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bioRxiv · 10.1101/2024.11.25.625259

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

Lo, T. W.·Cutler, K. J.·Choi, H. J.·Wiggins, P. A.
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Abstract

Time-lapse microscopy is a powerful tool for studying the cell 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 OmniSegger, an updated version of our SuperSegger 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 Escherichia 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.

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Lo, T. W., Cutler, K. J., Choi, H. J., Wiggins, P. A.. 2024-11-28. OmniSegger: A time-lapse image analysis pipeline for bacterial cells. https://doi.org/10.1101/2024.11.25.625259

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