BACteria in Mother Machine Analyzer (BACMMAN) Tutorials

A series of open licensed tutorials by Dr Daniel Thedie on how to use the BACMMAN software. BACteria in Mother Machine Analyzer (BACMMAN) is a software allowing fast and reliable automated image analysis of high-throughput 2D/3D time-series images from mother machine. Mother machine is a very popular microfluidic device allowing investigating biological processes in bacteria at the single-cell level.

Dr Daniel Thedie is part of the El Karoui Lab at The University of Edinburgh.

About the El Karoui Lab

A population of cells growing in identical environments can display substantial phenotypic heterogeneity between individuals. It has been shown that even genetically identical cells behave differently because many central processes involve molecules present in small numbers. The inherent randomness of chemical reactions in these concentration regimes generates spontaneous fluctuations that can enslave all dependent processes.

Some key proteins involved in DNA repair, replication control and cell division in bacteria are present at low levels and are therefore likely subject to significant fluctuations. While fluctuations in gene expression are transient by nature, cell to cell variability in central DNA metabolism might have a direct impact on the evolution of microbes. Indeed, fluctuations in DNA repair mechanisms can modify mutation rates, acting as a generating force of genetic diversity. Work in the El Karoui laboratory aims to explore the contribution of molecular stochasticity to genetic variability in bacteria. We combine single molecule microscopy, microfluidics, genetics and modeling to address this question. We expect that connecting phenotypic variability caused by the stochastic nature of chemical reactions with genetic variability will shed new light on the dynamics of bacterial genomes evolution.

Video Tutorials

Using selections to visualise objects

Click here to view ‘Using selections to visualise objects’ directly on Media Hopper Create 


How to visualise and edit segmentation results

Click here to view ‘How to visualise and edit segmentation results’ 


Add an object to a segmentation mask

Click here to view ‘Add an object to a segmentation mask’ directly on Media Hopper Create 



Header Image: Screenshot from tutorial ‘Add an object to a segmentation mask