ChipSeg

ChipSeg segments bacterial and mammalian cells in microfluidic devices from time-lapse microscopy images to quantify single-cell fluorescent protein expression and provide segmentation outputs for external feedback control experiments.

Key Features:

• Thresholding-based segmentation: Uses thresholding techniques to delineate cell boundaries from microscopy images.
• Unified segmentation approach: Applies the same segmentation strategy to both bacterial and mammalian cells.
• Time-lapse image processing: Operates on time-lapse microscopy datasets to enable temporal analyses.
• High cell-density handling: Maintains segmentation performance in high cell-density regions typical of microfluidic devices.
• Fluorescent protein quantification: Extracts per-cell fluorescent protein expression measurements across time points.
• Support for external feedback control: Produces segmentation outputs suitable for informing control algorithms in feedback experiments.
• Customizability for experimental settings: Allows adjustment for different experimental configurations and imaging conditions.

Scientific Applications:

• Single-cell fluorescence dynamics: Quantifies temporal changes in fluorescent protein expression at single-cell resolution.
• External feedback control experiments: Supplies real-time segmentation data to drive control strategies in microfluidic studies.
• Gene expression regulation studies: Enables measurement of expression dynamics relevant to regulatory investigations.
• Cellular response to stimuli: Supports analysis of population and single-cell responses to environmental or experimental perturbations.
• Developmental and temporal process tracking: Facilitates tracking of cellular behaviors and development over time in microfluidic contexts.

Methodology:

Segmentation is performed using thresholding techniques applied to time-lapse microscopy images with a unified approach for bacterial and mammalian cells, including handling of high cell-density regions.