9,300 research outputs found

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

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    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

    A model-based approach to recovering the structure of a plant from images

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    We present a method for recovering the structure of a plant directly from a small set of widely-spaced images. Structure recovery is more complex than shape estimation, but the resulting structure estimate is more closely related to phenotype than is a 3D geometric model. The method we propose is applicable to a wide variety of plants, but is demonstrated on wheat. Wheat is made up of thin elements with few identifiable features, making it difficult to analyse using standard feature matching techniques. Our method instead analyses the structure of plants using only their silhouettes. We employ a generate-and-test method, using a database of manually modelled leaves and a model for their composition to synthesise plausible plant structures which are evaluated against the images. The method is capable of efficiently recovering accurate estimates of plant structure in a wide variety of imaging scenarios, with no manual intervention

    Robust virtual unrolling of historical parchment XMT images

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    We develop a framework to virtually unroll fragile historical parchment scrolls, which cannot be physically unfolded via a sequence of X-ray tomographic slices, thus providing easy access to those parchments whose contents have remained hidden for centuries. The first step is to produce a topologically correct segmentation, which is challenging as the parchment layers vary significantly in thickness, contain substantial interior textures and can often stick together in places. For this purpose, our method starts with linking the broken layers in a slice using the topological structure propagated from its previous processed slice. To ensure topological correctness, we identify fused regions by detecting junction sections, and then match them using global optimization efficiently solved by the blossom algorithm, taking into account the shape energy of curves separating fused layers. The fused layers are then separated using as-parallel-as-possible curves connecting junction section pairs. To flatten the segmented parchment, pixels in different frames need to be put into alignment. This is achieved via a dynamic programming-based global optimization, which minimizes the total matching distances and penalizes stretches. Eventually, the text of the parchment is revealed by ink projection. We demonstrate the effectiveness of our approach using challenging real-world data sets, including the water damaged fifteenth century Bressingham scroll

    CPM: a deformable model for shape recovery and segmentation based on charged particles

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