High-throughput live imaging of microcolonies to measure heterogeneity in growth and gene expression

Federica M.O. Sartori, Cassandra Buzby, Yevgeniy Plavskin, Mark L. Siegal

Research output: Contribution to journalArticlepeer-review


Precise measurements of between-and within-strain heterogeneity in microbial growth rates are essential for understanding genetic and environmental inputs into stress tolerance, pathogenicity, and other key components of fitness. This manuscript describes a microscope-based assay that tracks approximately 105 Saccharomyces cerevisiae microcolonies per experiment. After automated time-lapse imaging of yeast immobilized in a multiwell plate, microcolony growth rates are easily analyzed with custom image-analysis software. For each microcolony, expression and localization of fluorescent proteins and survival of acute stress can also be monitored. This assay allows precise estimation of strains' average growth rates, as well as comprehensive measurement of heterogeneity in growth, gene expression, and stress tolerance within clonal populations.

Original languageEnglish (US)
Article numbere62038
JournalJournal of Visualized Experiments
Issue number170
StatePublished - Apr 2021

ASJC Scopus subject areas

  • General Neuroscience
  • General Chemical Engineering
  • General Biochemistry, Genetics and Molecular Biology
  • General Immunology and Microbiology


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