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

Geodesic boundary value problems with symmetry

This paper shows how left and right actions of Lie groups on a manifold may be used to complement one another in a variational reformulation of optimal control problems equivalently as geodesic boundary value problems with symmetry. We prove an equivalence theorem to this effect and illustrate it with several examples. In finite-dimensions, we discuss geodesic flows on the Lie groups SO(3) and SE(3) under the left and right actions of their respective Lie algebras. In an infinite-dimensional example, we discuss optimal large-deformation matching of one closed curve to another embedded in the same plane. In the curve-matching example, the manifold \Emb(S^1, \mathbb{R}^2) comprises the space of closed curves $S^1$ embedded in the plane $\mathbb{R}^2$. The diffeomorphic left action \Diff(\mathbb{R}^2) deforms the curve by a smooth invertible time-dependent transformation of the coordinate system in which it is embedded, while leaving the parameterisation of the curve invariant. The diffeomorphic right action \Diff(S^1) corresponds to a smooth invertible reparameterisation of the $S^1$ domain coordinates of the curve. As we show, this right action unlocks an important degree of freedom for geodesically matching the curve shapes using an equivalent fixed boundary value problem, without being constrained to match corresponding points along the template and target curves at the endpoint in time.Comment: First version -- comments welcome

Wing and body motion during flight initiation in Drosophila revealed by automated visual tracking

The fruit fly Drosophila melanogaster is a widely used model organism in studies of genetics, developmental biology and biomechanics. One limitation for exploiting Drosophila as a model system for behavioral neurobiology is that measuring body kinematics during behavior is labor intensive and subjective. In order to quantify flight kinematics during different types of maneuvers, we have developed a visual tracking system that estimates the posture of the fly from multiple calibrated cameras. An accurate geometric fly model is designed using unit quaternions to capture complex body and wing rotations, which are automatically fitted to the images in each time frame. Our approach works across a range of flight behaviors, while also being robust to common environmental clutter. The tracking system is used in this paper to compare wing and body motion during both voluntary and escape take-offs. Using our automated algorithms, we are able to measure stroke amplitude, geometric angle of attack and other parameters important to a mechanistic understanding of flapping flight. When compared with manual tracking methods, the algorithm estimates body position within 4.4±1.3% of the body length, while body orientation is measured within 6.5±1.9 deg. (roll), 3.2±1.3 deg. (pitch) and 3.4±1.6 deg. (yaw) on average across six videos. Similarly, stroke amplitude and deviation are estimated within 3.3 deg. and 2.1 deg., while angle of attack is typically measured within 8.8 deg. comparing against a human digitizer. Using our automated tracker, we analyzed a total of eight voluntary and two escape take-offs. These sequences show that Drosophila melanogaster do not utilize clap and fling during take-off and are able to modify their wing kinematics from one wingstroke to the next. Our approach should enable biomechanists and ethologists to process much larger datasets than possible at present and, therefore, accelerate insight into the mechanisms of free-flight maneuvers of flying insects

Non-Rigid Structure from Motion for Complex Motion

Recovering deformable 3D motion from temporal 2D point tracks in a monocular video is an open problem with many everyday applications throughout science and industry, or the new augmented reality. Recently, several techniques have been proposed to deal the problem called Non-Rigid Structure from Motion (NRSfM), however, they can exhibit poor reconstruction performance on complex motion. In this project, we will analyze these situations for primitive human actions such as walk, run, sit, jump, etc. on different scenarios, reviewing first the current techniques to finally present our novel method. This approach is able to model complex motion into a union of subspaces, rather than the summation occurring in standard low-rank shape methods, allowing better reconstruction accuracy. Experiments in a wide range of sequences and types of motion illustrate the benefits of this new approac

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

Shape basis interpretation for monocular deformable 3D reconstruction

© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.In this paper, we propose a novel interpretable shape model to encode object non-rigidity. We first use the initial frames of a monocular video to recover a rest shape, used later to compute a dissimilarity measure based on a distance matrix measurement. Spectral analysis is then applied to this matrix to obtain a reduced shape basis, that in contrast to existing approaches, can be physically interpreted. In turn, these pre-computed shape bases are used to linearly span the deformation of a wide variety of objects. We introduce the low-rank basis into a sequential approach to recover both camera motion and non-rigid shape from the monocular video, by simply optimizing the weights of the linear combination using bundle adjustment. Since the number of parameters to optimize per frame is relatively small, specially when physical priors are considered, our approach is fast and can potentially run in real time. Validation is done in a wide variety of real-world objects, undergoing both inextensible and extensible deformations. Our approach achieves remarkable robustness to artifacts such as noisy and missing measurements and shows an improved performance to competing methods.Peer ReviewedPostprint (author's final draft