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High-throughput microcolony growth analysis from suboptimal low-magnification micrographs

By Yevgeniy Plavskin, Shuang Li, Hyun Jung, Federica M. O. Sartori, Cassandra Buzby, Heiko Mueller, Naomi Ziv, Sasha F Levy, Mark L Siegal

Posted 25 Jan 2018
bioRxiv DOI: 10.1101/253724

New technological advances have enabled high-throughput phenotyping at the single-cell level, yet analyzing the large amount of data generated by high throughput phenotyping experiments automatically and accurately is a considerable challenge. Here we introduce Processing Images Easily (PIE), software that automatically tracks growth of microbial colonies in low-magnification brightfield images by combining adaptive object-center recognition with gradient-based object-outline recognition. PIE recognizes colony outlines very robustly and accurately across a wide range of image brightnesses, focal depths, and organisms. Beyond accurate colony recognition, PIE is designed to easily integrate with complex experiments, allowing colony tracking across multiple experimental phases and classification based on fluorescence intensity. We show that PIE can be used to accurately measure the growth rates of large numbers (>90,000) of bacterial or yeast microcolonies in a single-time-lapse experiment, allowing calculation of population-wide growth properties. Finally, PIE is able to track individual colonies across multiple experimental phases, measuring both growth and fluorescence properties of the microcolonies.

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