ArticleScientific reports2019
MMHelper: An automated framework for the analysis of microscopy images acquired with the mother machine.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Raman imaging for the investigation of Mycobacterium smegmatis in a mother machine.Analytical and bioanalytical chemistry · 2026Article
- Heterogeneous efflux pump expression underpins phenotypic resistance to antimicrobial peptides.eLife · 2025Article
- Article
- Phage-induced efflux down-regulation boosts antibiotic efficacy.PLoS pathogens · 2024Article
- Article
- Microfluidic approaches in microbial ecology.Lab on a chip · 2024Review
- Tools and methods for high-throughput single-cell imaging with the mother machine.bioRxiv : the preprint server for biology · 2024Article
- Quantitative microbiology with widefield microscopy: navigating optical artefacts for accurate interpretations.Npj imaging · 2024Article
- Slow growing bacteria survive bacteriophage in isolation.ISME communications · 2023Article
- Single Cell Killing Kinetics Differentiate Phenotypic Bacterial Responses to Different Antibacterial Classes.Microbiology spectrum · 2023Article
- Article
- Nutrient and salt depletion synergistically boosts glucose metabolism in individual Escherichia coli cells.Communications biology · 2022Article
- LIM Tracker: a software package for cell tracking and analysis with advanced interactivity.Scientific reports · 2022Article
- Microfluidics for long-term single-cell time-lapse microscopy: Advances and applications.Frontiers in bioengineering and biotechnology · 2022Review
- Individual bacteria in structured environments rely on phenotypic resistance to phage.PLoS biology · 2021Article
- Article
- Advances and opportunities in image analysis of bacterial cells and communities.FEMS microbiology reviews · 2021Article
- Challenges of analysing stochastic gene expression in bacteria using single-cell time-lapse experiments.Essays in biochemistry · 2021Article
- ChipSeg: An Automatic Tool to Segment Bacterial and Mammalian Cells Cultured in Microfluidic Devices.ACS omega · 2021Article
- Fluorescent macrolide probes - synthesis and use in evaluation of bacterial resistance.RSC chemical biology · 2020Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Live-cell imaging in microfluidic devices now allows the investigation of cellular heterogeneity within microbial populations. In particular, the mother machine technology developed by Wang et al. has been widely employed to investigate single-cell physiological parameters including gene expression, growth rate, mutagenesis, and response to antibiotics. One of the advantages of the mother machine technology is the ability to generate vast amounts of images; however, the time consuming analysis of these images constitutes a severe bottleneck. Here we overcome this limitation by introducing MMHelper ( https://doi.org/10.5281/zenodo.3254394 ), a publicly available custom software implemented in Python which allows the automated analysis of brightfield or phase contrast, and any associated fluorescence, images of bacteria confined in the mother machine. We show that cell data extracted via MMHelper from tens of thousands of individual cells imaged in brightfield are consistent with results obtained via semi-automated image analysis based on ImageJ. Furthermore, we benchmark our software capability in processing phase contrast images from other laboratories against other publicly available software. We demonstrate that MMHelper has over 90% detection efficiency for brightfield and phase contrast images and provides a new open-source platform for the extraction of single-bacterium data, including cell length, area, and fluorescence intensity.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.