their correct functioning. The debugger was unable to properly execute code that interacted with such devices because its execution modes introduced a large overhead, making it impossible to meet their time requirements. This project seeks to implement a new execution mode for !UCDebug that provides execution times similar to those of the execution in the native system. This would allow a greater variety of peripherals to be used in these courses. Before starting the development of this new mode, a test suite was developed to address the lack of a mechanism that checks the debugger behavior. This test suite was developed in order to verify that the debugger's functionalities match a specific intended behavior. The new mode, called Go-Fast mode, employs a strategy based on the development of a SWI handler. As a further development, a way for the user to interact with the debugger while running in this mode was sought, for which a periodic interrupt mechanism was chosen. With the development conducted in this work, the debugger has shown that it can successfully execute the same ARM assembly codes as the native system, to the extent that the debugger has been tested.Grado en Ingeniería Informátic

Diseño y construcción de un banco de ensayos para un bogie de tren a escala

El objeto de este proyecto es analizar, diseñar y construir un banco de ensayos para un bogie de tren a escala reducida. Los procesos experimentales que se pretenden realizar son: Estimación de los parámetros inerciales, a partir del movimiento del sistema y las fuerzas que actúan en él ; Estimación del estado, es decir, coordenadas y velocidades generalizadas que definan el movimiento del sistema; Estimación de coeficientes de fricción entre rueda y vía. Los aspectos más importantes en el desarrollo del proyecto son: La elección de la escala óptima a partir de las características de los elementos ya disponibles, el presupuesto y las dimensiones del prototipo; Análisis punto de contacto rueda – vía; El estudio dinámico del conjunto del bogie; El diseño de componentes para facilitar el montaje; Los sensores a utilizar y su ubicación en el sistema. Las características del banco de ensayos son: Posibilidad de reproducir diversas condiciones de trabajo; Posibilidad de regular la velocidad de giro adecuadamente y con precisión, manteniendo la estabilidad en cualquier régimen; Diseño que no comprometa la seguridad del usuario y permita un fácil y cómodo manejo; Sistema de medida que permita una interpretación de datos sencilla y fiable; Posibilidad de incorporar nuevos elementos. En este proyecto se ha realizado toda la parte correspondiente al análisis previo del prototipo: diseño de piezas, selección de componentes y sensores, así como la construcción y puesta en funcionamiento del banco de ensayos. El apartado correspondiente al sistema eléctrico, conectar los sensores y obtener resultados con las diferentes pruebas realizadas, ha quedado pendiente para futuros trabajos, los cuales tendrán como referencia este proyecto para entender el funcionamiento del prototipo y la función de los sensores.Ingeniería IndustrialIndustria Ingeniaritz

Influence of Short Carbon-Chain Alcohol (Ethanol and 1-Propanol)/Diesel Fuel Blends over Diesel Engine Emissions

Oxygenated fuels, in this case short carbon-chain alcohols, have been investigated as alternative fuels to power compression ignition engines. A major advantage of short-chain alcohols is that they can be produced from renewable resources, i.e., cultivated commodities or biomass-based biorefineries. However, before entering the market, the effects of short-chain alcohols on engine performance, exhaust emissions, noise and sound quality need to be understood. This work sheds light on the relationship between the physicochemical properties of the alcohol/diesel fuel blends (ethanol and 1-propanol) on engine performance, exhaust emissions and, for the first time, on noise and sound quality. It has been demonstrated that when the content of alcohol in blends increased, soot and soluble organic material emissions drastically decreased, mainly due to the increase of oxygen content in the fuel. Reduction in soot emissions combined with higher thermodynamic efficiency of alcohol fuels, with respect to diesel fuel, enable their utilization on compression ignition engines. There is also an improvement in the soot-NOx trade off, leading to large reductions on soot with a small effect on NOx emissions. The oxygen content within the fuel reduces CO and THC emissions at extra-urban driving operation conditions. However, hydrocarbons and CO emissions increased at urban driving conditions, due to the high heat of vaporization of the alcohol fuels which reduces cylinder temperature worsening fuel atomization, vaporization and mixing with air being more significant at lower cylinder temperature conditions (low engine loads and speeds). Similarly, the higher the presence of alcohol in the blend, the higher the noise emitted by the engine due to their low tendency to auto-ignition. The optimization of alcohol quantity and the calibration of engine control parameters (e.g., injection settings) which is out of the scope of this work, will be required to overcome noise emission penalty. Furthermore, under similar alcohol content in the blend (10% v/v), the use of propanol is preferred over ethanol, as it exhibits lower exhaust emissions and better sound quality than ethanol

Ventricular Tachycardia and Early Fibrillation in Patients With Brugada Syndrome and Ischemic Cardiomyopathy Show Predictable Frequency-Phase Properties on the Precordial ECG Consistent With the Respective Arrhythmogenic Substrate

[EN] Background¿ Ventricular fibrillation (VF) has been proposed to be maintained by localized high-frequency sources. We tested whether spectral-phase analysis of the precordial ECG enabled identification of periodic activation patterns generated by such sources. Methods and Results¿Precordial ECGs were recorded from 15 ischemic cardiomyopathy and 15 Brugada syndrome (type 1 ECG) patients during induced VF and analyzed in the frequency-phase domain. Despite temporal variability, induced VF episodes lasting 19.6±7.9 s displayed distinctly high power at a common frequency (shared frequency, 5.7±1.1 Hz) in all leads about half of the time. In patients with Brugada syndrome, phase analysis of shared frequency showed a V1¿V6 sequence as would be expected from patients displaying a type 1 ECG pattern (P<0.001). Hilbert-based phases confirmed that the most stable sequence over the whole VF duration was V1¿V6. Analysis of shared frequency in ischemic cardiomyopathy patients with anteroseptal (n=4), apical (n=3), and inferolateral (n=4) myocardial infarction displayed a sequence starting at V1¿V2, V3¿V4, and V5¿V6, respectively, consistent with an activation origin at the scar location (P=0.005). Sequences correlated with the Hilbert-based phase analysis (P<0.001). Posterior infarction (n=4) displayed no specific sequence. On paired comparison, phase sequences during monomorphic ventricular tachycardia correlated moderately with VF (P<0.001). Moreover, there was a dominant frequency gradient from precordial leads facing the scar region to the contralateral leads (5.8±0.8 versus 5.4±1.1 Hz; P=0.004). Conclusions¿Noninvasive analysis of ventricular tachycardia and early VF in patients with Brugada syndrome and ischemic cardiomyopathy shows a predictable sequence in the frequency-phase domain, consistent with anatomic location of the arrhythmogenic substrate.This study was supported by the National Heart, Lung and Blood Institute (P01-HL039707, P01-HL087226 R01-HL118304); the Spanish Society of Cardiology, Arrhythmia and Electrophysiology Section; the Leducq Foundation, Paris, France; Centro Nacional de Investigaciones Cientificas, Madrid, Spain; Generalitat Valenciana, Valencia, Spain (PROMETEO/2012/030); VI Plan Nacional de Investigacion Cientifica, Desarrollo e Innovacion Tecnologica from the Ministerio de Economia y Competitividad of Spain (TIN2012-37546-C03-01); and the European Commission (European Regional Development Funds [ERDF]-FEDER)Calvo, D.; Atienza, F.; Saiz Rodríguez, FJ.; Martinez, L.; Ávila, P.; Rubín, J.; Herreros, B.... (2015). 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