title: Spotsizer: High-throughput quantitative analysis of microbial growth.
abstract: Microbial colony growth can serve as a useful readout in assays for studying complex genetic interactions or the effects of chemical compounds. Although computational tools for acquiring quantitative measurements of microbial colonies have been developed, their utility can be compromised by inflexible input image requirements, non-trivial installation procedures, or complicated operation. Here, we present the Spotsizer software tool for automated colony size measurements in images of robotically arrayed microbial colonies. Spotsizer features a convenient graphical user interface (GUI), has both single-image and batch-processing capabilities, and works with multiple input image formats and different colony grid types. We demonstrate how Spotsizer can be used for high-throughput quantitative analysis of fission yeast growth. The user-friendly Spotsizer tool provides rapid, accurate, and robust quantitative analyses of microbial growth in a high-throughput format. Spotsizer is freely available at https://data.csiro.au/dap/landingpage?pid=csiro:15330 under a proprietary CSIRO license.
authors.affiliation: CSIRO Digital Productivity, North Ryde, Australia.
authors.forename: Leanne
authors.initials: L
authors.lastname: Bischof
authors.affiliation: Department of Cell Biology, Charles University in Prague, Faculty of Science, Prague, Czech Republic.|Department of Genetics, Evolution and Environment and Institute of Healthy Ageing, University College London, London, UK.
authors.forename: Martin
authors.initials: M
authors.lastname: Převorovský
authors.affiliation: Department of Genetics, Evolution and Environment and Institute of Healthy Ageing, University College London, London, UK.
authors.forename: Charalampos
authors.initials: C
authors.lastname: Rallis
authors.affiliation: Department of Genetics, Evolution and Environment and Institute of Healthy Ageing, University College London, London, UK.
authors.forename: Daniel C
authors.initials: DC
authors.lastname: Jeffares
authors.affiliation: CSIRO Digital Productivity, North Ryde, Australia.
authors.forename: Yulia
authors.initials: Y
authors.lastname: Arzhaeva
authors.affiliation: Department of Genetics, Evolution and Environment and Institute of Healthy Ageing, University College London, London, UK.
authors.forename: Jürg
authors.initials: J
authors.lastname: Bähler
mesh_terms: D000465:Algorithms; D057166:High-Throughput Screening Assays / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D012568:Schizosaccharomyces / Q000254:growth & development*; D012984:Software
keywords: bacteria; colony array; large-scale screen; microorganism; synthetic genetic array; yeast