Spotsizer: High-throughput quantitative analysis of microbial growth

Leanne Bischof, Martin Prěvorovský*, Charalampos Rallis, Daniel C. Jeffares, Yulia Arzhaeva, Jürg Bähler

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


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 under a proprietary CSIRO license.

Original languageEnglish
Pages (from-to)191-201
Number of pages11
Issue number4
Publication statusPublished - Oct 2016


  • Bacteria
  • Colony array
  • Large-scale screen
  • Microorganism
  • Synthetic genetic array
  • Yeast

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