Image analysis for microbial cultures growing on solid agar surfaces
Image analysis software for estimating cell density in arrayed microbial cultures growing on solid agar. This module contains a set of functions for spot location, image segmentation and spot size estimation, suitable for quantifying culture size/cell density for libraries of microbial cultures growing on a solid agar surface.
There are also a set of console scripts available for specific analysis jobs. For example, after installation, executing:
on the commandline, will run a script to analyse a batch of timecourse images of microbial colonies growing up over time. Detailed documentation can be found at the website below:
Website describing current, stable release.
Open access manuscript describing Colonyzer algorithms:
Open access video and manuscript demonstrating the use of Colonyzer within a Quantitative Fitness Analysis workflow