WormLib documentation

WormLib is a modular open-source image analysis library for quantifying microscopy images of Caenorhabditis elegans embryos. It provides an end-to-end pipeline from image loading, embryo segmentation, cell identity prediction, single-molecule FISH (smFISH) spot detection, and spatial mRNA analysis.

BASICS:

• Installation
  • Quick Install with Conda
  • Core Dependencies
  • Troubleshooting
  • Next Steps
• Input
  • Supported Image Formats
  • File Organization Best Practice
  • Loading Images in Code
• Configuration (YAML Settings)
  • Configuration Structure
  • Input Section
  • Microscope Section
  • Channels Section
  • Segmentation Section
  • Pipeline Section
  • Example Configs
  • Using Configuration Files
  • Next Steps
• Output Files and Results Structure
  • Output Directory Structure
  • Visualization Outputs (PNG)
  • Quantification Outputs (CSV)
  • PDF Report
  • Interpreting Results
  • Troubleshooting Output Issues
  • Next Steps
• Pre-Trained Models
  • Cell Classification Models (Random Forest)
  • Cellpose Segmentation Model
  • Using Models in Code
  • Disabling Classification
  • Model Limitations and Best Practices
  • Training Custom Models
  • Citation
  • Next Steps