RT Journal Article
SR Electronic
T1 Robust cell tracking in epithelial tissues through identification of maximum common subgraphs
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 049551
DO 10.1101/049551
A1 Jochen Kursawe
A1 Rémi Bardenet
A1 Jeremiah J. Zartman
A1 Ruth E. Baker
A1 Alexander G. Fletcher
YR 2016
UL http://biorxiv.org/content/early/2016/09/08/049551.abstract
AB Tracking of cells in live-imaging microscopy videos of epithelial sheets is a powerful tool for investigating fundamental processes in embryonic development. Characterising 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 photoxicity. 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.