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Mother machine image analysis with MM3

Sauls, J. T.; Schroeder, J. W.; Brown, S. D.; Le Treut, G.; Si, F.; Li, D.; Wang, J. D.; Jun, S.

2019-10-18 systems biology
10.1101/810036 bioRxiv
Show abstract

The mother machine is a microfluidic device for high-throughput time-lapse imaging of microbes. Here, we present MM3, a complete and modular image analysis pipeline. MM3 turns raw mother machine images, both phase contrast and fluorescence, into a data structure containing cells with their measured features. MM3 employs machine learning and non-learning algorithms, and is implemented in Python. MM3 is easy to run as a command line tool with the occasional graphical user interface on a PC or Mac. A typical mother machine experiment can be analyzed within one day. It has been extensively tested, is well documented and publicly available via Github.

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