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.

Evaluation of a PET Prototype Using LYSO:Ce Monolithic Detector Block

We have analyzed the performance of a PET demonstrator formed by two sectors of four monolithic detector blocks placed face-to-face. Both front-end and read-out electronics have been evaluated by means of coincidence measurements using a rotating 22Na source placed at the center of the sectors in order to emulate the behavior of a complete full ring. A continuous training method based on neural network (NN) algorithms has been carried out to determine the entrance points over the surface of the detectors. Reconstructed images from 1 MBq 22Na point source and 22Na Derenzo phantom have been obtained using both filtered back projection (FBP) analytic methods and the OSEM 3D iterative algorithm available in the STIR software package [1]. Preliminary data on image reconstruction from a 22Na point source with Ø = 0.25 mm show spatial resolutions from 1.7 to 2.1 mm FWHM in the transverse plane. The results confirm the viability of this design for the development of a full-ring brain PET scanner compatible with magnetic resonance imaging for human studies.

Aspectos metodológicos para la evaluación de sistemas de tomografía por emisión de positrones empleando técnicas Montecarlo, protocolos estandarizados y diferentes trazadores

Esta tesis analiza los elementos que afectan a la evaluación del rendimiento dentro de la técnica de radiodiagnóstico mediante tomografía por emisión de positrones (PET), centrándose en escáneres preclínicos. Se exploran las posibilidades de los protocolos estándar de evaluación sobre los siguientes aspectos: su uso como herramienta para validar programas de simulación Montecarlo, como método para la comparación de escáneres y su validez en el estudio del efecto sobre la calidad de imagen al utilizar radioisótopos alternativos. Inicialmente se estudian los métodos de evaluación orientados a la validación de simulaciones PET, para ello se presenta el programa GAMOS como entorno de simulación y se muestran los resultados de su validación basada en el estándar NEMA NU 4-2008 para escáneres preclínicos. Esta validación se ha realizado mediante la comparación de los resultados simulados frente a adquisiciones reales en el equipo ClearPET, describiendo la metodología de evaluación y selección de los parámetros NEMA. En este apartado también se mencionan las aportaciones desarrolladas en GAMOS para aplicaciones PET, como la inclusión de herramientas para la reconstrucción de imágenes. Por otro lado, la evaluación NEMA del ClearPET es utilizada para comparar su rendimiento frente a otro escáner preclínico: el sistema rPET-1. Esto supone la primera caracterización NEMA NU 4 completa de ambos equipos; al mismo tiempo que se analiza cómo afectan las importantes diferencias de diseño entre ellos, especialmente el tamaño axial del campo de visión y la configuración de los detectores. El 68Ga es uno de los radioisótopos no convencionales en imagen PET que está experimentando un mayor desarrollo, sin embargo, presenta la desventaja del amplio rango o distancia recorrida por el positrón emitido. Además del rango del positrón, otra propiedad física característica de los radioisótopos PET que puede afectar a la imagen es la emisión de fotones gamma adicionales, tal como le ocurre al isótopo 48V. En esta tesis se evalúan dichos efectos mediante estudios de resolución espacial y calidad de imagen NEMA. Finalmente, se analiza el alcance del protocolo NEMA NU 4-2008 cuando se utiliza para este propósito, adaptándolo a tal fin y proponiendo posibles modificaciones. Abstract This thesis analyzes the factors affecting the performance evaluation in positron emission tomography (PET) imaging, focusing on preclinical scanners. It explores the possibilities of standard protocols of assessment on the following aspects: their use as tools to validate Monte Carlo simulation programs, their usefulness as a method for comparing scanners and their validity in the study of the effect of alternative radioisotopes on image quality. Initially we study the methods of performance evaluation oriented to validate PET simulations. For this we present the GAMOS program as a simulation framework and show the results of its validation based on the standard NEMA NU 4-2008 for preclinical PET scanners. This has been accomplished by comparing simulated results against experimental acquisitions in the ClearPET scanner, describing the methodology for the evaluation and selection of NEMA parameters. This section also mentions the contributions developed in GAMOS for PET applications, such as the inclusion of tools for image reconstruction. Furthermore, the evaluation of the ClearPET scanner is used to compare its performance against another preclinical scanner, specifically the rPET-1 system. This is the first complete NEMA NU 4 based characterization study of both systems. At the same time we analyze how do the significant design differences of these two systems, especially the size of the axial field of view and the detectors configuration affect their performance characteristics. 68Ga is one of the unconventional radioisotopes in PET imaging the use of which is currently significantly increasing; however, it presents the disadvantage of the long positron range (distance traveled by the emitted positron before annihilating with an electron). Besides the positron range, additional gamma photon emission is another physical property characteristic of PET radioisotopes that can affect the reconstructed image quality, as it happens to the isotope 48V. In this thesis we assess these effects through studies of spatial resolution and image quality. Finally, we analyze the scope of the NEMA NU 4-2008 to carry out such studies, adapting it and proposing possible modifications.

Applications of image-based, multi-view stereo reconstruction methods = (Aplicaciones de los métodos de reconstrucción estéreo multivista)

These slides present several 3-D reconstruction methods to obtain the geometric structure of a scene that is viewed by multiple cameras. We focus on the combination of the geometric modeling in the image formation process with the use of standard optimization tools to estimate the characteristic parameters that describe the geometry of the 3-D scene. In particular, linear, non-linear and robust methods to estimate the monocular and epipolar geometry are introduced as cornerstones to generate 3-D reconstructions with multiple cameras. Some examples of systems that use this constructive strategy are Bundler, PhotoSynth, VideoSurfing, etc., which are able to obtain 3-D reconstructions with several hundreds or thousands of cameras. En esta presentación se tratan varios métodos de reconstrucción 3-D para la obtención de la estructura geométrica de una escena que es visualizada por varias cámaras. Se enfatiza la combinación de modelado geométrico del proceso de formación de la imagen con el uso de herramientas estándar de optimización para estimar los parámetros característicos que describen la geometría de la escena 3-D. En concreto, se presentan métodos de estimación lineales, no lineales y robustos de las geometrías monocular y epipolar como punto de partida para generar reconstrucciones con tres o más cámaras. Algunos ejemplos de sistemas que utilizan este enfoque constructivo son Bundler, PhotoSynth, VideoSurfing, etc., los cuales, en la práctica pueden llegar a reconstruir una escena con varios cientos o miles de cámaras.

Computerized Three-Dimmensional Craniofacial Reconstruction from Skulls Based on Landmarks.

Human identification from a skull is a critical process in legal and forensic medicine, specially when no other means are available. Traditional clay-based methods attempt to generate the human face, in order to identify the corresponding person. However, these reconstructions lack of objectivity and consistence, since they depend on the practitioner. Current computerized techniques are based on facial models, which introduce undesired facial features when the final reconstruction is built. This paper presents an objective 3D craniofacial reconstruction technique, implemented in a graphic application, without using any facial template. The only information required by the software tool is the 3D image of the target skull and three parameters: age, gender and Body Mass Index (BMI) of the individual. Complexity is minimized, since the application database only consists of the anthropological information provided by soft tissue depth values in a set of points of the skull.

Assembling models of embryo development: Image analysis and the construction of digital atlases

Digital atlases of animal development provide a quantitative description of morphogenesis, opening the path toward processes modeling. Prototypic atlases offer a data integration framework where to gather information from cohorts of individuals with phenotypic variability. Relevant information for further theoretical reconstruction includes measurements in time and space for cell behaviors and gene expression. The latter as well as data integration in a prototypic model, rely on image processing strategies. Developing the tools to integrate and analyze biological multidimensional data are highly relevant for assessing chemical toxicity or performing drugs preclinical testing. This article surveys some of the most prominent efforts to assemble these prototypes, categorizes them according to salient criteria and discusses the key questions in the field and the future challenges toward the reconstruction of multiscale dynamics in model organisms.

Massively parallelizable list-mode reconstruction using a Monte Carlo-based elliptical Gaussian model

Purpose: A fully three-dimensional (3D) massively parallelizable list-mode ordered-subsets expectation-maximization (LM-OSEM) reconstruction algorithm has been developed for high-resolution PET cameras. System response probabilities are calculated online from a set of parameters derived from Monte Carlo simulations. The shape of a system response for a given line of response (LOR) has been shown to be asymmetrical around the LOR. This work has been focused on the development of efficient region-search techniques to sample the system response probabilities, which are suitable for asymmetric kernel models, including elliptical Gaussian models that allow for high accuracy and high parallelization efficiency. The novel region-search scheme using variable kernel models is applied in the proposed PET reconstruction algorithm. Methods: A novel region-search technique has been used to sample the probability density function in correspondence with a small dynamic subset of the field of view that constitutes the region of response (ROR). The ROR is identified around the LOR by searching for any voxel within a dynamically calculated contour. The contour condition is currently defined as a fixed threshold over the posterior probability, and arbitrary kernel models can be applied using a numerical approach. The processing of the LORs is distributed in batches among the available computing devices, then, individual LORs are processed within different processing units. In this way, both multicore and multiple many-core processing units can be efficiently exploited. Tests have been conducted with probability models that take into account the noncolinearity, positron range, and crystal penetration effects, that produced tubes of response with varying elliptical sections whose axes were a function of the crystal's thickness and angle of incidence of the given LOR. The algorithm treats the probability model as a 3D scalar field defined within a reference system aligned with the ideal LOR. Results: This new technique provides superior image quality in terms of signal-to-noise ratio as compared with the histogram-mode method based on precomputed system matrices available for a commercial small animal scanner. Reconstruction times can be kept low with the use of multicore, many-core architectures, including multiple graphic processing units. Conclusions: A highly parallelizable LM reconstruction method has been proposed based on Monte Carlo simulations and new parallelization techniques aimed at improving the reconstruction speed and the image signal-to-noise of a given OSEM algorithm. The method has been validated using simulated and real phantoms. A special advantage of the new method is the possibility of defining dynamically the cut-off threshold over the calculated probabilities thus allowing for a direct control on the trade-off between speed and quality during the reconstruction.

Image processing methods for human brain connectivity analysis from in-vivo diffusion MRI

The structural connectivity of the brain is considered to encode species-wise and subject-wise patterns that will unlock large areas of understanding of the human brain. Currently, diffusion MRI of the living brain enables to map the microstructure of tissue, allowing to track the pathways of fiber bundles connecting the cortical regions across the brain. These bundles are summarized in a network representation called connectome that is analyzed using graph theory. The extraction of the connectome from diffusion MRI requires a large processing flow including image enhancement, reconstruction, segmentation, registration, diffusion tracking, etc. Although a concerted effort has been devoted to the definition of standard pipelines for the connectome extraction, it is still crucial to define quality assessment protocols of these workflows. The definition of quality control protocols is hindered by the complexity of the pipelines under test and the absolute lack of gold-standards for diffusion MRI data. Here we characterize the impact on structural connectivity workflows of the geometrical deformation typically shown by diffusion MRI data due to the inhomogeneity of magnetic susceptibility across the imaged object. We propose an evaluation framework to compare the existing methodologies to correct for these artifacts including whole-brain realistic phantoms. Additionally, we design and implement an image segmentation and registration method to avoid performing the correction task and to enable processing in the native space of diffusion data. We release PySDCev, an evaluation framework for the quality control of connectivity pipelines, specialized in the study of susceptibility-derived distortions. In this context, we propose Diffantom, a whole-brain phantom that provides a solution to the lack of gold-standard data. The three correction methodologies under comparison performed reasonably, and it is difficult to determine which method is more advisable. We demonstrate that susceptibility-derived correction is necessary to increase the sensitivity of connectivity pipelines, at the cost of specificity. Finally, with the registration and segmentation tool called regseg we demonstrate how the problem of susceptibility-derived distortion can be overcome allowing data to be used in their original coordinates. This is crucial to increase the sensitivity of the whole pipeline without any loss in specificity.

Haptically assisted connection procedure for the reconstruction of dendritic spines

Dendritic spines are thin protrusions that cover the dendritic surface of numerous neurons in the brain and whose function seems to play a key role in neural circuits. The correct segmentation of those structures is difficult due to their small size and the resulting spines can appear incomplete. This paper presents a four-step procedure for the complete reconstruction of dendritic spines. The haptically driven procedure is intended to work as an image processing stage before the automatic segmentation step giving the final representation of the dendritic spines. The procedure is designed to allow both the navigation and the volume image editing to be carried out using a haptic device. A use case employing our procedure together with a commercial software package for the segmentation stage is illustrated. Finally, the haptic editing is evaluated in two experiments; the first experiment concerns the benefits of the force feedback and the second checks the suitability of the use of a haptic device as input. In both cases, the results shows that the procedure improves the editing accuracy.

Multi-textured 3D humanoid reconstruction through passive and active automatic techniques = Reconstrucción de humanoides 3D multi-texturados mediante técnicas pasivas y activas automáticas

The proliferation of video games and other applications of computer graphics in everyday life demands a much easier way to create animatable virtual human characters. Traditionally, this has been the job of highly skilled artists and animators that painstakingly model, rig and animate their avatars, and usually have to tune them for each application and transmission/rendering platform. The emergence of virtual/mixed reality environments also calls for practical and costeffective ways to produce custom models of actual people. The purpose of the present dissertation is bringing 3D human scanning closer to the average user. For this, two different techniques are presented, one passive and one active. The first one is a fully automatic system for generating statically multi-textured avatars of real people captured with several standard cameras. Our system uses a state-of-the-art shape from silhouette technique to retrieve the shape of subject. However, to deal with the lack of detail that is common in the facial region for these kind of techniques, which do not handle concavities correctly, our system proposes an approach to improve the quality of this region. This face enhancement technique uses a generic facial model which is transformed according to the specific facial features of the subject. Moreover, this system features a novel technique for generating view-independent texture atlases computed from the original images. This static multi-texturing system yields a seamless texture atlas calculated by combining the color information from several photos. We suppress the color seams due to image misalignments and irregular lighting conditions that multi-texturing approaches typically suffer from, while minimizing the blurring effect introduced by color blending techniques. The second technique features a system to retrieve a fully animatable 3D model of a human using a commercial depth sensor. Differently to other approaches in the current state of the art, our system does not require the user to be completely still through the scanning process, and neither the depth sensor is moved around the subject to cover all its surface. Instead, the depth sensor remains static and the skeleton tracking information is used to compensate the user’s movements during the scanning stage. RESUMEN La popularización de videojuegos y otras aplicaciones de los gráficos por ordenador en el día a día requiere una manera más sencilla de crear modelos virtuales humanos animables. Tradicionalmente, estos modelos han sido creados por artistas profesionales que cuidadosamente los modelan y animan, y que tienen que adaptar específicamente para cada aplicación y plataforma de transmisión o visualización. La aparición de los entornos de realidad virtual/mixta aumenta incluso más la demanda de técnicas prácticas y baratas para producir modelos 3D representando personas reales. El objetivo de esta tesis es acercar el escaneo de humanos en 3D al usuario medio. Para ello, se presentan dos técnicas diferentes, una pasiva y una activa. La primera es un sistema automático para generar avatares multi-texturizados de personas reales mediante una serie de cámaras comunes. Nuestro sistema usa técnicas del estado del arte basadas en shape from silhouette para extraer la forma del sujeto a escanear. Sin embargo, este tipo de técnicas no gestiona las concavidades correctamente, por lo que nuestro sistema propone una manera de incrementar la calidad en una región del modelo que se ve especialmente afectada: la cara. Esta técnica de mejora facial usa un modelo 3D genérico de una cara y lo modifica según los rasgos faciales específicos del sujeto. Además, el sistema incluye una novedosa técnica para generar un atlas de textura a partir de las imágenes capturadas. Este sistema de multi-texturización consigue un atlas de textura sin transiciones abruptas de color gracias a su manera de mezclar la información de color de varias imágenes sobre cada triángulo. Todas las costuras y discontinuidades de color debidas a las condiciones de iluminación irregulares son eliminadas, minimizando el efecto de desenfoque de la interpolación que normalmente introducen este tipo de métodos. La segunda técnica presenta un sistema para conseguir un modelo humano 3D completamente animable utilizando un sensor de profundidad. A diferencia de otros métodos del estado de arte, nuestro sistema no requiere que el usuario esté completamente quieto durante el proceso de escaneado, ni mover el sensor alrededor del sujeto para cubrir toda su superficie. Por el contrario, el sensor se mantiene estático y el esqueleto virtual de la persona, que se va siguiendo durante el proceso, se utiliza para compensar sus movimientos durante el escaneado.