RT Journal Article
SR Electronic
T1 Mother machine image analysis with MM3
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 810036
DO 10.1101/810036
A1 John T. Sauls
A1 Jeremy W. Schroeder
A1 Steven D. Brown
A1 Guillaume Le Treut
A1 Fangwei Si
A1 Dongyang Li
A1 Jue D. Wang
A1 Suckjoon Jun
YR 2019
UL http://biorxiv.org/content/early/2019/10/18/810036.abstract
AB 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.