Efficient methodologies for system matrix modelling in iterative image reconstruction for rotating high-resolution PET

A fully 3D iterative image reconstruction algorithm has been developed for high-resolution PET cameras composed of pixelated scintillator crystal arrays and rotating planar detectors, based on the ordered subsets approach. The associated system matrix is precalculated with Monte Carlo methods that incorporate physical effects not included in analytical models, such as positron range effects and interaction of the incident gammas with the scintillator material. Custom Monte Carlo methodologies have been developed and optimized for modelling of system matrices for fast iterative image reconstruction adapted to specific scanner geometries, without redundant calculations. According to the methodology proposed here, only one-eighth of the voxels within two central transaxial slices need to be modelled in detail. The rest of the system matrix elements can be obtained with the aid of axial symmetries and redundancies, as well as in-plane symmetries within transaxial slices. Sparse matrix techniques for the non-zero system matrix elements are employed, allowing for fast execution of the image reconstruction process. This 3D image reconstruction scheme has been compared in terms of image quality to a 2D fast implementation of the OSEM algorithm combined with Fourier rebinning approaches. This work confirms the superiority of fully 3D OSEM in terms of spatial resolution, contrast recovery and noise reduction as compared to conventional 2D approaches based on rebinning schemes. At the same time it demonstrates that fully 3D methodologies can be efficiently applied to the image reconstruction problem for high-resolution rotational PET cameras by applying accurate pre-calculated system models and taking advantage of the system's symmetries.

UV laser-induced high resolution cleaving of Si wafers for micro-nano devices and polymeric waveguide characterization

In this work we propose a method for cleaving silicon-based photonic chips by using a laser based micromachining system, consisting of a ND:YVO4laser emitting at 355 nm in nanosecond pulse regime and a micropositioning system. The laser makes grooved marks placed at the desired locations and directions where cleaves have to be initiated, and after several processing steps, a crack appears and propagate along the crystallographic planes of the silicon wafer. This allows cleavage of the chips automatically and with high positioning accuracy, and provides polished vertical facets with better quality than the obtained with other cleaving process, which eases the optical characterization of photonic devices. This method has been found to be particularly useful when cleaving small-sized chips, where manual cleaving is hard to perform; and also for polymeric waveguides, whose facets get damaged or even destroyed with polishing or manual cleaving processing. Influence of length of the grooved line and speed of processing is studied for a variety of silicon chips. An application for cleaving and characterizing sol–gel waveguides is presented. The total amount of light coupled is higher than when using any other procedure.

High resolution system for nanoparticles hyperthermia efficiency evaluation

A system to evaluate nanoparticles efficiency in hyperthermia applications is presented. The method allows a direct measurement of the power dissipated by the nanoparticles through the determination of the first harmonic component of the in quadrature magnetic moment induced by the applied field. The magnetic moment is measured by using an induction method. To avoid errors and reduce the noise signal a double in phase demodulation technique is used. To test the system viability we have measured nanowires, nanoparticles and copper samples of different volumes to prove by comparing experimental and modeled results

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.

On the acquisition of high-resolution maps with open source software and commercials off-the-shelf quad-rotors

Mosaics are high-resolution images obtained aerially and employed in several scientific research areas, such for example, in the field of environmental monitoring and precision agriculture. Although many high resolution maps are obtained by commercial demand, they can also be acquired with commercial aerial vehicles which provide more experimental autonomy and availability. For what regard to mosaicing-based aerial mission planners, there are not so many - if any - free of charge software. Therefore, in this paper is presented a framework designed with open source tools and libraries as an alternative to commercial tools to carry out mosaicing tasks.

Fast Correction of Tiled Display Systems on Planar Surfaces

A method for fast colour and geometric correction of a tiled display system is presented in this paper. Such kind of displays are a common choice for virtual reality applications and simulators, where a high resolution image is required. They are the cheapest and more flexible alternative for large image generation but they require a precise geometric and colour correction. The purpose of the proposed method is to correct the projection system as fast as possible so in case the system needs to be recalibrated it doesn’t interfere with the normal operation of the simulator or virtual reality application. This technique makes use of a single conventional webcam for both geometric and photometric correction. Some previous assumptions are made, like planar projection surface and negligibleintra-projector colour variation and black-offset levels. If these assumptions hold true, geometric and photometric seamlessness can be achievedfor this kind of display systems. The method described in this paper is scalable for an undefined number of projectors and completely automatic.

Metodología para el desarrollo de un sistema de visualización multi-proyector con características cromáticas uniformes

Los sistemas de proyección multi-proyector han adquirido gran popularidad en los últimos años para su uso en un amplio rango de aplicaciones como sistemas de realidad virtual, simuladores y visualización de datos. Esto es debido a que normalmente estas aplicaciones necesitan representar sus datos a muy alta resolución y a lo largo de una gran superficie. Este tipo de sistemas de proyección son baratos en comparación con las resoluciones que pueden conseguir, se pueden configurar para proyectar sobre prácticamente cualquier tipo de superficie, sea cual sea su forma, y son fácilmente escalables. Sin embargo, para hacer que este tipo de sistemas generen una imagen sin discontinuidades geométricas o colorimétricas requieren de un ajuste preciso. En la presente tesis se analizan en detalle todos los problemas a los que hay que enfrentarse a la hora de diseñar y calibrar un sistema de proyección de este tipo y se propone una metodología con una serie de optimizaciones para hacer el ajuste de estos sistemas más sencillo y rápido. Los resultados de esta metodología se muestran aplicados a la salida gráfica de un simulador de entrenamiento. Multi-projector display systems have gained high popularity over the past years for its use in a wide range of applications such as virtual reality systems, simulators or data visualization where a high resolution image over a large projection surface is required. Such systems are cheap for the resolutions they can provide, can be configured to project images on almost any kind of screen shapes and are easily scalable, but in order to provide a seamless image with no photometric discontinuities they require a precise geometric and colour correction. In this thesis, we analyze all the problems that have to be faced in order to design and calibrate a multi-projector display. We propose a calibration methodology with some optimizations that make the adjustment of this kind of displays easier and faster. The results of the implementation of this methodology on a training simulator are presented and discussed

Aerial Coverage Path Planning applied to Mapping

In the last decade we have seen how small and light weight aerial platforms - aka, Mini Unmanned Aerial Vehicles (MUAV) - shipped with heterogeneous sensors have become a 'most wanted' Remote Sensing (RS) tool. Most of the off-the-shelf aerial systems found in the market provide way-point navigation. However, they do not rely on a tool that compute the aerial trajectories considering all the aspects that allow optimizing the aerial missions. One of the most demanded RS applications of MUAV is image surveying. The images acquired are typically used to build a high-resolution image, i.e., a mosaic of the workspace surface. Although, it may be applied to any other application where a sensor-based map must be computed. This thesis provides a study of this application and a set of solutions and methods to address this kind of aerial mission by using a fleet of MUAVs. In particular, a set of algorithms are proposed for map-based sampling, and aerial coverage path planning (ACPP). Regarding to map-based sampling, the approaches proposed consider workspaces with different shapes and surface characteristics. The workspace is sampled considering the sensor characteristics and a set of mission requirements. The algorithm applies different computational geometry approaches, providing a unique way to deal with workspaces with different shape and surface characteristics in order to be surveyed by one or more MUAVs. This feature introduces a previous optimization step before path planning. After that, the ACPP problem is theorized and a set of ACPP algorithms to compute the MUAVs trajectories are proposed. The problem addressed herein is the problem to coverage a wide area by using MUAVs with limited autonomy. Therefore, the mission must be accomplished in the shortest amount of time. The aerial survey is usually subject to a set of workspace restrictions, such as the take-off and landing positions as well as a safety distance between elements of the fleet. Moreover, it has to avoid forbidden zones to y. Three different algorithms have been studied to address this problem. The approaches studied are based on graph searching, heuristic and meta-heuristic approaches, e.g., mimic, evolutionary. Finally, an extended survey of field experiments applying the previous methods, as well as the materials and methods adopted in outdoor missions is presented. The reported outcomes demonstrate that the findings attained from this thesis improve ACPP mission for mapping purpose in an efficient and safe manner.

Aerial Coverage Path Planning applied to Mapping

In the last decade we have seen how small and light weight aerial platforms - aka, Mini Unmanned Aerial Vehicles (MUAV) - shipped with heterogeneous sensors have become a 'most wanted' Remote Sensing (RS) tool. Most of the off-the-shelf aerial systems found in the market provide way-point navigation. However, they do not rely on a tool that compute the aerial trajectories considering all the aspects that allow optimizing the aerial missions. One of the most demanded RS applications of MUAV is image surveying. The images acquired are typically used to build a high-resolution image, i.e., a mosaic of the workspace surface. Although, it may be applied to any other application where a sensor-based map must be computed. This thesis provides a study of this application and a set of solutions and methods to address this kind of aerial mission by using a fleet of MUAVs. In particular, a set of algorithms are proposed for map-based sampling, and aerial coverage path planning (ACPP). Regarding to map-based sampling, the approaches proposed consider workspaces with different shapes and surface characteristics. The workspace is sampled considering the sensor characteristics and a set of mission requirements. The algorithm applies different computational geometry approaches, providing a unique way to deal with workspaces with different shape and surface characteristics in order to be surveyed by one or more MUAVs. This feature introduces a previous optimization step before path planning. After that, the ACPP problem is theorized and a set of ACPP algorithms to compute the MUAVs trajectories are proposed. The problem addressed herein is the problem to coverage a wide area by using MUAVs with limited autonomy. Therefore, the mission must be accomplished in the shortest amount of time. The aerial survey is usually subject to a set of workspace restrictions, such as the take-off and landing positions as well as a safety distance between elements of the fleet. Moreover, it has to avoid forbidden zones to y. Three different algorithms have been studied to address this problem. The approaches studied are based on graph searching, heuristic and meta-heuristic approaches, e.g., mimic, evolutionary. Finally, an extended survey of field experiments applying the previous methods, as well as the materials and methods adopted in outdoor missions is presented. The reported outcomes demonstrate that the findings attained from this thesis improve ACPP mission for mapping purpose in an efficient and safe manner.

What is the optimal stitching orientation from an aerial survey perspective?

Mosaicing is a technique that allows obtaining a large high resolution image by stitching several images together. These base images are usually acquired from an elevated point of view. Until recently, low-altitude image acquisition has been performed typically by using using airplanes, as well as other manned platforms. However, mini unmanned aerial vehicles (MUAV) endowed with a camera have lately made this task more available for small for cicil applications, for example for small farmers in order to obtain accurate agronomic information about their crop fields. The stitching orientation, or the image acquisition orientation usually coincides with the aircraft heading assuming a downwards orientation of the camera. In this paper, the efect of the image orientation in the eficiency of the aerial coverage path planning is studied. Moreover, an algorithm to compute an optimal stitching orientation angle is proposed and results are numerically compared with classical approaches.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.

Self-organizing cultured neural networks: Image analysis techniques for longitudinal tracking and modeling of the underlying network structure (versión actualizada)

Esta tesis estudia la evolución estructural de conjuntos de neuronas como la capacidad de auto-organización desde conjuntos de neuronas separadas hasta que forman una red (clusterizada) compleja. Esta tesis contribuye con el diseño e implementación de un algoritmo no supervisado de segmentación basado en grafos con un coste computacional muy bajo. Este algoritmo proporciona de forma automática la estructura completa de la red a partir de imágenes de cultivos neuronales tomadas con microscopios de fase con una resolución muy alta. La estructura de la red es representada mediante un objeto matemático (matriz) cuyos nodos representan a las neuronas o grupos de neuronas y los enlaces son las conexiones reconstruidas entre ellos. Este algoritmo extrae también otras medidas morfológicas importantes que caracterizan a las neuronas y a las neuritas. A diferencia de otros algoritmos hasta el momento, que necesitan de fluorescencia y técnicas inmunocitoquímicas, el algoritmo propuesto permite el estudio longitudinal de forma no invasiva posibilitando el estudio durante la formación de un cultivo. Además, esta tesis, estudia de forma sistemática un grupo de variables topológicas que garantizan la posibilidad de cuantificar e investigar la progresión de las características principales durante el proceso de auto-organización del cultivo. Nuestros resultados muestran la existencia de un estado concreto correspondiente a redes con configuracin small-world y la emergencia de propiedades a micro- y meso-escala de la estructura de la red. Finalmente, identificamos los procesos físicos principales que guían las transformaciones morfológicas de los cultivos y proponemos un modelo de crecimiento de red que reproduce el comportamiento cuantitativamente de las observaciones experimentales. ABSTRACT The thesis analyzes the morphological evolution of assemblies of living neurons, as they self-organize from collections of separated cells into elaborated, clustered, networks. In particular, it contributes with the design and implementation of a graph-based unsupervised segmentation algorithm, having an associated very low computational cost. The processing automatically retrieves the whole network structure from large scale phase-contrast images taken at high resolution throughout the entire life of a cultured neuronal network. The network structure is represented by a mathematical object (a matrix) in which nodes are identified neurons or neurons clusters, and links are the reconstructed connections between them. The algorithm is also able to extract any other relevant morphological information characterizing neurons and neurites. More importantly, and at variance with other segmentation methods that require fluorescence imaging from immunocyto- chemistry techniques, our measures are non invasive and entitle us to carry out a fully longitudinal analysis during the maturation of a single culture. In turn, a systematic statistical analysis of a group of topological observables grants us the possibility of quantifying and tracking the progression of the main networks characteristics during the self-organization process of the culture. Our results point to the existence of a particular state corresponding to a small-world network configuration, in which several relevant graphs micro- and meso-scale properties emerge. Finally, we identify the main physical processes taking place during the cultures morphological transformations, and embed them into a simplified growth model that quantitatively reproduces the overall set of experimental observations.