9,300 research outputs found
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
A model-based approach to recovering the structure of a plant from images
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
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
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