Extracting road centrelines from binary road images by optimizing geodesic lines

Binary road images can be obtained from remotely sensed images with the aid of classification and segmentation techniques. Extracting road centrelines from these binary images are crucial to update a Geographic Information System (GIS) database. A current state of art method of centreline extraction needs to remove road junctions and depends on the accuracy of the endpoints, leading to three main limitations: (1) causing small gaps in the roads, (2) wrongly treating short non-road segments as roads, and (3) producing centrelines of low accuracy around the road end regions. To overcome these limitations, we propose to use an iteratively searching scheme to obtain the longest geodesic line in the preprocessed road skeleton images. Several image pixels at each end of the geodesic lines were removed to avoid noise, and the remaining parts were optimized using a dynamic programming snake model. The proposed method is applied to three types of binary road images and compared with the state of art method. It shows that the proposed method is less affected by the end regions of the roads, and is effective in filling the gaps in the roads. It also has an advantage on processing short non-road segments. © 2015 IEEE.International Conference Image and Vision Computing New Zealan

Human and environmental exposure to hydrocarbon pollution in the Niger Delta:A geospatial approach

This study undertook an integrated geospatial assessment of human and environmental exposure to oil pollution in the Niger Delta using primary and secondary spatial data. This thesis begins by presenting a clear rationale for the study of extensive oil pollution in the Niger Delta, followed by a critical literature review of the potential application of geospatial techniques for monitoring and managing the problem. Three analytical chapters report on the methodological developments and applications of geospatial techniques that contribute to achieving the aim of the study. Firstly, a quantitative assessment of human and environmental exposure to oil pollution in the Niger Delta was performed using a government spill database. This was carried out using Spatial Analysis along Networks (SANET), a geostatistical tool, since oil spills in the region tend to follow the linear patterns of the pipelines. Spatial data on pipelines, oil spills, population and land cover data were analysed in order to quantify the extent of human and environmental exposure to oil pollution. The major causes of spills and spatial factors potentially reinforcing reported causes were analysed. Results show extensive general exposure and sabotage as the leading cause of oil pollution in the Niger Delta. Secondly, a method of delineating the river network in the Niger Delta using Sentinel-1 SAR data was developed, as a basis for modelling potential flow of pollutants in the distributary pathways of the network. The cloud penetration capabilities of SAR sensing are particularly valuable for this application since the Niger Delta is notorious for cloud cover. Vector and raster-based river networks derived from Sentinel-1 were compared to alternative river map products including those from the USGS and ESA. This demonstrated the superiority of the Sentinel-1 derived river network, which was subsequently used in a flow routing analysis to demonstrate the potential for understanding oil spill dispersion. Thirdly, the study applied optical remote sensing for indirect detection and mapping of oil spill impacts on vegetation. Multi-temporal Landsat data was used to delineate the spill impact footprint of a notable 2008 oil spill incident in Ogoniland and population exposure was evaluated. The optical data was effective in impact area delineation, demonstrating extensive and long-lasting population exposure to oil pollution. Overall, this study has successfully assembled and produced relevant spatial and attribute data sets and applied integrated geostatistical analytical techniques to understand the distribution and impacts of oil spills in the Niger Delta. The study has revealed the extensive level of human and environmental exposure to hydrocarbon pollution in the Niger Delta and introduced new methods that will be valuable fo

Open-source virtual bronchoscopy for image guided navigation

This thesis describes the development of an open-source system for virtual bronchoscopy used in combination with electromagnetic instrument tracking. The end application is virtual navigation of the lung for biopsy of early stage cancer nodules. The open-source platform 3D Slicer was used for creating freely available algorithms for virtual bronchscopy. Firstly, the development of an open-source semi-automatic algorithm for prediction of solitary pulmonary nodule malignancy is presented. This approach may help the physician decide whether to proceed with biopsy of the nodule. The user-selected nodule is segmented in order to extract radiological characteristics (i.e., size, location, edge smoothness, calcification presence, cavity wall thickness) which are combined with patient information to calculate likelihood of malignancy. The overall accuracy of the algorithm is shown to be high compared to independent experts' assessment of malignancy. The algorithm is also compared with two different predictors, and our approach is shown to provide the best overall prediction accuracy. The development of an airway segmentation algorithm which extracts the airway tree from surrounding structures on chest Computed Tomography (CT) images is then described. This represents the first fundamental step toward the creation of a virtual bronchoscopy system. Clinical and ex-vivo images are used to evaluate performance of the algorithm. Different CT scan parameters are investigated and parameters for successful airway segmentation are optimized. Slice thickness is the most affecting parameter, while variation of reconstruction kernel and radiation dose is shown to be less critical. Airway segmentation is used to create a 3D rendered model of the airway tree for virtual navigation. Finally, the first open-source virtual bronchoscopy system was combined with electromagnetic tracking of the bronchoscope for the development of a GPS-like system for navigating within the lungs. Tools for pre-procedural planning and for helping with navigation are provided. Registration between the lungs of the patient and the virtually reconstructed airway tree is achieved using a landmark-based approach. In an attempt to reduce difficulties with registration errors, we also implemented a landmark-free registration method based on a balanced airway survey. In-vitro and in-vivo testing showed good accuracy for this registration approach. The centreline of the 3D airway model is extracted and used to compensate for possible registration errors. Tools are provided to select a target for biopsy on the patient CT image, and pathways from the trachea towards the selected targets are automatically created. The pathways guide the physician during navigation, while distance to target information is updated in real-time and presented to the user. During navigation, video from the bronchoscope is streamed and presented to the physician next to the 3D rendered image. The electromagnetic tracking is implemented with 5 DOF sensing that does not provide roll rotation information. An intensity-based image registration approach is implemented to rotate the virtual image according to the bronchoscope's rotations. The virtual bronchoscopy system is shown to be easy to use and accurate in replicating the clinical setting, as demonstrated in the pre-clinical environment of a breathing lung method. Animal studies were performed to evaluate the overall system performance

Image Processing and Simulation Toolboxes of Microscopy Images of Bacterial Cells

Recent advances in microscopy imaging technology have allowed the characterization of the dynamics of cellular processes at the single-cell and single-molecule level. Particularly in bacterial cell studies, and using the E. coli as a case study, these techniques have been used to detect and track internal cell structures such as the Nucleoid and the Cell Wall and fluorescently tagged molecular aggregates such as FtsZ proteins, Min system proteins, inclusion bodies and all the different types of RNA molecules. These studies have been performed with using multi-modal, multi-process, time-lapse microscopy, producing both morphological and functional images. To facilitate the finding of relationships between cellular processes, from small-scale, such as gene expression, to large-scale, such as cell division, an image processing toolbox was implemented with several automatic and/or manual features such as, cell segmentation and tracking, intra-modal and intra-modal image registration, as well as the detection, counting and characterization of several cellular components. Two segmentation algorithms of cellular component were implemented, the first one based on the Gaussian Distribution and the second based on Thresholding and morphological structuring functions. These algorithms were used to perform the segmentation of Nucleoids and to identify the different stages of FtsZ Ring formation (allied with the use of machine learning algorithms), which allowed to understand how the temperature influences the physical properties of the Nucleoid and correlated those properties with the exclusion of protein aggregates from the center of the cell. Another study used the segmentation algorithms to study how the temperature affects the formation of the FtsZ Ring. The validation of the developed image processing methods and techniques has been based on benchmark databases manually produced and curated by experts. When dealing with thousands of cells and hundreds of images, these manually generated datasets can become the biggest cost in a research project. To expedite these studies in terms of time and lower the cost of the manual labour, an image simulation was implemented to generate realistic artificial images. The proposed image simulation toolbox can generate biologically inspired objects that mimic the spatial and temporal organization of bacterial cells and their processes, such as cell growth and division and cell motility, and cell morphology (shape, size and cluster organization). The image simulation toolbox was shown to be useful in the validation of three cell tracking algorithms: Simple Nearest-Neighbour, Nearest-Neighbour with Morphology and DBSCAN cluster identification algorithm. It was shown that the Simple Nearest-Neighbour still performed with great reliability when simulating objects with small velocities, while the other algorithms performed better for higher velocities and when there were larger clusters present

Proceedings of the 2018 Canadian Society for Mechanical Engineering (CSME) International Congress

Published proceedings of the 2018 Canadian Society for Mechanical Engineering (CSME) International Congress, hosted by York University, 27-30 May 2018