SOFI

SOFI simulates and analyzes super-resolution optical fluctuation imaging (SOFI) data to evaluate microscope and sample parameters, perform high-order cross-cumulant reconstruction across all three spatial dimensions, and compare simulated outputs with experimental data.

Key Features:

• High-order cross-cumulant analysis: Employs high-order cross-cumulant analysis to reconstruct super-resolution images from SOFI image sequences across all three spatial dimensions.
• Integration with STORM algorithms: Incorporates algorithms from stochastic optical reconstruction microscopy (STORM) to extend reconstruction and analysis capabilities.
• Simulation of microscope and sample parameters: Simulates SOFI images by integrating technical parameters of the microscope setup and intrinsic properties of biological samples for realistic condition modeling.
• Parameter optimization in silico: Enables rapid testing of imaging and analysis parameters within the simulation environment to assess their effects on reconstructed images.
• Performance validation against experimental data: Compares simulated results with experimentally acquired data to validate simulation realism and reconstruction outcomes.

Scientific Applications:

• Sub-diffraction fluorescence microscopy optimization: Supports planning and optimization of sub-diffraction fluorescence microscopy experiments by evaluating parameter impacts on SOFI reconstructions.
• Live-cell imaging studies: Enables assessment of imaging conditions for studies involving living cells to visualize cellular structures beyond the diffraction limit.
• Imaging protocol refinement: Facilitates refinement of imaging protocols and parameter selection through in silico simulation of experimental conditions.

Methodology:

Simulates SOFI image sequences by combining microscope technical parameters and intrinsic sample properties; applies high-order cross-cumulant analysis (including three-dimensional reconstruction), can incorporate STORM algorithms, and compares simulated outputs with experimentally acquired data.