AnalyzER

AnalyzER quantifies endoplasmic reticulum (ER) architecture and dynamics in plant cells from multi-dimensional fluorescence images to enable analysis of ER structure, topology, protein-localization patterns, and responses relevant to protein translocation, folding, glycosylation, quality control, lipid synthesis, calcium signaling, and metabolon formation.

Key Features:

• Automated Extraction: Automated extraction of ER tubules and cisternae from multi-dimensional fluorescence images.
• Quantitative Metrics: Computation of spatial, intensity-based, and graph-theoretic metrics to quantify ER structure, topology, protein-localization patterns, and dynamics.
• Validation and Calibration: Validation against manually-traced ground-truth networks and calibration of sub-resolution width estimates using profiles from serial block-face scanning electron microscopy (SEM) images.
• Application Versatility: Enables comparative analysis of ER morphology under drug treatments, abiotic stress conditions, and genetic modifications including over-expression of proteins that shape tubules or modify cisternae.

Scientific Applications:

• Abiotic stress analysis: Assessing impacts of abiotic and environmental stressors on ER architecture in plant cells.
• Protein function studies: Investigating roles of specific proteins in maintaining ER structure and function.
• Secretory pathway research: Studying mechanisms of protein processing and trafficking within the secretory pathway.

Methodology:

Processes multi-dimensional fluorescence microscopy data with automated extraction of ER tubules and cisternae, computes spatial, intensity-based, and graph-theoretic metrics, validates outputs against manually-traced ground-truth networks, and calibrates sub-resolution width estimates using serial block-face SEM profiles.