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TAMMiCol: tool for analysis of the morphology of microbial colonies

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dc.contributor.authorTronnolone, H.
dc.contributor.authorGardner, J.
dc.contributor.authorSundstrom, J.
dc.contributor.authorJiranek, V.
dc.contributor.authorOliver, S.
dc.contributor.authorBinder, B.
dc.contributor.editorSchneidman-Duhovny, D.
dc.date.issued2018
dc.description.abstractMany microbes are studied by examining colony morphology via two-dimensional top-down images. The quantification of such images typically requires each pixel to be labelled as belonging to either the colony or background, producing a binary image. While this may be achieved manually for a single colony, this process is infeasible for large datasets containing thousands of images. The software Tool for Analysis of the Morphology of Microbial Colonies (TAMMiCol) has been developed to efficiently and automatically convert colony images to binary. TAMMiCol exploits the structure of the images to choose a thresholding tolerance and produce a binary image of the colony. The images produced are shown to compare favourably with images processed manually, while TAMMiCol is shown to outperform standard segmentation methods. Multiple images may be imported together for batch processing, while the binary data may be exported as a CSV or MATLAB MAT file for quantification, or analysed using statistics built into the software. Using the in-built statistics, it is found that images produced by TAMMiCol yield values close to those computed from binary images processed manually. Analysis of a new large dataset using TAMMiCol shows that colonies of Saccharomyces cerevisiae reach a maximum level of filamentous growth once the concentration of ammonium sulfate is reduced to 200 μM. TAMMiCol is accessed through a graphical user interface, making it easy to use for those without specialist knowledge of image processing, statistical methods or coding.
dc.description.statementofresponsibilityHayden Tronnolone, Jennifer M. Gardner, Joanna F. Sundstrom, Vladimir Jiranek, Stephen G. Oliver, Benjamin J. Binder
dc.identifier.citationPLoS Computational Biology, 2018; 14(12):e1006629-1-e1006629-15
dc.identifier.doi10.1371/journal.pcbi.1006629
dc.identifier.issn1553-734X
dc.identifier.issn1553-7358
dc.identifier.orcidTronnolone, H. [0000-0003-4532-2030]
dc.identifier.orcidGardner, J. [0000-0002-4215-955X]
dc.identifier.orcidSundstrom, J. [0000-0002-4898-3101]
dc.identifier.orcidJiranek, V. [0000-0002-9775-8963]
dc.identifier.orcidBinder, B. [0000-0002-1812-6715]
dc.identifier.urihttp://hdl.handle.net/2440/117863
dc.language.isoen
dc.publisherPLoS - Public Library of Science
dc.relation.granthttp://purl.org/au-research/grants/arc/DP160102644
dc.relation.granthttp://purl.org/au-research/grants/arc/DP130103547
dc.rights© 2018 Tronnolone et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.source.urihttps://doi.org/10.1371/journal.pcbi.1006629
dc.subjectBiofilms
dc.subjectBacillus subtilis
dc.subjectSaccharomyces cerevisiae
dc.subjectAmmonium Sulfate
dc.subjectCulture Media
dc.subjectComputational Biology
dc.subjectImage Processing, Computer-Assisted
dc.subjectSoftware
dc.subjectDatabases, Factual
dc.subjectMicrobiota
dc.titleTAMMiCol: tool for analysis of the morphology of microbial colonies
dc.typeJournal article
pubs.publication-statusPublished

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