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bioRxiv · 10.1101/810036

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.
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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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Sauls, J. T., Schroeder, J. W., Brown, S. D., Le Treut, G., Si, F., Li, D., Wang, J. D., Jun, S.. 2019-10-18. Mother machine image analysis with MM3. https://doi.org/10.1101/810036

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