OmniSegger: A time-lapse image analysis pipeline for bacterial cells

Time-lapse microscopy is a powerful tool to study the biology of bacterial cells. The development of pipelines that facilitate the automated analysis of these datasets is a long-standing goal of the field. In this paper, we describe the OmniSegger pipeline developed as an open-source, modular, and holistic suite of algorithms whose input is raw microscopy images and whose output is a wide range of quantitative cellular analyses, including dynamical cell cytometry data and cellular visualizations. The updated version described in this paper introduces two principal refinements: (i) robustness to cell morphologies and (ii) support for a range of common imaging modalities. To demonstrate robustness to cell morphology, we present an analysis of the proliferation dynamics of Escherchia coli treated with a drug that induces filamentation. To demonstrate extended support for new image modalities, we analyze cells imaged by five distinct modalities: phase-contrast, two brightfield modalities, and cytoplasmic and membrane fluorescence. Together, this pipeline should greatly increase the scope of tractable analyses for bacterial microscopists.