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

Area of Science:

• Microbiology
• Cell Biology
• Bioimaging

Background:

• Time-lapse microscopy is crucial for bacterial cell biology research.
• Automated analysis pipelines are needed for efficient processing of microscopy data.

Purpose of the Study:

• To introduce OmniSegger, an enhanced open-source pipeline for automated bacterial cell analysis.
• To improve robustness to diverse cell morphologies and expand support for various imaging modalities.

Main Methods:

• OmniSegger processes raw microscopy images to generate quantitative cellular analyses.
• The pipeline was tested on *Escherichia coli* undergoing filamentation induced by a drug.
• Analysis included five imaging modalities: phase-contrast, two brightfield, and fluorescence (cytoplasmic and membrane).

Main Results:

• OmniSegger demonstrated robustness in analyzing bacterial proliferation dynamics with altered cell morphologies.
• The pipeline successfully processed data from multiple imaging modalities, including fluorescence microscopy.
• Quantitative cellular data and visualizations were generated, showcasing the pipeline's capabilities.

Conclusions:

• OmniSegger significantly expands the scope of tractable analyses for bacterial microscopists.
• The pipeline's modularity and enhanced features facilitate deeper insights into bacterial cell behavior.
• This tool supports a wider range of research questions in bacterial cell biology.