ArticlePLoS computational biology2025
OmniSegger: A time-lapse image analysis pipeline for bacterial cells.
Article in PLoS computational biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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4 citing papers in PubMed.
- Partaker: deep-learning-based single-cell-resolution analysis of multi-dimensional, long-term, microfluidic-based time-lapse microscopy data.Bioinformatics (Oxford, England) · 2026Article
- The transcription factor Vca0578 (DsvR) mediated expression of ZapC is required to promote cell division during lytic transglycosylase insufficiency inbioRxiv : the preprint server for biology · 2026Article
- Protein overabundance is driven by growth robustness.Science advances · 2026Article
- mAIcrobe: an open-source framework for high-throughput bacterial image analysis.Communications AI & computing · 2026Article
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4 authors.
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Abstract
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.
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