Active-Meshes

This paper describes the implementation of an active mesh that is to be automatically created and configured directly from a single frame of an image sequence The aim of this approach is to use the derived mesh to perform visual tracking in unconstrained motion environments allowing movement of the camera the scene and even the inclusion of background independent moving objects The main problem in initializing this mesh comes from the fact that there is little a priori information about the scene available The paper will discuss methods that are currently available for determining the initial position of active contour models within images also suggesting a method of initializing the active mesh The approach is further extended to using multiple meshes and region initialized meshes

Speeding up active mesh segmentation by local termination of nodes.

This article outlines a procedure for speeding up segmentation of images using active mesh systems. Active meshes and other deformable models are very popular in image segmentation due to their ability to capture weak or missing boundary information; however, where strong edges exist, computations are still done after mesh nodes have settled on the boundary. This can lead to extra computational time whilst the system continues to deform completed regions of the mesh. We propose a local termination procedure, reducing these unnecessary computations and speeding up segmentation time with minimal loss of quality

Cut Finite Elements for Convection in Fractured Domains

We develop a cut finite element method (CutFEM) for the convection problem in a so called fractured domain which is a union of manifolds of different dimensions such that a $d$ dimensional component always resides on the boundary of a $d+1$ dimensional component. This type of domain can for instance be used to model porous media with embedded fractures that may intersect. The convection problem can be formulated in a compact form suitable for analysis using natural abstract directional derivative and divergence operators. The cut finite element method is based on using a fixed background mesh that covers the domain and the manifolds are allowed to cut through a fixed background mesh in an arbitrary way. We consider a simple method based on continuous piecewise linear elements together with weak enforcement of the coupling conditions and stabilization. We prove a priori error estimates and present illustrating numerical examples

A Cut Finite Element Method for Elliptic Bulk Problems with Embedded Surfaces

We propose an unfitted finite element method for flow in fractured porous media. The coupling across the fracture uses a Nitsche type mortaring, allowing for an accurate representation of the jump in the normal component of the gradient of the discrete solution across the fracture. The flow field in the fracture is modelled simultaneously, using the average of traces of the bulk variables on the fractured. In particular the Laplace-Beltrami operator for the transport in the fracture is included using the average of the projection on the tangential plane of the fracture of the trace of the bulk gradient. Optimal order error estimates are proven under suitable regularity assumptions on the domain geometry. The extension to the case of bifurcating fractures is discussed. Finally the theory is illustrated by a series of numerical examples

Active meshes for motion tracking

This thesis presents an integrated approach to modelling, extraction and tracking of deformable contour meshes through image sequences, with the aim of extracting motion information about the viewed scene. The thesis begins by reviewing the area of motion estimation in computer vision, leading to a review on the formulation and initialisation of active contour models. From this review the thesis develops and provides as its major contribution an active mesh structure that may be used for motion estimation. This active mesh structure approach is combined with feature matching to provide a stable, deformable motion tracking system for real-world scenes. This system is tested on various real-world scenes and varying conditions to provide extensive and rigorous experimental proof of the validity of the formulation. Further extensions to the system are implemented, including the use of multiple and region based active meshes. Future directions of research are also suggested

Active mesh and neural network pipeline for cell aggregate segmentation

Segmenting cells within cellular aggregates in 3D is a growing challenge in cell biology due to improvements in capacity and accuracy of microscopy techniques. Here, we describe a pipeline to segment images of cell aggregates in 3D. The pipeline combines neural network segmentations with active meshes. We apply our segmentation method to cultured mouse mammary gland organoids imaged over 24 h with oblique plane microscopy, a high-throughput light-sheet fluorescence microscopy technique. We show that our method can also be applied to images of mouse embryonic stem cells imaged with a spinning disc microscope. We segment individual cells based on nuclei and cell membrane fluorescent markers, and track cells over time. We describe metrics to quantify the quality of the automated segmentation. Our segmentation pipeline involves a Fiji plugin that implements active mesh deformation and allows a user to create training data, automatically obtain segmentation meshes from original image data or neural network prediction, and manually curate segmentation data to identify and correct mistakes. Our active meshes-based approach facilitates segmentation postprocessing, correction, and integration with neural network prediction

Active mesh coding and rate-distortion theory

This paper presents a video coding scheme for very low bit rate applications. The coding approach relies on active meshes and can be viewed as a particular case of region-based coding. The active mesh is used to efficiently represent and code the various regions of the scene and the motion information. The variation of the mesh topology as well as the strategy for coding the synthesis error are defined by an optimization technique following the rate-distortion criterion.Peer ReviewedPostprint (published version

Speeding Up Active Mesh Segmentation by Local Termination of Nodes

This article outlines a procedure for speeding up segmentation of images using active mesh systems. Active meshes and other deformable models are very popular in image segmentation due to their ability to capture weak or missing boundary information; however, where strong edges exist, computations are still done after mesh nodes have settled on the boundary. This can lead to extra computational time whilst the system continues to deform completed regions of the mesh. We propose a local termination procedure, reducing these unnecessary computations and speeding up segmentation time with minimal loss of quality