Cell Lineage Tracking. Implementation of automated lineage tracking on 4D confocal image data in the MorphoGraphX software.

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Perustieteiden korkeakoulu | Master's thesis
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Master's in Computational and Systems Biology
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Master's Degree Programme in Computational and Systems Biology (euSYSBIO)
76 + 8
Multicellular organisms comprise a multitude of cells belonging to diverse types. The cells undergo growth and differentiation to generate tissues and develop the shape of organs. This phenomenon is known as morphogenesis. In order to study morphogenesis, temporal analysis of cell populations in an organism is studied which requires the determination of cell lineage. This problem is generally known as lineage tracking. MorphoGraphX is a software used by biologists to study various aspects of morphogenesis, specifically in plant samples, as it enables visualization and analysis of 3D biological datasets or images obtained from confocal microscopy. Despite the importance of lineage tracking to study morphogenesis, it is not automated in the software. Its automation in the software is a challenging problem due to irregularities among the cells with respect to their behaviour, shape and division. However, its implementation would improve efficiency and make it feasible to track lineage in a wider variety of datasets. In the current work, a software is implemented to automate lineage tracking in MorphoGraphX. The method does a piecewise linear registration of the meshes (2D curved surfaces) extracted from their respective confocal microscopy images with a time lapse. The registration is based on non-rigid deformation of meshes created by user specified landmarks (parent cells and respective daughter cells). An algorithm is developed to triangulate the landmarks on the surface. The triangulation is then used to define cells’ location over time with the help of barycentric coordinates. The method uses local geometric coordinates to establish parent - daughter relationship between the cells on the two meshes. After the initial lineage assignment, neighbourhood relations are used to verify that the correct lineage was assigned. Cells which pass verification are then added to the triangulation and the process repeats. The method gave over 90 % accuracy for lineage tracking on a leaf sample of Arabidopsis thaliana, one of the largest dataset tested comprising 1411 cells.
Rousu, Juho
Thesis advisor
Smith, Richard
lineage tracking, 3D triangulation, meshes, delaunay triangulation, barycentric coordinates