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We present a high-throughput method to measure abundance dynamics in microbial communities sustained in continuous-culture. Our method uses custom epi-fluorescence microscopes to automatically image single cells drawn from a continuously-cultured population while precisely controlling culture conditions. For clonal populations of  Escherichia coli  our instrument reveals history-dependent resilience and growth rate dependent aggregation.

Quantitative high-throughput population dynamics in continuous-culture by automated microscopy