MotilA documentation

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

MotilA’s segmentation and microglial turnover rate assessment. This animation illustrates the structural changes that MotilA detects and quantifies. The left panel shows one representative Z-slice per time point after MotilA’s internal preprocessing steps. The right panel shows the corresponding \(\Delta B\) classification maps, which are computed as difference images between two consecutive time points \(t_i\) and \(t_{i+1}\).

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.