Robust cell tracking in epithelial tissues through identification of maximum common subgraphs

Tracking of cells in live-imaging microscopy videos of epithelial sheets is a powerful tool for investigating fundamental processes in embryonic development. Characterizing cell growth, proliferation, intercalation and apoptosis in epithelia helps us to understand how morphogenetic processes such as tissue invagination and extension are locally regulated and controlled. Accurate cell tracking requires correctly resolving cells entering or leaving the field of view between frames, cell neighbour exchanges, cell removals and cell divisions. However, current tracking methods for epithelial sheets are not robust to large morphogenetic deformations and require significant manual interventions. Here, we present a novel algorithm for epithelial cell tracking, exploiting the graph-theoretic concept of a ‘maximum common subgraph’ to track cells between frames of a video. Our algorithm does not require the adjustment of tissue-specific parameters, and scales in sub-quadratic time with tissue size. It does not rely on precise positional information, permitting large cell movements between frames and enabling tracking in datasets acquired at low temporal resolution due to experimental constraints such as phototoxicity. To demonstrate the method, we perform tracking on the Drosophila embryonic epidermis and compare cell–cell rearrangements to previous studies in other tissues. Our implementation is open source and generally applicable to epithelial tissues

Modelling and tracking objects with a topology preserving self-organising neural network

Human gestures form an integral part in our everyday communication. We use gestures not only to reinforce meaning, but also to describe the shape of objects, to play games, and to communicate in noisy environments. Vision systems that exploit gestures are often limited by inaccuracies inherent in handcrafted models. These models are generated from a collection of training examples which requires segmentation and alignment. Segmentation in gesture recognition typically involves manual intervention, a time consuming process that is feasible only for a limited set of gestures. Ideally gesture models should be automatically acquired via a learning scheme that enables the acquisition of detailed behavioural knowledge only from topological and temporal observation. The research described in this thesis is motivated by a desire to provide a framework for the unsupervised acquisition and tracking of gesture models. In any learning framework, the initialisation of the shapes is very crucial. Hence, it would be beneficial to have a robust model not prone to noise that can automatically correspond the set of shapes. In the first part of this thesis, we develop a framework for building statistical 2D shape models by extracting, labelling and corresponding landmark points using only topological relations derived from competitive hebbian learning. The method is based on the assumption that correspondences can be addressed as an unsupervised classification problem where landmark points are the cluster centres (nodes) in a high-dimensional vector space. The approach is novel in that the network can be used in cases where the topological structure of the input pattern is not known a priori thus no topology of fixed dimensionality is imposed onto the network. In the second part, we propose an approach to minimise the user intervention in the adaptation process, which requires to specify a priori the number of nodes needed to represent an object, by utilising an automatic criterion for maximum node growth. Furthermore, this model is used to represent motion in image sequences by initialising a suitable segmentation that separates the object of interest from the background. The segmentation system takes into consideration some illumination tolerance, images as inputs from ordinary cameras and webcams, some low to medium cluttered background avoiding extremely cluttered backgrounds, and that the objects are at close range from the camera. In the final part, we extend the framework for the automatic modelling and unsupervised tracking of 2D hand gestures in a sequence of k frames. The aim is to use the tracked frames as training examples in order to build the model and maintain correspondences. To do that we add an active step to the Growing Neural Gas (GNG) network, which we call Active Growing Neural Gas (A-GNG) that takes into consideration not only the geometrical position of the nodes, but also the underlined local feature structure of the image, and the distance vector between successive images. The quality of our model is measured through the calculation of the topographic product. The topographic product is our topology preserving measure which quantifies the neighbourhood preservation. In our system we have applied specific restrictions in the velocity and the appearance of the gestures to simplify the difficulty of the motion analysis in the gesture representation. The proposed framework has been validated on applications related to sign language. The work has great potential in Virtual Reality (VR) applications where the learning and the representation of gestures becomes natural without the need of expensive wear cable sensors

Configraphics:

This dissertation reports a PhD research on mathematical-computational models, methods, and techniques for analysis, synthesis, and evaluation of spatial configurations in architecture and urban design. Spatial configuration is a technical term that refers to the particular way in which a set of spaces are connected to one another as a network. Spatial configuration affects safety, security, and efficiency of functioning of complex buildings by facilitating certain patterns of movement and/or impeding other patterns. In cities and suburban built environments, spatial configuration affects accessibilities and influences travel behavioural patterns, e.g. choosing walking and cycling for short trips instead of travelling by cars. As such, spatial configuration effectively influences the social, economic, and environmental functioning of cities and complex buildings, by conducting human movement patterns. In this research, graph theory is used to mathematically model spatial configurations in order to provide intuitive ways of studying and designing spatial arrangements for architects and urban designers. The methods and tools presented in this dissertation are applicable in: arranging spatial layouts based on configuration graphs, e.g. by using bubble diagrams to ensure certain spatial requirements and qualities in complex buildings; and analysing the potential effects of decisions on the likely spatial performance of buildings and on mobility patterns in built environments for systematic comparison of designs or plans, e.g. as to their aptitude for pedestrians and cyclists. The dissertation reports two parallel tracks of work on architectural and urban configurations. The core concept of the architectural configuration track is the ‘bubble diagram’ and the core concept of the urban configuration track is the ‘easiest paths’ for walking and cycling. Walking and cycling have been chosen as the foci of this theme as they involve active physical, cognitive, and social encounter of people with built environments, all of which are influenced by spatial configuration. The methodologies presented in this dissertation have been implemented in design toolkits and made publicly available as freeware applications

Parity and Spin CFT with boundaries and defects

This paper is a follow-up to [arXiv:2001.05055] in which two-dimensional conformal field theories in the presence of spin structures are studied. In the present paper we define four types of CFTs, distinguished by whether they need a spin structure or not in order to be well-defined, and whether their fields have parity or not. The cases of spin dependence without parity, and of parity without the need of a spin structure, have not, to our knowledge, been investigated in detail so far. We analyse these theories by extending the description of CFT correlators via three-dimensional topological field theory developed in [arXiv:hep-th/0204148] to include parity and spin. In each of the four cases, the defining data are a special Frobenius algebra $F$ in a suitable ribbon fusion category, such that the Nakayama automorphism of $F$ is the identity (oriented case) or squares to the identity (spin case). We use the TFT to define correlators in terms of $F$ and we show that these satisfy the relevant factorisation and single-valuedness conditions. We allow for world sheets with boundaries and topological line defects, and we specify the categories of boundary labels and the fusion categories of line defect labels for each of the four types. The construction can be understood in terms of topological line defects as gauging a possibly non-invertible symmetry. We analyse the case of a $\mathbb{Z}_2$-symmetry in some detail and provide examples of all four types of CFT, with Bershadsky-Polyakov models illustrating the two new types.Comment: v2 - expanded some discussions in the introduction and in the examples section - 112 page

The scaling limits of near-critical and dynamical percolation

We prove that near-critical percolation and dynamical percolation on the triangular lattice $\eta \mathbb{T}$ have a scaling limit as the mesh $\eta \to 0$, in the "quad-crossing" space $\mathcal{H}$ of percolation configurations introduced by Schramm and Smirnov. The proof essentially proceeds by "perturbing" the scaling limit of the critical model, using the pivotal measures studied in our earlier paper. Markovianity and conformal covariance of these new limiting objects are also established.Comment: 72 pages, 7 figures. Slightly revised, final versio

Label Efficient 3D Scene Understanding

3D scene understanding models are becoming increasingly integrated into modern society. With applications ranging from autonomous driving, Augmented Real- ity, Virtual Reality, robotics and mapping, the demand for well-behaved models is rapidly increasing. A key requirement for training modern 3D models is high- quality manually labelled training data. Collecting training data is often the time and monetary bottleneck, limiting the size of datasets. As modern data-driven neu- ral networks require very large datasets to achieve good generalisation, finding al- ternative strategies to manual labelling is sought after for many industries. In this thesis, we present a comprehensive study on achieving 3D scene under- standing with fewer labels. Specifically, we evaluate 4 approaches: existing data, synthetic data, weakly-supervised and self-supervised. Existing data looks at the potential of using readily available national mapping data as coarse labels for train- ing a building segmentation model. We further introduce an energy-based active contour snake algorithm to improve label quality by utilising co-registered LiDAR data. This is attractive as whilst the models may still require manual labels, these labels already exist. Synthetic data also exploits already existing data which was not originally designed for training neural networks. We demonstrate a pipeline for generating a synthetic Mobile Laser Scanner dataset. We experimentally evalu- ate if such a synthetic dataset can be used to pre-train smaller real-world datasets, increasing the generalisation with less data. A weakly-supervised approach is presented which allows for competitive per- formance on challenging real-world benchmark 3D scene understanding datasets with up to 95% less data. We propose a novel learning approach where the loss function is learnt. Our key insight is that the loss function is a local function and therefore can be trained with less data on a simpler task. Once trained our loss function can be used to train a 3D object detector using only unlabelled scenes. Our method is both flexible and very scalable, even performing well across datasets. Finally, we propose a method which only requires a single geometric represen- tation of each object class as supervision for 3D monocular object detection. We discuss why typical L2-like losses do not work for 3D object detection when us- ing differentiable renderer-based optimisation. We show that the undesirable local- minimas that the L2-like losses fall into can be avoided with the inclusion of a Generative Adversarial Network-like loss. We achieve state-of-the-art performance on the challenging 6DoF LineMOD dataset, without any scene level labels

Automatic face recognition using stereo images

Face recognition is an important pattern recognition problem, in the study of both natural and artificial learning problems. Compaxed to other biometrics, it is non-intrusive, non- invasive and requires no paxticipation from the subjects. As a result, it has many applications varying from human-computer-interaction to access control and law-enforcement to crowd surveillance. In typical optical image based face recognition systems, the systematic vaxiability arising from representing the three-dimensional (3D) shape of a face by a two-dimensional (21)) illumination intensity matrix is treated as random vaxiability. Multiple examples of the face displaying vaxying pose and expressions axe captured in different imaging conditions. The imaging environment, pose and expressions are strictly controlled and the images undergo rigorous normalisation and pre-processing. This may be implemented in a paxtially or a fully automated system. Although these systems report high classification accuracies (>90%), they lack versatility and tend to fail when deployed outside laboratory conditions. Recently, more sophisticated 3D face recognition systems haxnessing the depth information have emerged. These systems usually employ specialist equipment such as laser scanners and structured light projectors. Although more accurate than 2D optical image based recognition, these systems are equally difficult to implement in a non-co-operative environment. Existing face recognition systems, both 2D and 3D, detract from the main advantages of face recognition and fail to fully exploit its non-intrusive capacity. This is either because they rely too much on subject co-operation, which is not always available, or because they cannot cope with noisy data. The main objective of this work was to investigate the role of depth information in face recognition in a noisy environment. A stereo-based system, inspired by the human binocular vision, was devised using a pair of manually calibrated digital off-the-shelf cameras in a stereo setup to compute depth information. Depth values extracted from 2D intensity images using stereoscopy are extremely noisy, and as a result this approach for face recognition is rare. This was cofirmed by the results of our experimental work. Noise in the set of correspondences, camera calibration and triangulation led to inaccurate depth reconstruction, which in turn led to poor classifier accuracy for both 3D surface matching and 211) 2 depth maps. Recognition experiments axe performed on the Sheffield Dataset, consisting 692 images of 22 individuals with varying pose, illumination and expressions