An integrated approach for reconstructing a surface model of the proximal femur from sparse input data and a multi-resolution point distribution model: an in vitro study

Background: Accurate reconstruction of a patient-specific surface model of the proximal femur from preoperatively or intraoperatively available sparse data plays an important role in planning and supporting various computer-assisted surgical procedures. Methods: In this paper, we present an integrated approach using a multi-resolution point distribution model (MR-PDM) to reconstruct a patient-specific surface model of the proximal femur from sparse input data, which may consist of sparse point data or a limited number of calibrated X-ray images. Depending on the modality of the input data, our approach chooses different PDMs. When 3D sparse points are used, which may be obtained intraoperatively via a pointer-based digitization or from a calibrated ultrasound, a fine level point distribution model (FL-PDM) is used in the reconstruction process. In contrast, when calibrated X-ray images are used, which may be obtained preoperatively or intraoperatively, a coarse level point distribution model (CL-PDM) will be used. Results: The present approach was verified on 31 femurs. Three different types of input data, i.e., sparse points, calibrated fluoroscopic images, and calibrated X-ray radiographs, were used in our experiments to reconstruct a surface model of the associated bone. Our experimental results demonstrate promising accuracy of the present approach. Conclusions: A multi-resolution point distribution model facilitate the reconstruction of a patient-specific surface model of the proximal femur from sparse input dat

Statistical Modelling of Craniofacial Shape

With prior knowledge and experience, people can easily observe rich shape and texture variation for a certain type of objects, such as human faces, cats or chairs, in both 2D and 3D images. This ability helps us recognise the same person, distinguish different kinds of creatures and sketch unseen samples of the same object class. The process of capturing this prior knowledge is mathematically interpreted as statistical modelling. The outcome is a morphable model, a vector space representation of objects, that captures the variation of shape and texture. This thesis presents research aimed at constructing 3DMMs of craniofacial shape and texture using new algorithms and processing pipelines to offer enhanced modelling abilities over existing techniques. In particular, we present several fully automatic modelling approaches and apply them to a large dataset of 3D images of the human head, the Headspace dataset, thus generating the first public shape-and- texture 3D Morphable Model (3DMM) of the full human head. We call this the Liverpool-York Head Model, reflecting the data collection and statistical modelling respectively. We also explore the craniofacial symmetry and asymmetry in template morphing and statistical modelling. We propose a Symmetry-aware Coherent Point Drift (SA-CPD) algorithm, which mitigates the tangential sliding problem seen in competing morphing algorithms. Based on the symmetry-constrained correspondence output of SA-CPD, we present a symmetry-factored statistical modelling method for craniofacial shape. Also, we propose an iterative process of refinement for a 3DMM of the human ear that employs data augmentation. Then we merge the proposed 3DMMs of the ear with the full head model. As craniofacial clinicians like to look at head profiles, we propose a new pipeline to build a 2D morphable model of the craniofacial sagittal profile and augment it with profile models from frontal and top-down views. Our models and data are made publicly available online for research purposes

Registration based respiratory motion models for use in lung radiotherapy.

Respiratory motion is a major factor contributing to errors and uncertainties in Radiotherapy (RT) treatment of lung tumours. Knowledge of this motion may improve the planning and delivery of RT treatment for lung cancer patients. This thesis develops and evaluates methods of building patient specific respiratory motion models. These relate the internal motion to respiratory parameters derived from an external surrogate signal that can be measured during data acquisition and treatment delivery. The models offer a number of advantages over current methods of imaging and analysing respiratory motion, in particular their ability to account for variations in the respiratory motion. Computer Tomography (CT) data is acquired over several respiratory cycles to sample some of the variation in the respiratory motion. B-spline registrations are used to recover the motion and deformation from the CT data. The models are then constructed by fitting functions that relate the registration results to the respiratory parameters. This thesis describes the CT data and respiratory parameters that have been used to construct the motion models. It details the registrations protocols used and evaluates their results. The initial models presented in the thesis relate the registration results to a single parameter, the phase of the respiratory cycle, and average out any variation in the respiratory motion. The later models relate the registration results to two respiratory parameters, with the intention of modelling some of the variation. A number of different functions are assessed for both the single and two parameter models. The results show that the models can predict the respiratory motion in the CT data very accurately (mean error < 1.4 mm). This thesis also discusses some of the uses of the motion models in RT and, in particular, explores the use of the motion models for 'tracking' respiratory motion while delivering intensity modulated RT.

Mathematical Modelling and Machine Learning Methods for Bioinformatics and Data Science Applications

Mathematical modeling is routinely used in physical and engineering sciences to help understand complex systems and optimize industrial processes. Mathematical modeling differs from Artificial Intelligence because it does not exclusively use the collected data to describe an industrial phenomenon or process, but it is based on fundamental laws of physics or engineering that lead to systems of equations able to represent all the variables that characterize the process. Conversely, Machine Learning methods require a large amount of data to find solutions, remaining detached from the problem that generated them and trying to infer the behavior of the object, material or process to be examined from observed samples. Mathematics allows us to formulate complex models with effectiveness and creativity, describing nature and physics. Together with the potential of Artificial Intelligence and data collection techniques, a new way of dealing with practical problems is possible. The insertion of the equations deriving from the physical world in the data-driven models can in fact greatly enrich the information content of the sampled data, allowing to simulate very complex phenomena, with drastically reduced calculation times. Combined approaches will constitute a breakthrough in cutting-edge applications, providing precise and reliable tools for the prediction of phenomena in biological macro/microsystems, for biotechnological applications and for medical diagnostics, particularly in the field of precision medicine

Computational neuroanatomy of the central complex of drosophila melanogaster

In many different insect species the highly conserved neuropil regions known as the central complex or central body complex have been shown to be important in behaviours such as locomotion, visual memory and courtship conditioning. The aim of this project is to generate accurate quantitative neuroanatomy of the central complex in the fruit fly Drosophila melanogaster. Much of the authoritative neuroanatomy of the fruit fly from past literature has been derived using Golgi stains, and in important cases these data are available only from 2D camera lucida drawings of the neurons and linguistic descriptions of connectivity. These cannot easily be mapped onto 3D template brains or compared directly to our own data. Using GAL4 driver and reporter constructs, some of the findings within these studies could be visualized using immunohistochemistry and confocal microscopy. A range of GAL4 driver lines were selected that particularly had prominent expression in the fan-shaped body. Images of brains from these lines were archived using a web-based 3D image stack archive developed for the sharing and backup of large confocal stacks. This is also the platform which we use to publish the data, so that other researchers can reuse this catalogue and compare their results directly. Each brain was annotated using desktop-based tools for labelling neuropil regions, locating landmarks in image stacks and tracing fine neuronal processes both manually and automatically. The development of the tracing and landmark annotation tools is described, and all of the tools used in this work are available as free software. In order to compare and aggregate these data, which are from many different brains, it is necessary to register each image stack onto some standard template brain. Although this is a well-studied problem in medical imaging, these high resolution scans of the central fly brain are unusual in a number of respects. The relative effectiveness of various methods currently available were tested on this data set. The best registrations were produced by a method that generates free-form deformations based on B-splines (the Computational Morphometry Toolkit), but for much faster registrations, the thin plate spline method based on manual landmarks may be sufficient. The annotated and registered data allows us to produce central complex template images and also files that accurately represent the possible central complex connectivity apparent in these images. One interesting result to arise from these efforts was evidence for a possible connection between the inferior region of the fan-shaped body and the beta lobe of the mushroom body which had previously been missed in these GAL4 lines. In addition, we can identify several connections which appear to be similar to those described in [Hanesch et al., 1989], the canonical paper on the architecture of the Drosophila melanogaster central complex, and describe for the first time their variation statistically. This registered data was also used to suggest a method for classifying layers of expression within the fan-shaped body

Computational intelligence approaches to robotics, automation, and control [Volume guest editors]

No abstract available