Colony Size Characterization and Quantification
Keio wild-type and ∆ybeX strains were grown overnight in LB or
defined MOPS minimal media (Neidhardt et al. , 1974). Well-grown
bacterial cell cultures were serially diluted and plated on LB agar
plates using glass beads (Hecht Assistent, #41401004). We aimed to have
approximately 100-125 colonies per plate. The plates were incubated
overnight at 37°C or 42°C and scanned using EPSON Expression 1680pro
scanner. The images were subjected to AutoCellSeg software (Khanet al. , 2018). The colonies were first picked automatically using
program default settings, and then, as a second step, manual picking was
applied (picking small colonies, deselecting adherent colonies, etc.).
The data were analysed in the R::tidyverse package (Wickham et
al. , 2019; R Core Team, 2022).