MMHelper: An automated framework for the analysis of microscopy images acquired with the mother machine
dc.contributor.author | Smith, A | |
dc.contributor.author | Metz, J | |
dc.contributor.author | Pagliara, S | |
dc.date.accessioned | 2019-11-11T11:37:34Z | |
dc.date.issued | 2019-07-12 | |
dc.description.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. | en_GB |
dc.description.sponsorship | Royal Society | en_GB |
dc.description.sponsorship | Wellcome Trust | en_GB |
dc.description.sponsorship | MRC | en_GB |
dc.description.sponsorship | BBSRC | en_GB |
dc.identifier.citation | Vol. 9, 10123 | en_GB |
dc.identifier.doi | 10.1038/s41598-019-46567-0 | |
dc.identifier.grantnumber | RG180007 | en_GB |
dc.identifier.grantnumber | WT097835/Z/11/Z | en_GB |
dc.identifier.grantnumber | MCPC17189 | en_GB |
dc.identifier.grantnumber | BB/M009122/1 | en_GB |
dc.identifier.grantnumber | WT097835MF | en_GB |
dc.identifier.uri | http://hdl.handle.net/10871/39584 | |
dc.language.iso | en | en_GB |
dc.publisher | Nature Research | en_GB |
dc.rights | Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. | en_GB |
dc.subject | bacterial techniques and applications | en_GB |
dc.subject | biological fluorescence | en_GB |
dc.subject | imaging techniques | en_GB |
dc.subject | lab on a chip | en_GB |
dc.title | MMHelper: An automated framework for the analysis of microscopy images acquired with the mother machine | en_GB |
dc.type | Article | en_GB |
dc.date.available | 2019-11-11T11:37:34Z | |
dc.description | This is the final version. Available from Nature Research via the DOI in this record. | en_GB |
dc.identifier.eissn | 2045-2322 | |
dc.identifier.journal | Scientific Reports | en_GB |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | en_GB |
dcterms.dateAccepted | 2019-06-26 | |
rioxxterms.version | VoR | en_GB |
rioxxterms.licenseref.startdate | 2019-07-12 | |
rioxxterms.type | Journal Article/Review | en_GB |
refterms.dateFCD | 2019-11-11T11:33:31Z | |
refterms.versionFCD | VoR | |
refterms.dateFOA | 2019-11-11T11:37:44Z | |
refterms.panel | A | en_GB |
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Except where otherwise noted, this item's licence is described as Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.