TAMMiCol: Tool for analysis of the morphology of microbial colonies

Hayden Tronnolone, Jennifer M. Gardner, Joanna F. Sundstrom, Vladimir Jiranek, Stephen G. Oliver, Benjamin J. Binder

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Many 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.

Original languageEnglish
Article numbere1006629
Number of pages15
JournalPLOS Computational Biology
Volume14
Issue number12
DOIs
Publication statusPublished - 3 Dec 2018

Bibliographical note

© 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.

Keywords

  • colony morphology images
  • binary images
  • software
  • graphical user interface

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  • Cite this

    Tronnolone, H., Gardner, J. M., Sundstrom, J. F., Jiranek, V., Oliver, S. G., & Binder, B. J. (2018). TAMMiCol: Tool for analysis of the morphology of microbial colonies. PLOS Computational Biology, 14(12), [e1006629]. https://doi.org/10.1371/journal.pcbi.1006629