MotilA documentation

MotilA is a Python-based pipeline for microglial fine process motility analysis from 4D and 5D multiphoton imaging data.

This documentation provides:

• an overview of the pipeline and its scientific context,

• installation and basic usage instructions,

• a detailed description of the processing steps and parameters,

• an automatically generated API reference.

Contents:

• Overview
  • What does MotilA do?
  • How is motility determined?
  • Pipeline overview
  • Installation
  • Example dataset and tutorials
  • License
  • Citation
  • Acknowledgments and contact
• Data Prerequisites and Project Structure
  • TIFF file format and image axis order
  • Channel specification
  • Image registration pre-requirements
  • Project folder structure for batch processing
  • Metadata file (metadata.xls – for batch processing only)
  • Summary
• Tutorials and Example Datasets
  • Example dataset
  • Tutorial notebooks
  • Example Python scripts
  • Reproducing manuscript figures
  • Additional example datasets
  • Example usage
  • Assessing your results
  • Summary
• Parameters Overview
  • Input/output parameters for single-file processing
  • Input/output parameters for batch processing
  • General processing settings
  • Input/output parameters for batch collection
• API reference
  • Core functions
  • Additional functions
  • Utility functions
• Contributing and Community Guidelines
  • How to contribute
  • Contribution guidelines
  • Code of Conduct
  • Where to start

MotilA is free and open-source software (FOSS) distributed under the GPL-3.0 license.