PyCLM Documentation

PyCLM is a python-based closed-loop microscopy software designed for running many dynamic and/or feedback-controlled optogenetic experiments simultaneously.

Contents:

• First-Time Setup Guide
  • 1. Install PyCLM
  • 2. Configure MicroManager
  • 3. Create pyclm_config.toml
  • 4. Choose or Implement a PositionMover
  • 5. Export a Position List from MicroManager
  • 6. Write Experiment TOML Files
  • 7. Write schedule.toml
  • 8. Experiment Directory Layout
  • 9. Run the Experiment
  • 10. Custom Pattern and Segmentation Methods
• Usage
  • 1. Designing a multi-experiment
  • 2. Running a multi-experiment
  • 3. Analyzing a completed multi-experiment
• Experiment TOMLs
• Writing Custom Pattern Methods
  • Overview
  • Example 1 — static (open-loop) pattern
  • Example 2 — feedback-controller (closed-loop)
  • Base class API
• Method Zoo
  • Stimulation / Pattern Methods
• Pattern Method API Reference
  • Base Classes
  • Embryo Axis Patterns
  • Bar Patterns
  • Intensity Control Patterns
  • Wave Patterns
  • Static Patterns
  • Feedback Control Patterns