bacto_tracker: a method for single-cell tracking of M. xanthus in dense and multispecies colonies
Résumé
Cell motility and predation are important for the dynamics of many multi-cellular ecosystems, such as the gut or the soil. Approaches to image cell dynamics in such complex systems are scant, and high-throughput analysis methods to segment and track single-cell behaviors are currently lacking. Here, we addressed these limitations by implementing a fast fluorescence microscopy technique enabling the high-resolution acquisition of cell movement over large areas and long time periods. Next, we applied deep learning to semantically segment two different bacteria species within complex micro-environments . We implemented a method to build single cell traces by combining the cell masks from different time points to follow the dynamics of single cells with high spatial and temporal resolutions and over long periods of time. We applied and validated these methods by characterizing the dynamics of Escherichia coli predation by Myxococcus xanthus .
Mots clés
time-lapse imaging
biofilm
deep-learning Author roles: Rombouts S: Conceptualization
Data Curation
Formal Analysis
Methodology
Resources
Software
Validation
Visualization
Writing -Original Draft Preparation
Writing -Review & Editing Fiche JB: Conceptualization
Supervision
Writing -Review & Editing Mignot T: Conceptualization
Writing -Review & Editing Nollmann M: Conceptualization
Funding Acquisition
Writing -Review & Editing
Fiche JB: Conceptualization
Mignot T: Conceptualization
Nollmann M: Conceptualization
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