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

EIT Reconstruction Algorithms: Pitfalls, Challenges and Recent Developments

We review developments, issues and challenges in Electrical Impedance Tomography (EIT), for the 4th Workshop on Biomedical Applications of EIT, Manchester 2003. We focus on the necessity for three dimensional data collection and reconstruction, efficient solution of the forward problem and present and future reconstruction algorithms. We also suggest common pitfalls or ``inverse crimes'' to avoid.Comment: A review paper for the 4th Workshop on Biomedical Applications of EIT, Manchester, UK, 200

Intersubject Regularity in the Intrinsic Shape of Human V1

Previous studies have reported considerable intersubject variability in the three-dimensional geometry of the human primary visual cortex (V1). Here we demonstrate that much of this variability is due to extrinsic geometric features of the cortical folds, and that the intrinsic shape of V1 is similar across individuals. V1 was imaged in ten ex vivo human hemispheres using high-resolution (200 μm) structural magnetic resonance imaging at high field strength (7 T). Manual tracings of the stria of Gennari were used to construct a surface representation, which was computationally flattened into the plane with minimal metric distortion. The instrinsic shape of V1 was determined from the boundary of the planar representation of the stria. An ellipse provided a simple parametric shape model that was a good approximation to the boundary of flattened V1. The aspect ration of the best-fitting ellipse was found to be consistent across subject, with a mean of 1.85 and standard deviation of 0.12. Optimal rigid alignment of size-normalized V1 produced greater overlap than that achieved by previous studies using different registration methods. A shape analysis of published macaque data indicated that the intrinsic shape of macaque V1 is also stereotyped, and similar to the human V1 shape. Previoud measurements of the functional boundary of V1 in human and macaque are in close agreement with these results

Tools for quantitative form description : an evaluation of different software packages for semi-landmark analysis

The challenging complexity of biological structures has led to the development of several methods for quantitative analyses of form. Bones are shaped by the interaction of historical (phylogenetic), structural, and functional constrains. Consequently, bone shape has been investigated intensively in an evolutionary context. Geometric morphometric approaches allow the description of the shape of an object in all of its biological complexity. However, when biological objects present only few anatomical landmarks, sliding semi-landmarks may provide good descriptors of shape. The sliding procedure, mandatory for sliding semi-landmarks, requires several steps that may be time-consuming. We here compare the time required by two different software packages ('Edgewarp' and 'Morpho') for the same sliding task, and investigate potential differences in the results and biological interpretation. 'Morpho' is much faster than 'Edgewarp,' notably as a result of the greater computational power of the 'Morpho' software routines and the complexity of the 'Edgewarp' workflow. Morphospaces obtained using both software packages are similar and provide a consistent description of the biological variability. The principal differences between the two software packages are observed in areas characterized by abrupt changes in the bone topography. In summary, both software packages perform equally well in terms of the description of biological structures, yet differ in the simplicity of the workflow and time needed to performthe analyses

On the Origin of Frictional Adhesion in Geckos: Small Morphological Changes Lead to a Major Biomechanical Transition in the Genus \u3cem\u3eGonatodes\u3c/em\u3e

The evolutionary history of vertebrate locomotion is punctuated by innovations that have permitted expansion into novel ecological niches. Frictional adhesion of geckos is an innovation renowned for enabling locomotion on vertical and inverted smooth surfaces. Much is known about the microstructure and function of the fully-expressed gekkotan adhesive apparatus, although how it originated is poorly understood. Therefore, identifying species that exhibit the earliest stages of expression of frictional adhesion will provide significant insights into the evolution of this trait. Our previous investigation of digital proportions, shape, scalation, skeletal form, and subdigital epidermal micro-ornamentation in the genus Gonatodes led us to hypothesize that Gonatodes humeralisexpresses incipient frictional adhesion. To test this, we first conducted a phylogenetic analysis of Gonatodes and related sphaerodactyl genera to clarify the historical context of the evolution of frictional adhesive capability in the genus. We then measured the ability of G. humeralis and its close relatives to generate frictional adhesive force, examined their locomotor capabilities on low-friction surfaces, and observed animals in their natural habitat. After accounting for body mass and phylogenetic relationships, we found that G. humeralis generates frictional adhesive force essentially equivalent to that of Anolis, and can scale vertical smooth surfaces. Gonatodes vittatus, a species that lacks elaborated epidermal setae, generates negligible frictional adhesive force and can only ascend smooth inclined surfaces with a pitch of ≤ 40°. We conclude that the ostensibly padless G. humeralis, with feet lacking the musculoskeletal, tendinous, and vascular modifications typical of pad-bearing geckos, nevertheless can employ frictional adhesive contact to assist locomotion. As in Anolis, the release of frictional adhesive contact occurs when the foot is plantar flexed after the heel has lifted from the surface. Our findings indicate that the origin of frictional adhesion was likely gradual but that, ultimately, this led to major shifts in ecology and function

Optical techniques for 3D surface reconstruction in computer-assisted laparoscopic surgery

One of the main challenges for computer-assisted surgery (CAS) is to determine the intra-opera- tive morphology and motion of soft-tissues. This information is prerequisite to the registration of multi-modal patient-specific data for enhancing the surgeon’s navigation capabilites by observ- ing beyond exposed tissue surfaces and for providing intelligent control of robotic-assisted in- struments. In minimally invasive surgery (MIS), optical techniques are an increasingly attractive approach for in vivo 3D reconstruction of the soft-tissue surface geometry. This paper reviews the state-of-the-art methods for optical intra-operative 3D reconstruction in laparoscopic surgery and discusses the technical challenges and future perspectives towards clinical translation. With the recent paradigm shift of surgical practice towards MIS and new developments in 3D opti- cal imaging, this is a timely discussion about technologies that could facilitate complex CAS procedures in dynamic and deformable anatomical regions

Sexual Dimorphism in Homo erectus Inferred from 1.5 Ma Footprints Near Ileret, Kenya

Sexual dimorphism can be one of the most important indicators of social behavior in fossil species, but the effects of time averaging, geographic variation, and differential preservation can complicate attempts to determine this measure from preserved skeletal anatomy. Here we present an alternative, using footprints from near Ileret, Kenya, to assess the sexual dimorphism of presumptive African Homo erectus at 1.5 Ma. Footprint sites have several unique advantages not typically available to fossils: a single surface can sample a population over a very brief time (in this case likely not more than a single day), and the data are geographically constrained. Further, in many cases, the samples can be much larger than those from skeletal fossil assemblages. Our results indicate that East African Homo erectus was more dimorphic than modern Homo sapiens, although less so than highly dimorphic apes, suggesting that the Ileret footprints offer a unique window into an important transitional period in hominin social behavior

Geometry Processing of Conventionally Produced Mouse Brain Slice Images

Brain mapping research in most neuroanatomical laboratories relies on conventional processing techniques, which often introduce histological artifacts such as tissue tears and tissue loss. In this paper we present techniques and algorithms for automatic registration and 3D reconstruction of conventionally produced mouse brain slices in a standardized atlas space. This is achieved first by constructing a virtual 3D mouse brain model from annotated slices of Allen Reference Atlas (ARA). Virtual re-slicing of the reconstructed model generates ARA-based slice images corresponding to the microscopic images of histological brain sections. These image pairs are aligned using a geometric approach through contour images. Histological artifacts in the microscopic images are detected and removed using Constrained Delaunay Triangulation before performing global alignment. Finally, non-linear registration is performed by solving Laplace's equation with Dirichlet boundary conditions. Our methods provide significant improvements over previously reported registration techniques for the tested slices in 3D space, especially on slices with significant histological artifacts. Further, as an application we count the number of neurons in various anatomical regions using a dataset of 51 microscopic slices from a single mouse brain. This work represents a significant contribution to this subfield of neuroscience as it provides tools to neuroanatomist for analyzing and processing histological data.Comment: 14 pages, 11 figure

Human-activity-centered measurement system:challenges from laboratory to the real environment in assistive gait wearable robotics

Assistive gait wearable robots (AGWR) have shown a great advancement in developing intelligent devices to assist human in their activities of daily living (ADLs). The rapid technological advancement in sensory technology, actuators, materials and computational intelligence has sped up this development process towards more practical and smart AGWR. However, most assistive gait wearable robots are still confined to be controlled, assessed indoor and within laboratory environments, limiting any potential to provide a real assistance and rehabilitation required to humans in the real environments. The gait assessment parameters play an important role not only in evaluating the patient progress and assistive device performance but also in controlling smart self-adaptable AGWR in real-time. The self-adaptable wearable robots must interactively conform to the changing environments and between users to provide optimal functionality and comfort. This paper discusses the performance parameters, such as comfortability, safety, adaptability, and energy consumption, which are required for the development of an intelligent AGWR for outdoor environments. The challenges to measuring the parameters using current systems for data collection and analysis using vision capture and wearable sensors are presented and discussed