Computer-assisted polyp matching between optical colonoscopy and CT colonography: a phantom study

Potentially precancerous polyps detected with CT colonography (CTC) need to be removed subsequently, using an optical colonoscope (OC). Due to large colonic deformations induced by the colonoscope, even very experienced colonoscopists find it difficult to pinpoint the exact location of the colonoscope tip in relation to polyps reported on CTC. This can cause unduly prolonged OC examinations that are stressful for the patient, colonoscopist and supporting staff. We developed a method, based on monocular 3D reconstruction from OC images, that automatically matches polyps observed in OC with polyps reported on prior CTC. A matching cost is computed, using rigid point-based registration between surface point clouds extracted from both modalities. A 3D printed and painted phantom of a 25 cm long transverse colon segment was used to validate the method on two medium sized polyps. Results indicate that the matching cost is smaller at the correct corresponding polyp between OC and CTC: the value is 3.9 times higher at the incorrect polyp, comparing the correct match between polyps to the incorrect match. Furthermore, we evaluate the matching of the reconstructed polyp from OC with other colonic endoluminal surface structures such as haustral folds and show that there is a minimum at the correct polyp from CTC. Automated matching between polyps observed at OC and prior CTC would facilitate the biopsy or removal of true-positive pathology or exclusion of false-positive CTC findings, and would reduce colonoscopy false-negative (missed) polyps. Ultimately, such a method might reduce healthcare costs, patient inconvenience and discomfort.Comment: This paper was presented at the SPIE Medical Imaging 2014 conferenc

3D surface reconstruction for lower limb prosthetic model using modified radon transform

Computer vision has received increased attention for the research and innovation on three-dimensional surface reconstruction with aim to obtain accurate results. Although many researchers have come up with various novel solutions and feasibility of the findings, most require the use of sophisticated devices which is computationally expensive. Thus, a proper countermeasure is needed to resolve the reconstruction constraints and create an algorithm that is able to do considerably fast reconstruction by giving attention to devices equipped with appropriate specification, performance and practical affordability. This thesis describes the idea to realize three-dimensional surface of the residual limb models by adopting the technique of tomographic imaging coupled with the strategy based on multiple-views from a digital camera and a turntable. The surface of an object is reconstructed from uncalibrated two-dimensional image sequences of thirty-six different projections with the aid of Radon transform algorithm and shape-from-silhouette. The results show that the main objective to reconstruct three-dimensional surface of lower limb model has been successfully achieved with reasonable accuracy as the starting point to reconstruct three-dimensional surface and extract digital reading of an amputated lower limb model where the maximum percent error obtained from the computation is approximately 3.3 % for the height whilst 7.4%, 7.9% and 8.1% for the diameters at three specific heights of the objects. It can be concluded that the reconstruction of three-dimensional surface for the developed method is particularly dependent to the effects the silhouette generated where high contrast two-dimensional images contribute to higher accuracy of the silhouette extraction. The advantage of the concept presented in this thesis is that it can be done with simple experimental setup and the reconstruction of three-dimensional model neither involves expensive equipment nor require any service by an expert to handle sophisticated mechanical scanning system

Specular reflection removal and bloodless vessel segmentation for 3-D heart model reconstruction from single view images

Three Dimensional (3D) human heart model is attracting attention for its role in medical images for education and clinical purposes. Analysing 2D images to obtain meaningful information requires a certain level of expertise. Moreover, it is time consuming and requires special devices to obtain aforementioned images. In contrary, a 3D model conveys much more information. 3D human heart model reconstruction from medical imaging devices requires several input images, while reconstruction from a single view image is challenging due to the colour property of the heart image, light reflections, and its featureless surface. Lights and illumination condition of the operating room cause specular reflections on the wet heart surface that result in noises forming of the reconstruction process. Image-based technique is used for the proposed human heart surface reconstruction. It is important the reflection is eliminated to allow for proper 3D reconstruction and avoid imperfect final output. Specular reflections detection and correction process examine the surface properties. This was implemented as a first step to detect reflections using the standard deviation of RGB colour channel and the maximum value of blue channel to establish colour, devoid of specularities. The result shows the accurate and efficient performance of the specularities removing process with 88.7% similarity with the ground truth. Realistic 3D heart model reconstruction was developed based on extraction of pixel information from digital images to allow novice surgeons to reduce the time for cardiac surgery training and enhancing their perception of the Operating Theatre (OT). Cardiac medical imaging devices such as Magnetic Resonance Imaging (MRI), Computed Tomography (CT) images, or Echocardiography provide cardiac information. However,these images from medical modalities are not adequate, to precisely simulate the real environment and to be used in the training simulator for cardiac surgery. The propose method exploits and develops techniques based on analysing real coloured images taken during cardiac surgery in order to obtain meaningful information of the heart anatomical structures. Another issue is the different human heart surface vessels. The most important vessel region is the bloodless, lack of blood, vessels. Surgeon faces some difficulties in locating the bloodless vessel region during surgery. The thesis suggests a technique of identifying the vessels’ Region of Interest (ROI) to avoid surgical injuries by examining an enhanced input image. The proposed method locates vessels’ ROI by using Decorrelation Stretch technique. This Decorrelation Stretch can clearly enhance the heart’s surface image. Through this enhancement, the surgeon become enables effectively identifying the vessels ROI to perform the surgery from textured and coloured surface images. In addition, after enhancement and segmentation of the vessels ROI, a 3D reconstruction of this ROI takes place and then visualize it over the 3D heart model. Experiments for each phase in the research framework were qualitatively and quantitatively evaluated. Two hundred and thirteen real human heart images are the dataset collected during cardiac surgery using a digital camera. The experimental results of the proposed methods were compared with manual hand-labelling ground truth data. The cost reduction of false positive and false negative of specular detection and correction processes of the proposed method was less than 24% compared to other methods. In addition, the efficient results of Root Mean Square Error (RMSE) to measure the correctness of the z-axis values to reconstruction of the 3D model accurately compared to other method. Finally, the 94.42% accuracy rate of the proposed vessels segmentation method using RGB colour space achieved is comparable to other colour spaces. Experimental results show that there is significant efficiency and robustness compared to existing state of the art methods

Semi-automated parallel programming in heterogeneous intelligent reconfigurable environments (SAPPHIRE)

In recent years, as we come closer to approaching physical limits in making smaller (and faster) computer processors, focus has instead been turned toward including multiple processor cores in each device. While this technically allows for more computational power as compared with only one traditional processor core, conventional software can typically only make use of a single processor. Furthermore, we see an increasing number of stream programs that process streams of data such as a stream of images or audio. For stream programs to effectively utilize multi-core processors, multithreading is the key, but it may be difficult to implement in practice depending on the complexity of the programs. We present SAPPHIRE: Semi-Automated Parallel Programming in Heterogeneous Intelligent Reconfigurable Environment, a middleware and SDK for developing multithreaded stream programs. In this middleware, we implement our semi-automated program construction technique which is designed to aid in writing multithreaded software by reducing needed complexity and lines of code written by software developers. We also present a novel static task-scheduling algorithm for stream programs with heterogeneous implementation choices. Our algorithm is capable of scheduling stream programs with provably near-optimal results given a specific set of assumptions, without requiring the unrolling of the task graph. Unrolling the task graph greatly increases the size of the input to the NP-Complete part of the task-scheduling problem as in related work. Finally, we present two case study programs implemented using SAPPHIRE. One case study, EM-Capture, has analyzed over 50 billion frames of endoscopy video in real-time in a real hospital, discerning over 71,000 unique endoscopy procedures. The other case study, EM-Feedback-RT, is a collaborative extension to EM-Capture, and is an attempt to provide real-time quality analysis feedback to physicians during a colonoscopy exam

Characterization and modelling of complex motion patterns

Movement analysis is the principle of any interaction with the world and the survival of living beings completely depends on the effciency of such analysis. Visual systems have remarkably developed eficient mechanisms that analyze motion at different levels, allowing to recognize objects in dynamical and cluttered environments. In artificial vision, there exist a wide spectrum of applications for which the study of complex movements is crucial to recover salient information. Yet each domain may be different in terms of scenarios, complexity and relationships, a common denominator is that all of them require a dynamic understanding that captures the relevant information. Overall, current strategies are highly dependent on the appearance characterization and usually they are restricted to controlled scenarios. This thesis proposes a computational framework that is inspired in known motion perception mechanisms and structured as a set of modules. Each module is in due turn composed of a set of computational strategies that provide qualitative and quantitative descriptions of the dynamic associated to a particular movement. Diverse applications were herein considered and an extensive validation was performed for each of them. Each of the proposed strategies has shown to be reliable at capturing the dynamic patterns of different tasks, identifying, recognizing, tracking and even segmenting objects in sequences of video.Resumen. El análisis del movimiento es el principio de cualquier interacción con el mundo y la supervivencia de los seres vivos depende completamente de la eficiencia de este tipo de análisis. Los sistemas visuales notablemente han desarrollado mecanismos eficientes que analizan el movimiento en diferentes niveles, lo cual permite reconocer objetos en entornos dinámicos y saturados. En visión artificial existe un amplio espectro de aplicaciones para las cuales el estudio de los movimientos complejos es crucial para recuperar información saliente. A pesar de que cada dominio puede ser diferente en términos de los escenarios, la complejidad y las relaciones de los objetos en movimiento, un común denominador es que todos ellos requieren una comprensión dinámica para capturar información relevante. En general, las estrategias actuales son altamente dependientes de la caracterización de la apariencia y por lo general están restringidos a escenarios controlados. Esta tesis propone un marco computacional que se inspira en los mecanismos de percepción de movimiento conocidas y esta estructurado como un conjunto de módulos. Cada módulo esta a su vez compuesto por un conjunto de estrategias computacionales que proporcionan descripciones cualitativas y cuantitativas de la dinámica asociada a un movimiento particular. Diversas aplicaciones fueron consideradas en este trabajo y una extensa validación se llevó a cabo para cada uno de ellas. Cada una de las estrategias propuestas ha demostrado ser fiable en la captura de los patrones dinámicos de diferentes tareas identificando, reconociendo, siguiendo e incluso segmentando objetos en secuencias de video.Doctorad