Submitted in fulfillment of the requirements of the degree of the Master of Technology : Radiography, Durban University of Technology, 2014. / Research Aims The purpose of this study is to compare 2D HDR Brachytherapy planning and 3D HDR Brachytherapy planning in terms of dose distribution in order to accurately determine bladder and rectal doses. Further research questions were explored to determine whether relationships existed between Computer Tomography volumes and bladder and rectum dose. Methodology The 30 female patients that volunteered for the study were conveniently selected. Their age and ethnic group did not contribute to their selection. All participants were prepared for cervical HDR Brachytherapy. The Brachytherapy templates were computer generated and treatments were given based on the templates. They then had a Computer Tomography (CT) scan (3D data set) of the pelvis. The computer generated templates for 2D Brachytherapy planning were applied to the CT data set i.e. 2DBP. The plans were optimised to take into consideration the dose to the bladder and the rectum i.e. 3DBP. The 2DBP and the 3DBP were then evaluated in order to determine which method of planning yielded more acceptable dose distributions to the bladder and rectum. Results Significant differences in dose distribution were noted on comparison of 2DBP and 3DBP. A significant relationship was noted in respect of bladder mean dose and rectum mean dose. 3DBP proved to be more efficient in yielding lower mean dose to the bladder and the rectum. Whilst a significant relationship was noted in respect of bladder maximum dose, an insignificant relationship was noted for rectum maximum dose. Therefore, the efficiency of 3DBP to yield lower bladder maximum dose was established but its efficiency to yield lower rectum maximum dose is questionable. This has implications for the management of patients’ with cervical cancer who require cervical Brachytherapy. Recommendations It is imperative that imaging modalities be used for the accurate planning of cervical Brachytherapy. This study recommends that CT be used for HDR Brachytherapy planning by proving its greater efficiency compared to template planning.

Real-world radiance values can range over eight orders of magnitude from starlight to direct sunlight but few digital cameras capture more than three orders in a single Low Dynamic Range (LDR) image. We approach this problem using established High Dynamic Range (HDR) techniques in which multiple images are captured with different exposure times so that all portions of the scene are correctly exposed at least once. These images are then combined to create an HDR image capturing the full range of the scene. HDR capture introduces new challenges; movement in the scene creates faded copies of moving objects, referred to as ghosts. Many techniques have been introduced to handle ghosting, but typically they either address specific types of ghosting, or are computationally very expensive. We address ghosting by first detecting moving objects, then reducing their contribution to the final composite on a frame-by-frame basis. The detection of motion is addressed by performing change detection on exposure-normalized images. Additional special cases are developed based on a priori knowledge of the changing exposures; for example, if exposure is increasing every shot, then any decrease in intensity in the LDR images is a strong indicator of motion. Recent Superpixel over-segmentation techniques are used to refine the detection. We also propose a novel solution for areas that see motion throughout the capture, such as foliage blowing in the wind. Such areas are detected as always moving, and are replaced with information from a single input image, and the replacement of corrupted regions can be tailored to the scenario. We present our approach in the context of a panoramic tele-presence system. Tele-presence systems allow a user to experience a remote environment, aiming to create a realistic sense of "being there" and such a system should therefore provide a high quality visual rendition of the environment. Furthermore, panoramas, by virtue of capturing a greater proportion of a real-world scene, are often exposed to a greater dynamic range than standard photographs. Both facets of this system therefore stand to benefit from HDR imaging techniques. We demonstrate the success of our approach on multiple challenging ghosting scenarios, and compare our results with state-of-the-art methods previously proposed. We also demonstrate computational savings over these methods.

Real-world radiance values can range over eight orders of magnitude from starlight to direct sunlight but few digital cameras capture more than three orders in a single Low Dynamic Range (LDR) image. We approach this problem using established High Dynamic Range (HDR) techniques in which multiple images are captured with different exposure times so that all portions of the scene are correctly exposed at least once. These images are then combined to create an HDR image capturing the full range of the scene. HDR capture introduces new challenges; movement in the scene creates faded copies of moving objects, referred to as ghosts. Many techniques have been introduced to handle ghosting, but typically they either address specific types of ghosting, or are computationally very expensive. We address ghosting by first detecting moving objects, then reducing their contribution to the final composite on a frame-by-frame basis. The detection of motion is addressed by performing change detection on exposure-normalized images. Additional special cases are developed based on a priori knowledge of the changing exposures; for example, if exposure is increasing every shot, then any decrease in intensity in the LDR images is a strong indicator of motion. Recent Superpixel over-segmentation techniques are used to refine the detection. We also propose a novel solution for areas that see motion throughout the capture, such as foliage blowing in the wind. Such areas are detected as always moving, and are replaced with information from a single input image, and the replacement of corrupted regions can be tailored to the scenario. We present our approach in the context of a panoramic tele-presence system. Tele-presence systems allow a user to experience a remote environment, aiming to create a realistic sense of "being there" and such a system should therefore provide a high quality visual rendition of the environment. Furthermore, panoramas, by virtue of capturing a greater proportion of a real-world scene, are often exposed to a greater dynamic range than standard photographs. Both facets of this system therefore stand to benefit from HDR imaging techniques. We demonstrate the success of our approach on multiple challenging ghosting scenarios, and compare our results with state-of-the-art methods previously proposed. We also demonstrate computational savings over these methods.

Real-world radiance values can range over eight orders of magnitude from starlight to direct sunlight but few digital cameras capture more than three orders in a single Low Dynamic Range (LDR) image. We approach this problem using established High Dynamic Range (HDR) techniques in which multiple images are captured with different exposure times so that all portions of the scene are correctly exposed at least once. These images are then combined to create an HDR image capturing the full range of the scene. HDR capture introduces new challenges; movement in the scene creates faded copies of moving objects, referred to as ghosts. Many techniques have been introduced to handle ghosting, but typically they either address specific types of ghosting, or are computationally very expensive. We address ghosting by first detecting moving objects, then reducing their contribution to the final composite on a frame-by-frame basis. The detection of motion is addressed by performing change detection on exposure-normalized images. Additional special cases are developed based on a priori knowledge of the changing exposures; for example, if exposure is increasing every shot, then any decrease in intensity in the LDR images is a strong indicator of motion. Recent Superpixel over-segmentation techniques are used to refine the detection. We also propose a novel solution for areas that see motion throughout the capture, such as foliage blowing in the wind. Such areas are detected as always moving, and are replaced with information from a single input image, and the replacement of corrupted regions can be tailored to the scenario. We present our approach in the context of a panoramic tele-presence system. Tele-presence systems allow a user to experience a remote environment, aiming to create a realistic sense of "being there" and such a system should therefore provide a high quality visual rendition of the environment. Furthermore, panoramas, by virtue of capturing a greater proportion of a real-world scene, are often exposed to a greater dynamic range than standard photographs. Both facets of this system therefore stand to benefit from HDR imaging techniques. We demonstrate the success of our approach on multiple challenging ghosting scenarios, and compare our results with state-of-the-art methods previously proposed. We also demonstrate computational savings over these methods.

Real-world radiance values can range over eight orders of magnitude from starlight to direct sunlight but few digital cameras capture more than three orders in a single Low Dynamic Range (LDR) image. We approach this problem using established High Dynamic Range (HDR) techniques in which multiple images are captured with different exposure times so that all portions of the scene are correctly exposed at least once. These images are then combined to create an HDR image capturing the full range of the scene. HDR capture introduces new challenges; movement in the scene creates faded copies of moving objects, referred to as ghosts. Many techniques have been introduced to handle ghosting, but typically they either address specific types of ghosting, or are computationally very expensive. We address ghosting by first detecting moving objects, then reducing their contribution to the final composite on a frame-by-frame basis. The detection of motion is addressed by performing change detection on exposure-normalized images. Additional special cases are developed based on a priori knowledge of the changing exposures; for example, if exposure is increasing every shot, then any decrease in intensity in the LDR images is a strong indicator of motion. Recent Superpixel over-segmentation techniques are used to refine the detection. We also propose a novel solution for areas that see motion throughout the capture, such as foliage blowing in the wind. Such areas are detected as always moving, and are replaced with information from a single input image, and the replacement of corrupted regions can be tailored to the scenario. We present our approach in the context of a panoramic tele-presence system. Tele-presence systems allow a user to experience a remote environment, aiming to create a realistic sense of "being there" and such a system should therefore provide a high quality visual rendition of the environment. Furthermore, panoramas, by virtue of capturing a greater proportion of a real-world scene, are often exposed to a greater dynamic range than standard photographs. Both facets of this system therefore stand to benefit from HDR imaging techniques. We demonstrate the success of our approach on multiple challenging ghosting scenarios, and compare our results with state-of-the-art methods previously proposed. We also demonstrate computational savings over these methods.

L'un des buts principaux de l'imagerie numérique est d'une part la capture et d'autre part la reproduction de scènes réelles ou synthétiques sur des dispositifs d'affichage aux capacités restreintes. Les techniques d'imagerie traditionnelles sont limitées par la gamme de luminance qu'elles peuvent capturer et afficher. L'imagerie à grande gamme de luminance (High Dynamic Range – HDR) vise à dépasser cette limitation en capturant, représentant et affichant les quantités physique de la lumière présente dans une scène. Cependant, les technologies d'affichage existantes ne vont pas disparaitre instantanément, la compatibilité entre ces nouveaux contenus HDR et les contenus classiques est donc requise. Cette compatibilité est assurée par une opération de réduction des gammes de luminance (tone mapping) qui adapte les contenus HDR aux capacités restreintes des écrans. Bien que de nombreux opérateurs de tone mapping existent, ceux-ci se focalisent principalement sur les images fixes. Les verrous scientifiques associés au tone mapping de vidéo HDR sont plus complexes du fait de la dimension temporelle. Les travaux recherche menés dans la thèse se sont focalisés sur la préservation de la cohérence temporelle du vidéo tone mapping. Deux principaux axes de recherche ont été traités : la qualité subjective de contenus tone mappés et l'efficacité de la compression des vidéos HDR. En effet, tone mapper individuellement chaque image d'une séquence vidéo HDR engendre des artefacts temporels. Ces artefacts affectent la qualité visuelle de la vidéo tone mappée et il est donc nécessaire de les minimiser. Au travers de tests effectués sur des vidéos HDR avec différents opérateurs de tone mapping, nous avons proposé une classification des artefacts temporels en six catégories. Après avoir testé les opérateurs de tone mapping vidéo existants sur les différents types d'artefacts temporels, nous avons observé que seulement trois des six types d'artefacts étaient résolus. Nous avons donc créé une technique de post-traitement qui permet de réduire les 3 types d'artefacts non-considérés. Le deuxième aspect considéré dans la thèse concerne les relations entre compression et tone mapping. Jusque là, les travaux effectués sur le tone mapping et la vidéo compression se focalisaient sur l'optimisation du tone mapping de manière à atteindre des taux de compression élevés. Ces techniques modifient fortement le rendu, c'est à dire l'aspect de la vidéo, modifiant ainsi l'intention artistique initiale en amont dans la chaine de distribution (avant la compression). Dans ce contexte, nous avons proposé une technique qui permet de réduire l'entropie d'une vidéo tone mappée sans en modifier son rendu. Notre méthode adapte la quantification afin d'accroitre les corrélations entre images successives d'une vidéo. / One of the main goals of digital imagery is to improve the capture and the reproduction of real or synthetic scenes on display devices with restricted capabilities. Standard imagery techniques are limited with respect to the dynamic range that they can capture and reproduce. High Dynamic Range (HDR) imagery aims at overcoming these limitations by capturing, representing and displaying the physical value of light measured in a scene. However, current commercial displays will not vanish instantly hence backward compatibility between HDR content and those displays is required. This compatibility is ensured through an operation called tone mapping that retargets the dynamic range of HDR content to the restricted dynamic range of a display device. Although many tone mapping operators exist, they focus mostly on still images. The challenges of tone mapping HDR videos are more complex than those of still images since the temporal dimensions is added. In this work, the focus was on the preservation of temporal coherency when performing video tone mapping. Two main research avenues are investigated: the subjective quality of tone mapped video content and their compression efficiency. Indeed, tone mapping independently each frame of a video sequence leads to temporal artifacts. Those artifacts impair the visual quality of the tone mapped video sequence and need to be reduced. Through experimentations with HDR videos and Tone Mapping Operators (TMOs), we categorized temporal artifacts into six categories. We tested video tone mapping operators (techniques that take into account more than a single frame) on the different types of temporal artifact and we observed that they could handle only three out of the six types. Consequently, we designed a post-processing technique that adapts to any tone mapping operator and reduces the three types of artifact not dealt with. A subjective evaluation reported that our technique always preserves or increases the subjective quality of tone mapped content for the sequences and TMOs tested. The second topic investigated was the compression of tone mapped video content. So far, work on tone mapping and video compression focused on optimizing a tone map curve to achieve high compression ratio. These techniques changed the rendering of the video to reduce its entropy hence removing any artistic intent or constraint on the final results. That is why, we proposed a technique that reduces the entropy of a tone mapped video without altering its rendering.

CRISPR/Cas9 induced DNA breaks can be precisely repaired by cellular homology-directed repair (HDR) pathways using exogenously provided template DNA (donor). However, the full potential of precision editing is hindered in many model systems by low cutting efficiencies, low HDR efficiencies and, cytotoxicity related to Cas9 and donor DNA. In this thesis, I address these challenges and present methods that we developed to increase HDR efficiencies in multiple model organisms. In Caenorhabditis elegans, we show that by reducing toxicity high editing efficiencies can be achieved with single stranded oligonucleotide (ssODN) donors. We demonstrate that melting dsDNA donors dramatically improves the knock-in efficiencies of longer (1kb) edits. In addition, we describe 5′-terminal modifications to the donor molecules that further increase the frequency of precision editing. With our methodology a single optimally injected animal can yield more than 100 Green Fluorescent Protein (GFP) positive progeny, dramatically enhancing efficiency of genome editing. Next, we demonstrate the generality of 5′ modified donors by extending our studies to human cell cultures and mice zygotes. In mammalian models, 2′OMe-RNA modifications consistently increase HDR efficiencies by several fold over unmodified donors. Furthermore, end-modified donors exhibited a striking reduction in end-joining reactions including reduced concatemer formation and reduced direct ligation into the host genome. Our study demonstrates that HDR can be improved without inhibiting competing end-joining pathways and provides a platform to identify new chemical modifications that could further increase the potency and efficacy of precision genome editing.