Doctor of Philosophy

dissertationConfocal microscopy has become a popular imaging technique in biology research in recent years. It is often used to study three-dimensional (3D) structures of biological samples. Confocal data are commonly multichannel, with each channel resulting from a different fluorescent staining. This technique also results in finely detailed structures in 3D, such as neuron fibers. Despite the plethora of volume rendering techniques that have been available for many years, there is a demand from biologists for a flexible tool that allows interactive visualization and analysis of multichannel confocal data. Together with biologists, we have designed and developed FluoRender. It incorporates volume rendering techniques such as a two-dimensional (2D) transfer function and multichannel intermixing. Rendering results can be enhanced through tone-mappings and overlays. To facilitate analyses of confocal data, FluoRender provides interactive operations for extracting complex structures. Furthermore, we developed the Synthetic Brainbow technique, which takes advantage of the asynchronous behavior in Graphics Processing Unit (GPU) framebuffer loops and generates random colorizations for different structures in single-channel confocal data. The results from our Synthetic Brainbows, when applied to a sequence of developing cells, can then be used for tracking the movements of these cells. Finally, we present an application of FluoRender in the workflow of constructing anatomical atlases

A Novel Image Encryption Scheme Based on Reversible Cellular Automata

In this paper, a new scheme for image encryption is presented by reversible cellular automata. The presented scheme is applied in three individual steps. Firstly, the image is blocked and the pixels are substituted by a reversible cellular automaton. Then, image pixels are scrambled by an elementary cellular automata and finally the blocks are attached and pixels are substituted by an individual reversible cellular automaton. Due to reversibility of used cellular automata, decryption scheme can reversely be applied. The experimental results show that encrypted image is suitable visually and this scheme has satisfied quantitative performance

An Approach for the Customized High-Dimensional Segmentation of Remote Sensing Hyperspectral Images

Abstract: This paper addresses three problems in the field of hyperspectral image segmentation: the fact that the way an image must be segmented is related to what the user requires and the application; the lack and cost of appropriately labeled reference images; and, finally, the information loss problem that arises in many algorithms when high dimensional images are projected onto lower dimensional spaces before starting the segmentation process. To address these issues, the Multi-Gradient based Cellular Automaton (MGCA) structure is proposed to segment multidimensional images without projecting them to lower dimensional spaces. The MGCA structure is coupled with an evolutionary algorithm (ECAS-II) in order to produce the transition rule sets required by MGCA segmenters. These sets are customized to specific segmentation needs as a function of a set of low dimensional training images in which the user expresses his segmentation requirements. Constructing high dimensional image segmenters from low dimensional training sets alleviates the problem of lack of labeled training images. These can be generated online based on a parametrization of the desired segmentation extracted from a set of examples. The strategy has been tested in experiments carried out using synthetic and real hyperspectral images, and it has been compared to state-of-the-art segmentation approaches over benchmark images in the area of remote sensing hyperspectral imaging.Ministerio de Economía y competitividad; TIN2015-63646-C5-1-RMinisterio de Economía y competitividad; RTI2018-101114-B-I00Xunta de Galicia: ED431C 2017/1

Automatic detection and classification of leukaemia cells

This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Today, there is a substantial number of software and research groups that focus on the development of image processing software to extract useful information from medical images, in order to assist and improve patient diagnosis. The work presented in this thesis is centred on processing of images of blood and bone marrow smears of patients suffering from leukaemia, a common type of cancer. In general, cancer is due to aberrant gene expression, which is caused by either mutations or epigenetic changes in DNA. Poor diet and unhealthy lifestyle may trigger or contribute to these changes, although the underlying mechanism is often unknown. Importantly, many cancer types including leukaemia are curable and patient survival and treatment can be improved, subject to prompt diagnosis. In particular, this study focuses on Acute Myeloid Leukaemia (AML), which can be of eight distinct types (M0 to M7), with the main objective to develop a methodology to automatically detect and classify leukaemia cells into one of the above types. The data was collected from the Department of Haematology, Universiti Sains Malaysia, in Malaysia. Three main methods, namely Cellular Automata, Heuristic Search and classification using Neural Networks are facilitated. In the case of Cellular Automata, an improved method based on the 8-neighbourhood and rules were developed to remove noise from images and estimate the radius of the potential blast cells contained in them. The proposed methodology selects the starting points, corresponding to potential blast cells, for the subsequent seeded heuristic search. The Seeded Heuristic employs a new fitness function for blast cell detection. Furthermore, the WEKA software is utilised for classification of blast cells and hence images, into AML subtypes. As a result accuracy of 97.22% was achieved in the classification of blasts into M3 and other AML subtypes. Finally, these algorithms are integrated into an automated system for image processing. In brief, the research presented in this thesis involves the use of advanced computational techniques for processing and classification of medical images, that is, images of blood samples from patients suffering from leukaemia.The Institute of Higher Education of Malaysia and the Universiti Sains Islam Malaysia (USIM)

Modelling angiogenesis in three dimensions

The process through which new blood vessels are formed within the body is known as angiogenesis. An essential part of our survival, it has also been implicated more recently in many diseases both in terms of induced growth, and abnormal vascular structure. Angiogenesis is characterized as two processes, the development of a vascular network during embryonic growth and the production of new blood vessels. This work focuses on the latter, and seeks to develop a robust, three-dimensional model for simulating blood vessel growth and the attendant processes of blood flow and mass transfer within the simulated system. A system was developed which utilises medical imaging scan data (specifically, MicroCT) as the initial conditions from which a network of vessels is grown. This is combined with GPU accelerated simulations of fluid dynamics, with the intention of providing a technique for future use in predictive medicine and therapeutic simulation

Modelling angiogenesis in three dimensions

The process through which new blood vessels are formed within the body is known as angiogenesis. An essential part of our survival, it has also been implicated more recently in many diseases both in terms of induced growth, and abnormal vascular structure. Angiogenesis is characterized as two processes, the development of a vascular network during embryonic growth and the production of new blood vessels. This work focuses on the latter, and seeks to develop a robust, three-dimensional model for simulating blood vessel growth and the attendant processes of blood flow and mass transfer within the simulated system. A system was developed which utilises medical imaging scan data (specifically, MicroCT) as the initial conditions from which a network of vessels is grown. This is combined with GPU accelerated simulations of fluid dynamics, with the intention of providing a technique for future use in predictive medicine and therapeutic simulation

An Affordable Portable Obstetric Ultrasound Simulator for Synchronous and Asynchronous Scan Training

The increasing use of Point of Care (POC) ultrasound presents a challenge in providing efficient training to new POC ultrasound users. In response to this need, we have developed an affordable, compact, laptop-based obstetric ultrasound training simulator. It offers freehand ultrasound scan on an abdomen-sized scan surface with a 5 degrees of freedom sham transducer and utilizes 3D ultrasound image volumes as training material. On the simulator user interface is rendered a virtual torso, whose body surface models the abdomen of a particular pregnant scan subject. A virtual transducer scans the virtual torso, by following the sham transducer movements on the scan surface. The obstetric ultrasound training is self-paced and guided by the simulator using a set of tasks, which are focused on three broad areas, referred to as modules: 1) medical ultrasound basics, 2) orientation to obstetric space, and 3) fetal biometry. A learner completes the scan training through the following three steps: (i) watching demonstration videos, (ii) practicing scan skills by sequentially completing the tasks in Modules 2 and 3, with scan evaluation feedback and help functions available, and (iii) a final scan exercise on new image volumes for assessing the acquired competency. After each training task has been completed, the simulator evaluates whether the task has been carried out correctly or not, by comparing anatomical landmarks identified and/or measured by the learner to reference landmark bounds created by algorithms, or pre-inserted by experienced sonographers. Based on the simulator, an ultrasound E-training system has been developed for the medical practitioners for whom ultrasound training is not accessible at local level. The system, composed of a dedicated server and multiple networked simulators, provides synchronous and asynchronous training modes, and is able to operate with a very low bit rate. The synchronous (or group-learning) mode allows all training participants to observe the same 2D image in real-time, such as a demonstration by an instructor or scan ability of a chosen learner. The synchronization of 2D images on the different simulators is achieved by directly transmitting the position and orientation of the sham transducer, rather than the ultrasound image, and results in a system performance independent of network bandwidth. The asynchronous (or self-learning) mode is described in the previous paragraph. However, the E-training system allows all training participants to stay networked to communicate with each other via text channel. To verify the simulator performance and training efficacy, we conducted several performance experiments and clinical evaluations. The performance experiment results indicated that the simulator was able to generate greater than 30 2D ultrasound images per second with acceptable image quality on medium-priced computers. In our initial experiment investigating the simulator training capability and feasibility, three experienced sonographers individually scanned two image volumes on the simulator. They agreed that the simulated images and the scan experience were adequately realistic for ultrasound training; the training procedure followed standard obstetric ultrasound protocol. They further noted that the simulator had the potential for becoming a good supplemental training tool for medical students and resident doctors. A clinic study investigating the simulator training efficacy was integrated into the clerkship program of the Department of Obstetrics and Gynecology, University of Massachusetts Memorial Medical Center. A total of 24 3rd year medical students were recruited and each of them was directed to scan six image volumes on the simulator in two 2.5-hour sessions. The study results showed that the successful scan times for the training tasks significantly decreased as the training progressed. A post-training survey answered by the students found that they considered the simulator-based training useful and suitable for medical students and resident doctors. The experiment to validate the performance of the E-training system showed that the average transmission bit rate was approximately 3-4 kB/s; the data loss was less than 1% and no loss of 2D images was visually detected. The results also showed that the 2D images on all networked simulators could be considered to be synchronous even though inter-continental communication existed

Image analysis methods for brain tumor treatment follow-up

Assessment of the progression of the tumors in current clinical practice is based on maximum diameter measurements, which are related to the volumetric changes. With the advent of the spatially localized radiotherapy techniques (i.e. Cyberknife, IMRT, Gammaknife, Tomotherapy) not only the volumes of the tumors but also the geometric changes need to be considered to measure the effectiveness and to improve the applied therapy. In this thesis, image analysis techniques are developed for assessment of the changes of the tumor geometry between MRI volumes acquired after and before the therapy. Three main parts of the thesis are: Segmentation of brain tumors on MRI; change quantification in temporal MRI series of brain tumors; and deformable registration of brain MRI volumes with tumors. The results obtained by the developed semi-automatic brain tumor segmentation method, Tumor-cut, are comparable with those of state-of-the-art techniques in the field. The quantification of tumor evolution using the invariants of the Lagrange strain tensor provide measures that are more correlated with the clinical outcome than the volumetric measures. The deformable registration of longitudinal data provides a novel framework to study brain deformations, in vivo, and more accurate assessment of the changes

A comprehensive approach for the efficient acquisition and processing of hyperspectral images and sequence

Programa Oficial de Doctorado en Computación. 5009P01[Abstract] Despite the scientific and technological developments achieved during the last two decades in the hyperspectral field, some methodological, operational and conceptual issues have restricted the progress, promotion and popular dissemination of this technology. These shortcomings include the specialized knowledge required for the acquisition of hyperspectral images, the shortage of publicly accessible hyperspectral image repositories with reliable ground truth images or the lack of methodologies that allow for the adaptation of algorithms to particular user or application processing needs. The work presented here has the objective of contributing to the hyperspectral field with procedures for the automatic acquisition of hyperspectral scenes, including the hardware adaptation of our own imagers and the development of methods for the calibration and correction of the hyperspectral datacubes, the creation of a publicly available hyperspectral repository of well categorized and labeled images and the design and implementation of novel computational intelligence based processing techniques that solve typical issues related to the segmentation and denoising of hyperspectral images as well as sequences of them taking into account their temporal evolution.[Resumen] A pesar de los desarrollos tecnológicos y científicos logrados en el campo hiperespectral durante las dos últimas décadas, alg\mas limitaciones de tipo metodológico, operacional y conceptual han restringido el progreso, difusión y popularización de esta tecnología, entre ellas, el conocimiento especializado requerido en la adquisición de imágenes hiperespectrales, la carencia de repositorios de imágenes hiperespectrales con etiquetados fiables y de acceso público o la falta de metodologías que posibiliten la adaptación de algoritmos a usuarios o necesidades de procesamiento concretas. Este trabajo doctoral tiene el objetivo de contribuir al campo hiperespectral con procedimientos para la adquisición automática de escenas hiperespectrales, incluyendo la adaptación hardware de cámaras hiperespectrales propias y el desarrollo de métodos para la calibración y corrección de cubos de datos hiperespectrales; la creación de un repositorio hiperespectral de acceso público con imágenes categorizadas y con verdades de terreno fiables; y el diseño e implementación de técnicas de procesamiento basadas en inteligencia computacional para la resolución de problemas típicamente relacionados con las tareas de segmentación y eliminación de ruido en imágenes estáticas y secuencias de imágenes hiperespectrales teniendo en consideración su evolución temporal.[Resumo] A pesar dos desenvolvementos tecnolóxicos e científicos logrados no campo hiperespectral durante as dúas últimas décadas, algunhas lirrútacións de tipo metodolóxico¡ operacional e conceptual restrinxiron o progreso) difusión e popularización desta tecnoloxía, entre elas, o coñecemento especializado requirido na adquisición de imaxes hiperespectrales¡ a carencia de repositorios de irnaxes hiperespectrales con etiquetaxes fiables e de acceso público ou a falta de metodoloxías que posibiliten a adaptación de algoritmos a usuarios ou necesidades de procesamento concretas. Este traballo doutoral ten o obxectívo de contribuir ao campo hiperespectral con procedementos para a adquisición automática de eicenas hiperespectrais, incluíndo a adaptación hardware de cámaras hiperespectrales propias e o desenvolvemento de métodos para a calibración e corrección de cubos de datos hiperespectrais; a creación dun repositorio hiperespectral de acceso público con imaxes categorizadas e con verdades de terreo fiables; e o deseño e implementación de técnicas de procesamento baseadas en intelixencia computacional para a resolución de problemas tipicamente relacionado~ coas tarefas de segmentación e eliminación de ruído en imaxes estáticas e secuencias de imaxes hiperespectrai~ tendo en consideración a súa evolución temporal