6,324 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
Developing a comprehensive framework for multimodal feature extraction
Feature extraction is a critical component of many applied data science
workflows. In recent years, rapid advances in artificial intelligence and
machine learning have led to an explosion of feature extraction tools and
services that allow data scientists to cheaply and effectively annotate their
data along a vast array of dimensions---ranging from detecting faces in images
to analyzing the sentiment expressed in coherent text. Unfortunately, the
proliferation of powerful feature extraction services has been mirrored by a
corresponding expansion in the number of distinct interfaces to feature
extraction services. In a world where nearly every new service has its own API,
documentation, and/or client library, data scientists who need to combine
diverse features obtained from multiple sources are often forced to write and
maintain ever more elaborate feature extraction pipelines. To address this
challenge, we introduce a new open-source framework for comprehensive
multimodal feature extraction. Pliers is an open-source Python package that
supports standardized annotation of diverse data types (video, images, audio,
and text), and is expressly with both ease-of-use and extensibility in mind.
Users can apply a wide range of pre-existing feature extraction tools to their
data in just a few lines of Python code, and can also easily add their own
custom extractors by writing modular classes. A graph-based API enables rapid
development of complex feature extraction pipelines that output results in a
single, standardized format. We describe the package's architecture, detail its
major advantages over previous feature extraction toolboxes, and use a sample
application to a large functional MRI dataset to illustrate how pliers can
significantly reduce the time and effort required to construct sophisticated
feature extraction workflows while increasing code clarity and maintainability
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