This thesis focuses on automated monitoring of human embryonic cells in time-lapse microscopy images of early stage developing embryos. Our primary biological motivation is to develop an automated system that would assist embryologist to study and analyze the dynamic behavior of developing embryos in an attempt to improve in vitro fertilisation (IVF) outcomes. However, all methods proposed in this thesis are applicable to a wide range of microscopy cellular image analysis applications.

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... analysis tasks involving cellular structures, in general, present significant difficulties (e.g., topological change and deformable objects). These difficulties are even more acute in the context of microscopy images of human embryonic cells. The individual cells in the developing embryos form a complex 3D structure, which, in a 2D projection, overlap immensely. We tackle these difficulties within a principled probabilistic framework and propose methods that can reliably and efficiently analyse growing embryos in a fully automated manner. An important and first step in automated analysis is being able to efficiently and reliably segment the embryo from background clutter. To this end, we propose a framework to segment the developing embryo by estimating the contour around the embryo. We formulate segmentation as an energy minimization problem and solved it efficiently via graph cuts. Next, we propose frameworks to spatially localize embryonic cells and temporally detect their divisions. Predicting the number of cells is a fundamental task in cell biology analysis. In the context of human embryonic cells its importance is prime as current embryo viability biomarkers require accurate cells counts. The number of cells prediction can either be performed directly from the microscopy images or by detecting (localizing) cells. In this thesis, we employ both approaches and propose frameworks that combine both approaches in a conditional random field (CRF) framework. For localization, we model cells as ellipses and derive a data-d [...]