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
    • Core pipeline steps
    • Batch processing steps
    • Main functions
  • Installation
  • Example dataset and tutorials
    • Running the example scripts and notebooks
  • License
  • Citation
  • Acknowledgments and contact
• Data prerequisites and project structure
  • Image file formats and 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
    • Single-file processing
    • Batch processing
    • Batch collection
  • Assessing your results
  • Summary
• Parameters overview
  • Input/output parameters for single-file processing
    • Input paths
    • Results output settings
  • Input/output parameters for batch processing
    • Expected project folder structure
    • Metadata override file (metadata.xls)
  • General processing settings
    • Projection settings
    • Thresholding settings
    • Image enhancement settings
    • Filter settings
    • Channel settings
    • Registration settings
    • Spectral unmixing settings
    • Debug settings
  • Input/output parameters for batch collection
• API reference
  • Core functions
    • batch_collect()
    • batch_process_stacks()
    • process_stack()
  • Additional functions
    • hello_world()
    • read_image_stack()
    • write_image_stack()
    • calc_projection_range()
    • plot_2D_image()
    • plot_2D_image_as_tif()
    • plot_histogram()
    • plot_histogram_of_projections()
    • plot_projected_stack()
    • plot_projected_stack_as_tif()
    • get_stack_dimensions()
    • extract_and_register_subvolume()
    • extract_subvolume()
    • spectral_unmix()
    • histogram_equalization()
    • histogram_equalization_on_projections()
    • histogram_matching()
    • histogram_matching_on_projections()
    • median_filtering_on_projections()
    • circular_median_filtering_on_projections()
    • single_slice_median_filtering()
    • single_slice_circular_median_filtering()
    • gaussian_blurr_filtering_on_projections()
    • single_slice_gaussian_blurr_filtering()
    • z_max_project()
    • compare_histograms()
    • plot_intensities()
    • reg_2D_images()
    • binarize_2D_images()
    • remove_small_blobs()
    • plot_pixel_areas()
    • motility()
  • Utility functions
    • MotilA Utilities Module
    • calc_process_time_logger()
    • check_folder_exist_create()
    • filterfiles_by_string()
    • filterfolder_by_string()
    • getfile()
    • hello_world_utils()
    • logger_object
    • print_ram_usage()
    • print_ram_usage_in_loop()
    • tiff_axes_check_and_correct()
• What’s new?
  • MotilA Changelog
    • 🚀 MotilA v1.1.3
    • 🚀 MotilA v1.1.2
    • 🚀 MotilA v1.1.1
    • 🚀 MotilA v1.1.0 Release notes
    • 🚀 MotilA v1.0.7 Release notes
    • 🚀 MotilA v1.0.6 Release notes
    • 🚀 MotilA v1.0.5 Release notes
    • 🚀 MotilA v1.0.4 Release notes
    • 🚀 MotilA v1.0.3 Release notes
    • 🚀 MotilA v1.0.2 Release notes
    • 🚀 MotilA v1.0.1 - Dummy release
    • 🚀 MotilA v1.0.0 – Initial public release
• 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.