Adaptive transfer functions: improved multiresolution visualization of medical models

The final publication is available at Springer via http://dx.doi.org/10.1007/s00371-016-1253-9Medical datasets are continuously increasing in size. Although larger models may be available for certain research purposes, in the common clinical practice the models are usually of up to 512x512x2000 voxels. These resolutions exceed the capabilities of conventional GPUs, the ones usually found in the medical doctors’ desktop PCs. Commercial solutions typically reduce the data by downsampling the dataset iteratively until it fits the available target specifications. The data loss reduces the visualization quality and this is not commonly compensated with other actions that might alleviate its effects. In this paper, we propose adaptive transfer functions, an algorithm that improves the transfer function in downsampled multiresolution models so that the quality of renderings is highly improved. The technique is simple and lightweight, and it is suitable, not only to visualize huge models that would not fit in a GPU, but also to render not-so-large models in mobile GPUs, which are less capable than their desktop counterparts. Moreover, it can also be used to accelerate rendering frame rates using lower levels of the multiresolution hierarchy while still maintaining high-quality results in a focus and context approach. We also show an evaluation of these results based on perceptual metrics.Peer ReviewedPostprint (author's final draft

Progressive ray casting for volumetric models on mobile devices

Mobile devices have experienced an incredible market penetration in the last decade. Currently, medium to premium smartphones are relatively affordable devices. With the increase in screen size and resolution, together with the improvements in performance of mobile CPUs and GPUs, more tasks have become possible. In this paper we explore the rendering of medium to large volumetric models on mobile and low performance devices in general. To do so, we present a progressive ray casting method that is able to obtain interactive frame rates and high quality results for models that not long ago were only supported by desktop computers.Peer ReviewedPostprint (author's final draft

Downsampling methods for medical datasets

Volume visualization software usually has to deal with datasets that are larger than the GPUs may hold. This is especially true in one of the most popular application scenarios: medical visualization. Typically, medical datasets are available for different personnel, but only radiologists have high-end systems that are able to cope with large data. For the rest of physicians, usually low-end systems are only available. As a result, most volume rendering packages downsample the data prior to uploading to the GPU. The most common approach consists in performing iterative subsampling along the longest axis, until the model fits inside the GPU memory. This causes important information loss that affects the final rendering. Some cleverer techniques may be developed to preserve the volumetric information. In this paper we explore the quality of different downsampling methods and present a new approach that produces smooth lower-resolution representations, yet still preserves small features that are prone to disappear with other approaches.Peer ReviewedPostprint (published version

Real-time quality visualization of medical models on commodity and mobile devices

This thesis concerns the specific field of visualization of medical models using commodity and mobile devices. Mechanisms for medical imaging acquisition such as MRI, CT, and micro-CT scanners are continuously evolving, up to the point of obtaining volume datasets of large resolutions (> 512^3). As these datasets grow in resolution, its treatment and visualization become more and more expensive due to their computational requirements. For this reason, special techniques such as data pre-processing (filtering, construction of multi-resolution structures, etc.) and sophisticated algorithms have to be introduced in different points of the visualization pipeline to achieve the best visual quality without compromising performance times. The problem of managing big datasets comes from the fact that we have limited computational resources. Not long ago, the only physicians that were rendering volumes were radiologists. Nowadays, the outcome of diagnosis is the data itself, and medical doctors need to render them in commodity PCs (even patients may want to render the data, and the DVDs are commonly accompanied with a DICOM viewer software). Furthermore, with the increasing use of technology in daily clinical tasks, small devices such as mobile phones and tablets can fit the needs of medical doctors in some specific areas. Visualizing diagnosis images of patients becomes more challenging when it comes to using these devices instead of desktop computers, as they generally have more restrictive hardware specifications. The goal of this Ph.D. thesis is the real-time, quality visualization of medium to large medical volume datasets (resolutions >= 512^3 voxels) on mobile phones and commodity devices. To address this problem, we use multiresolution techniques that apply downsampling techniques on the full resolution datasets to produce coarser representations which are easier to handle. We have focused our efforts on the application of Volume Visualization in the clinical practice, so we have a particular interest in creating solutions that require short pre-processing times that quickly provide the specialists with the data outcome, maximize the preservation of features and the visual quality of the final images, achieve high frame rates that allow interactive visualizations, and make efficient use of the computational resources. The contributions achieved during this thesis comprise improvements in several stages of the visualization pipeline. The techniques we propose are located in the stages of multi-resolution generation, transfer function design and the GPU ray casting algorithm itself.Esta tesis se centra en la visualización de modelos médicos de volumen en dispositivos móviles y de bajas prestaciones. Los sistemas médicos de captación tales como escáners MRI, CT y micro-CT, están en constante evolución, hasta el punto de obtener modelos de volumen de gran resolución (> 512^3). A medida que estos datos crecen en resolución, su manejo y visualización se vuelve más y más costoso debido a sus requisitos computacionales. Por este motivo, técnicas especiales como el pre-proceso de datos (filtrado, construcción de estructuras multiresolución, etc.) y algoritmos específicos se tienen que introducir en diferentes puntos de la pipeline de visualización para conseguir la mejor calidad visual posible sin comprometer el rendimiento. El problema que supone manejar grandes volumenes de datos es debido a que tenemos recursos computacionales limitados. Hace no mucho, las únicas personas en el ámbito médico que visualizaban datos de volumen eran los radiólogos. Hoy en día, el resultado de la diagnosis son los datos en sí, y los médicos necesitan renderizar estos datos en PCs de características modestas (incluso los pacientes pueden querer visualizar estos datos, pues los DVDs con los resultados suelen venir acompañados de un visor de imágenes DICOM). Además, con el reciente aumento del uso de las tecnologías en la clínica práctica habitual, dispositivos pequeños como teléfonos móviles o tablets son los más convenientes en algunos casos. La visualización de volumen es más difícil en este tipo de dispositivos que en equipos de sobremesa, pues las limitaciones de su hardware son superiores. El objetivo de esta tesis doctoral es la visualización de calidad en tiempo real de modelos grandes de volumen (resoluciones >= 512^3 voxels) en teléfonos móviles y dispositivos de bajas prestaciones. Para enfrentarnos a este problema, utilizamos técnicas multiresolución que aplican técnicas de reducción de datos a los modelos en resolución original, para así obtener modelos de menor resolución. Hemos centrado nuestros esfuerzos en la aplicación de la visualización de volumen en la práctica clínica, así que tenemos especial interés en diseñar soluciones que requieran cortos tiempos de pre-proceso para que los especialistas tengan rápidamente los resultados a su disposición. También, queremos maximizar la conservación de detalles de interés y la calidad de las imágenes finales, conseguir frame rates altos que faciliten visualizaciones interactivas y que hagan un uso eficiente de los recursos computacionales. Las contribuciones aportadas por esta tesis són mejoras en varias etapas de la pipeline de visualización. Las técnicas que proponemos se situan en las etapas de generación de la estructura multiresolución, el diseño de la función de transferencia y el algoritmo de ray casting en la GPU.Postprint (published version

Real-time quality visualization of medical models on commodity and mobile devices

This thesis concerns the specific field of visualization of medical models using commodity and mobile devices. Mechanisms for medical imaging acquisition such as MRI, CT, and micro-CT scanners are continuously evolving, up to the point of obtaining volume datasets of large resolutions (> 512^3). As these datasets grow in resolution, its treatment and visualization become more and more expensive due to their computational requirements. For this reason, special techniques such as data pre-processing (filtering, construction of multi-resolution structures, etc.) and sophisticated algorithms have to be introduced in different points of the visualization pipeline to achieve the best visual quality without compromising performance times. The problem of managing big datasets comes from the fact that we have limited computational resources. Not long ago, the only physicians that were rendering volumes were radiologists. Nowadays, the outcome of diagnosis is the data itself, and medical doctors need to render them in commodity PCs (even patients may want to render the data, and the DVDs are commonly accompanied with a DICOM viewer software). Furthermore, with the increasing use of technology in daily clinical tasks, small devices such as mobile phones and tablets can fit the needs of medical doctors in some specific areas. Visualizing diagnosis images of patients becomes more challenging when it comes to using these devices instead of desktop computers, as they generally have more restrictive hardware specifications. The goal of this Ph.D. thesis is the real-time, quality visualization of medium to large medical volume datasets (resolutions >= 512^3 voxels) on mobile phones and commodity devices. To address this problem, we use multiresolution techniques that apply downsampling techniques on the full resolution datasets to produce coarser representations which are easier to handle. We have focused our efforts on the application of Volume Visualization in the clinical practice, so we have a particular interest in creating solutions that require short pre-processing times that quickly provide the specialists with the data outcome, maximize the preservation of features and the visual quality of the final images, achieve high frame rates that allow interactive visualizations, and make efficient use of the computational resources. The contributions achieved during this thesis comprise improvements in several stages of the visualization pipeline. The techniques we propose are located in the stages of multi-resolution generation, transfer function design and the GPU ray casting algorithm itself.Esta tesis se centra en la visualización de modelos médicos de volumen en dispositivos móviles y de bajas prestaciones. Los sistemas médicos de captación tales como escáners MRI, CT y micro-CT, están en constante evolución, hasta el punto de obtener modelos de volumen de gran resolución (> 512^3). A medida que estos datos crecen en resolución, su manejo y visualización se vuelve más y más costoso debido a sus requisitos computacionales. Por este motivo, técnicas especiales como el pre-proceso de datos (filtrado, construcción de estructuras multiresolución, etc.) y algoritmos específicos se tienen que introducir en diferentes puntos de la pipeline de visualización para conseguir la mejor calidad visual posible sin comprometer el rendimiento. El problema que supone manejar grandes volumenes de datos es debido a que tenemos recursos computacionales limitados. Hace no mucho, las únicas personas en el ámbito médico que visualizaban datos de volumen eran los radiólogos. Hoy en día, el resultado de la diagnosis son los datos en sí, y los médicos necesitan renderizar estos datos en PCs de características modestas (incluso los pacientes pueden querer visualizar estos datos, pues los DVDs con los resultados suelen venir acompañados de un visor de imágenes DICOM). Además, con el reciente aumento del uso de las tecnologías en la clínica práctica habitual, dispositivos pequeños como teléfonos móviles o tablets son los más convenientes en algunos casos. La visualización de volumen es más difícil en este tipo de dispositivos que en equipos de sobremesa, pues las limitaciones de su hardware son superiores. El objetivo de esta tesis doctoral es la visualización de calidad en tiempo real de modelos grandes de volumen (resoluciones >= 512^3 voxels) en teléfonos móviles y dispositivos de bajas prestaciones. Para enfrentarnos a este problema, utilizamos técnicas multiresolución que aplican técnicas de reducción de datos a los modelos en resolución original, para así obtener modelos de menor resolución. Hemos centrado nuestros esfuerzos en la aplicación de la visualización de volumen en la práctica clínica, así que tenemos especial interés en diseñar soluciones que requieran cortos tiempos de pre-proceso para que los especialistas tengan rápidamente los resultados a su disposición. También, queremos maximizar la conservación de detalles de interés y la calidad de las imágenes finales, conseguir frame rates altos que faciliten visualizaciones interactivas y que hagan un uso eficiente de los recursos computacionales. Las contribuciones aportadas por esta tesis són mejoras en varias etapas de la pipeline de visualización. Las técnicas que proponemos se situan en las etapas de generación de la estructura multiresolución, el diseño de la función de transferencia y el algoritmo de ray casting en la GPU

Accurate geometry reconstruction of vascular structures using implicit splines

3-D visualization of blood vessel from standard medical datasets (e.g. CT or MRI) play an important role in many clinical situations, including the diagnosis of vessel stenosis, virtual angioscopy, vascular surgery planning and computer aided vascular surgery. However, unlike other human organs, the vasculature system is a very complex network of vessel, which makes it a very challenging task to perform its 3-D visualization. Conventional techniques of medical volume data visualization are in general not well-suited for the above-mentioned tasks. This problem can be solved by reconstructing vascular geometry. Although various methods have been proposed for reconstructing vascular structures, most of these approaches are model-based, and are usually too ideal to correctly represent the actual variation presented by the cross-sections of a vascular structure. In addition, the underlying shape is usually expressed as polygonal meshes or in parametric forms, which is very inconvenient for implementing ramification of branching. As a result, the reconstructed geometries are not suitable for computer aided diagnosis and computer guided minimally invasive vascular surgery. In this research, we develop a set of techniques associated with the geometry reconstruction of vasculatures, including segmentation, modelling, reconstruction, exploration and rendering of vascular structures. The reconstructed geometry can not only help to greatly enhance the visual quality of 3-D vascular structures, but also provide an actual geometric representation of vasculatures, which can provide various benefits. The key findings of this research are as follows: 1. A localized hybrid level-set method of segmentation has been developed to extract the vascular structures from 3-D medical datasets. 2. A skeleton-based implicit modelling technique has been proposed and applied to the reconstruction of vasculatures, which can achieve an accurate geometric reconstruction of the vascular structures as implicit surfaces in an analytical form. 3. An accelerating technique using modern GPU (Graphics Processing Unit) is devised and applied to rendering the implicitly represented vasculatures. 4. The implicitly modelled vasculature is investigated for the application of virtual angioscopy