MMHelper: Mother-machine analysis

While co-supervising Dr Ashley Smith during his doctoral candidacy, I oversaw the development of MMHelper¹², a Python-based framework for the automated analysis of Mother-Machine-based microscopy images. The underlying stack of libraries utilised the core scientific Python libraries - Numpy, Scipy, and Matplotlib, together with Scikit-Image for additional image processing functionality, and Pandas for report generation.

An interface was also developed using PyQT to allow users unfamiliar with scripting to run the software.

The MMHelper project has proved to perform very well, and has been used for a variety of research projects and produced numerous publications since it's initial development³⁴⁵.

References

Smith, A., Metz, J., & Pagliara, S. (2019). MMHelper: An automated framework for the analysis of microscopy images acquired with the mother machine. Scientific Reports, 9(1), 10123.

https://github.com/jmetz/mmhelper

Cama, J., Voliotis, M., Metz, J., Smith, A., Iannucci, J., Keyser, U. F., ... & Pagliara, S. (2020). Single-cell microfluidics facilitates the rapid quantification of antibiotic accumulation in Gram-negative bacteria. Lab on a Chip, 20(15), 2765-2775.

⁴

Goode, O., Smith, A., Łapińska, U., Bamford, R., Kahveci, Z., Glover, G., Attrill, E., Carr, A., Metz, J. and Pagliara, S. (2021). Heterologous protein expression favors the formation of protein aggregates in persister and viable but nonculturable bacteria. ACS Infectious Diseases, 7(6), pp.1848-1858.

⁵

Goode, O., Smith, A., Zarkan, A., Cama, J., Invergo, B.M., Belgami, D., Caño-Muñiz, S., Metz, J., O’Neill, P., Jeffries, A. and Norville, I.H., (2021). Persister Escherichia coli cells have a lower intracellular pH than susceptible cells but maintain their pH in response to antibiotic treatment. MBio, 12(4), pp.10-1128.