Show simple item record

dc.contributor.authorLeung, Tony Kin Shun 17:53:14 (GMT) 17:53:14 (GMT)
dc.description.abstractAdvances in computational modelling offer unprecedented potential for obtaining insights into the mechanics of cell-cell interactions. With the aid of such models, cell-level phenomena such as cell sorting and tissue self-organization are now being understood in terms of forces generated by specific sub-cellular structural components. Three-dimensional systems can behave differently from two-dimensional ones and since models cannot be validated without corresponding data, it is crucial to build accurate three-dimensional models of real cell aggregates. The lack of automated methods to determine which cell outlines in successive images of a confocal stack or time-lapse image set belong to the same cell is an important unsolved problem in the reconstruction process. This thesis addresses this problem through a contour grouping algorithm (CGA) designed to lead to unsupervised three-dimensional reconstructions of biological cells. The CGA associates contours obtained from fluorescently-labeled cell membranes in individual confocal slices using concepts from the fields of machine learning and combinatorics. The feature extraction step results in a set of association metrics. The algorithm then uses a probabilistic grouping step and a greedy-cost optimization step to produce grouped sets of contours. Groupings are representative of imaged cells and are manually evaluated for accuracy. The CGA presented here is able to produce accuracies greater than 96% when properly tuned. Parameter studies show that the algorithm is robust. That is, acceptable results are obtained under moderately varied probabilistic constraints and reasonable cost weightings. Image properties – such as slicing distance, image quality – affect the results. Sources of error are identified and enhancements based on fuzzy-logic and other optimization methods are considered. The successful grouping of cell contours, as realized here, is an important step toward the development of realistic, three-dimensional, cell-based finite element models.en
dc.publisherUniversity of Waterlooen
dc.subjectcontour groupingen
dc.subject3D reconstructionen
dc.subjectconfocal imagingen
dc.subjectbiological cellsen
dc.titleA Contour Grouping Algorithm for 3D Reconstruction of Biological Cellsen
dc.typeMaster Thesisen
dc.subject.programCivil Engineeringen and Environmental Engineeringen
uws-etd.degreeMaster of Applied Scienceen

Files in this item


This item appears in the following Collection(s)

Show simple item record


University of Waterloo Library
200 University Avenue West
Waterloo, Ontario, Canada N2L 3G1
519 888 4883

All items in UWSpace are protected by copyright, with all rights reserved.

DSpace software

Service outages