theatRICS

theatRICS is a GUI application for quantitative fluorescence microscopy analysis, integrating multiple workflows into a single interface.

Documentation

• Installation
  • Requirements
  • Install from PyPI
  • Install from source
  • Core Python dependencies
  • Optional dependencies by workflow
  • Example dependency installation
  • Virtual environment (recommended)
  • Tkinter notes
  • CZI support
  • Optional notes by workflow
  • Install documentation dependencies
  • Verify the installation
  • Common installation issues
  • Recommended workflow after installation
• Quickstart
  • Start the program
  • Workflow 1: RICS analysis from image stacks
  • Workflow 2: SFCS analysis
  • Workflow 3: FCS fitting from exported CSV curves
  • Workflow 4: FRAP analysis
  • Workflow 5: Simulated data generation
  • Workflow 6: Diffusion map generation
  • Workflow 6: ICS analysis
  • Workflow 7: AFM condensate analysis
  • Workflow 8: Vesicle / GUV detection and membrane analysis
  • Monitoring progress
  • Saving and exporting
  • Suggested starting points
• Modular Launcher
  • The launcher window
  • Multiple windows
  • One instance per category
  • Closing
  • Lazy imports
• GUI overview
  • General interface features
  • Image Simulation
  • RICS Export
  • RICS Fitting
  • SFCS
  • FCS Export
  • FCS Fitting
  • FRAP
  • ICS
  • AFM
  • Vesicle Finder
  • Results & Logs
  • Notes on responsiveness and background processing
  • Typical analysis routes
• Workflow: RICS export
  • Purpose
  • Steps
  • Output
• Workflow: RICS fitting
  • Purpose
  • Inputs
  • Steps (single file)
  • Batch mode
  • Outputs
• Workflow: pSFCS (perpendicular scanning FCS)
  • Purpose
  • Steps
  • Outputs
• Workflow: FCS fitting
  • Input data format
  • Single-file fitting
  • Batch fitting
  • Models
  • Initial parameters (model-dependent)
  • Calibration parameters (Given D)
  • Display and exported outputs
  • Troubleshooting
• Workflow: FRAP analysis
  • Overview
  • Input requirements
  • Single-file analysis
  • Batch analysis
  • Model
  • Control normalisation
  • Automatic detection steps
  • Display panels
  • Parameters in the GUI
  • Output files
  • Batch summary
  • Fit outputs and interpretation
  • Warnings
  • Troubleshooting
• Workflow: ICS (Image Correlation Spectroscopy)
  • Overview
  • Input requirements
  • Single-file analysis
  • Batch analysis
  • Parameters
  • ICS computation
  • Normalisation
  • Display
  • Outputs
  • Interpretation
  • Troubleshooting
• Workflow: AFM profile analysis
  • Overview
  • Input requirements
  • Loading a file
  • Drawing a line profile
  • Profile parameters
  • Display panels
  • Profile list
  • Wetting angle computation
  • Measurements
  • Actions
  • Outputs
  • Typical use
  • Troubleshooting
• Workflow: Vesicle Finder
  • Overview
  • Input requirements
  • Detection methods
  • Parameters
  • Unit conversion
  • Detection phase
  • Selection
  • Cropping phase
  • Membrane straightening
  • Debug images
  • Troubleshooting
• Workflow: Diffusion map
  • Purpose
  • Steps
  • Outputs
• Outputs
  • General output behavior
  • Image Simulation outputs
  • RICS Export outputs
  • RICS Fitting outputs
  • Diffusion map outputs
  • SFCS outputs
  • FCS Fitting outputs
  • FRAP outputs
  • ICS outputs
  • AFM outputs
  • Logs and session files
  • Vesicle Finder outputs
  • Notes on file placement
  • Reproducibility
• Troubleshooting
  • Installation and startup
  • RICS export and fitting
  • SFCS
  • FCS fitting
  • FRAP analysis
  • Vesicle Finder
  • ICS
  • AFM
  • GUI responsiveness and background tasks
  • Session and export issues
  • If problems continue
• API reference
  • Workers
  • Utilities