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bioRxiv · 10.1101/2020.04.13.036756

EllipTrack: A Global-Local Cell-Tracking Pipeline for 2D Fluorescence Time-Lapse Microscopy

Tian, C.·Yang, C.·Spencer, S. L.
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Abstract

Time-lapse microscopy provides an unprecedented opportunity to monitor single-cell dynamics. However, tracking cells for long periods of time remains a technical challenge, especially for multi-day, large-scale movies with rapid cell migration, high cell density, and drug treatments that alter cell morphology/behavior. Here, we present EllipTrack, a global-local cell-tracking pipeline optimized for tracking such movies. EllipTrack first implements a global track-linking algorithm to construct tracks that maximize the probability of cell lineages, and then corrects tracking mistakes with a local track-correction module where tracks generated by the global algorithm are systematically examined and amended if a more probable alternative can be found. Through benchmarking, we show that EllipTrack outperforms state-of-the-art cell trackers and generates nearly error-free cell lineages for multiple large-scale movies. In addition, EllipTrack can adapt to time- and cell density-dependent changes in cell migration speeds, requires minimal training datasets, and provides a user-friendly interface. EllipTrack is available at github.com/tianchengzhe/EllipTrack.

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Tian, C., Yang, C., Spencer, S. L.. 2020-04-13. EllipTrack: A Global-Local Cell-Tracking Pipeline for 2D Fluorescence Time-Lapse Microscopy. https://doi.org/10.1101/2020.04.13.036756

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