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Semi-automated colony-forming unit counting for biosafety level 3 laboratories. 2023

Soorya Janakiraman, and Sophie Engels, and Pariksheet Nanda, and Maral Budak, and Talia Greenstein, and Mariana Pereira Moraes, and Bree B Aldridge, and Denise E Kirschner
Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.

Biosafety level 3 decontamination precautions motivate measuring microbial colonies using consumable photography instead of expensive automated plate counters or smartphones, and assaying drug treatments-with multiple concentrations per treatment, replicates, and controls-produces hundreds of images. Here, we present a protocol for semi-automated image analysis by hand-tuning three parameters. The parameters control for non-uniform colony growth and artifacts such as lid condensation, reflections, and plating streaks. We describe steps to prepare images, tune parameters, and plot dose-response relationships. For complete details on the use and execution of this protocol, please refer to Larkins-Ford et al.1.

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