Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates

The study of cerebral anatomy in developing neonates is of great importance for the understanding of brain development during the early period of life. This dissertation therefore focuses on three challenges in the modelling of cerebral anatomy in neonates during brain development. The methods that have been developed all use Magnetic Resonance Images (MRI) as source data. To facilitate study of vascular development in the neonatal period, a set of image analysis algorithms are developed to automatically extract and model cerebral vessel trees. The whole process consists of cerebral vessel tracking from automatically placed seed points, vessel tree generation, and vasculature registration and matching. These algorithms have been tested on clinical Time-of- Flight (TOF) MR angiographic datasets. To facilitate study of the neonatal cortex a complete cerebral cortex segmentation and reconstruction pipeline has been developed. Segmentation of the neonatal cortex is not effectively done by existing algorithms designed for the adult brain because the contrast between grey and white matter is reversed. This causes pixels containing tissue mixtures to be incorrectly labelled by conventional methods. The neonatal cortical segmentation method that has been developed is based on a novel expectation-maximization (EM) method with explicit correction for mislabelled partial volume voxels. Based on the resulting cortical segmentation, an implicit surface evolution technique is adopted for the reconstruction of the cortex in neonates. The performance of the method is investigated by performing a detailed landmark study. To facilitate study of cortical development, a cortical surface registration algorithm for aligning the cortical surface is developed. The method first inflates extracted cortical surfaces and then performs a non-rigid surface registration using free-form deformations (FFDs) to remove residual alignment. Validation experiments using data labelled by an expert observer demonstrate that the method can capture local changes and follow the growth of specific sulcus

Autonomous Tissue Scanning under Free-Form Motion for Intraoperative Tissue Characterisation

In Minimally Invasive Surgery (MIS), tissue scanning with imaging probes is required for subsurface visualisation to characterise the state of the tissue. However, scanning of large tissue surfaces in the presence of deformation is a challenging task for the surgeon. Recently, robot-assisted local tissue scanning has been investigated for motion stabilisation of imaging probes to facilitate the capturing of good quality images and reduce the surgeon's cognitive load. Nonetheless, these approaches require the tissue surface to be static or deform with periodic motion. To eliminate these assumptions, we propose a visual servoing framework for autonomous tissue scanning, able to deal with free-form tissue deformation. The 3D structure of the surgical scene is recovered and a feature-based method is proposed to estimate the motion of the tissue in real-time. A desired scanning trajectory is manually defined on a reference frame and continuously updated using projective geometry to follow the tissue motion and control the movement of the robotic arm. The advantage of the proposed method is that it does not require the learning of the tissue motion prior to scanning and can deal with free-form deformation. We deployed this framework on the da Vinci surgical robot using the da Vinci Research Kit (dVRK) for Ultrasound tissue scanning. Since the framework does not rely on information from the Ultrasound data, it can be easily extended to other probe-based imaging modalities.Comment: 7 pages, 5 figures, ICRA 202

Adaptive object segmentation and tracking

Efficient tracking of deformable objects moving with variable velocities is an important current research problem. In this thesis a robust tracking model is proposed for the automatic detection, recognition and tracking of target objects which are subject to variable orientations and velocities and are viewed under variable ambient lighting conditions. The tracking model can be applied to efficiently track fast moving vehicles and other objects in various complex scenarios. The tracking model is evaluated on both colour visible band and infra-red band video sequences acquired from the air by the Sussex police helicopter and other collaborators. The observations made validate the improved performance of the model over existing methods. The thesis is divided in three major sections. The first section details the development of an enhanced active contour for object segmentation. The second section describes an implementation of a global active contour orientation model. The third section describes the tracking model and assesses it performance on the aerial video sequences. In the first part of the thesis an enhanced active contour snake model using the difference of Gaussian (DoG) filter is reported and discussed in detail. An acquisition method based on the enhanced active contour method developed that can assist the proposed tracking system is tested. The active contour model is further enhanced by the use of a disambiguation framework designed to assist multiple object segmentation which is used to demonstrate that the enhanced active contour model can be used for robust multiple object segmentation and tracking. The active contour model developed not only facilitates the efficient update of the tracking filter but also decreases the latency involved in tracking targets in real-time. As far as computational effort is concerned, the active contour model presented improves the computational cost by 85% compared to existing active contour models. The second part of the thesis introduces the global active contour orientation (GACO) technique for statistical measurement of contoured object orientation. It is an overall object orientation measurement method which uses the proposed active contour model along with statistical measurement techniques. The use of the GACO technique, incorporating the active contour model, to measure object orientation angle is discussed in detail. A real-time door surveillance application based on the GACO technique is developed and evaluated on the i-LIDS door surveillance dataset provided by the UK Home Office. The performance results demonstrate the use of GACO to evaluate the door surveillance dataset gives a success rate of 92%. Finally, a combined approach involving the proposed active contour model and an optimal trade-off maximum average correlation height (OT-MACH) filter for tracking is presented. The implementation of methods for controlling the area of support of the OT-MACH filter is discussed in detail. The proposed active contour method as the area of support for the OT-MACH filter is shown to significantly improve the performance of the OT-MACH filter's ability to track vehicles moving within highly cluttered visible and infra-red band video sequence