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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
        • Parameter selection
          • Projection parameters
          • Registration parameters
          • Histogram equalization and matching
          • Filtering parameters
          • Spectral unmixing parameters
        • Example parameter values
        • Calling the processing function
      • Batch processing
        • Example batch configuration
      • Batch collection
        • Example batch collection configuration
    • Assessing your results
  • 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
        • Contents:
        • Functions:
        • Classes:
        • Note:
      • calc_process_time_logger()
      • check_folder_exist_create()
      • filterfiles_by_string()
      • filterfolder_by_string()
      • getfile()
      • hello_world_utils()
      • logger_object
        • logger_object.log()
        • logger_object.logc()
        • logger_object.logt()
        • logger_object.stop()
        • logger_object.type()
      • print_ram_usage()
      • print_ram_usage_in_loop()
      • tiff_axes_check_and_correct()
  • What’s new?
    • MotilA Changelog
      • 🚀 MotilA v1.2.0
        • Internal package modularization
        • Development groundwork
        • Flexible BIDS-like batch processing
      • 🚀 MotilA v1.1.3
        • Optional CSV and YAML table exports
        • Documentation and tests
        • Logo
      • 🚀 MotilA v1.1.2
      • 🚀 MotilA v1.1.1
        • Flexible image I/O via OMIO
        • API and batch processing updates
        • Repository path cleanup
        • Tests and documentation
      • 🚀 MotilA v1.1.0 Release notes
        • 🚀 Major improvements: installation, API structure, CI, code coverage, documentation, and roadmap
        • 📚 Full Read the Docs documentation
        • 🔧 API improvements
          • ✔️ Clean top-level API
          • ✔️ Backward compatibility preserved
        • 🧹 Internal code cleanup
        • 🏷️ Citation metadata cleanup
        • 📦 Installation & environment handling
          • ✔️ Modernized installation instructions
          • ✔️ Example scripts updated
        • 📂 Example dataset externalization
        • 🧪 CI workflow modernization
        • 📊 Test coverage integration
        • 🧭 Contribution and community guidelines
        • 🗺️ Roadmap implementation
        • 🧹 Additional documentation refinements
        • Summary
      • 🚀 MotilA v1.0.7 Release notes
        • 🐞 Critical bugfix: PyStackReg support in batch processing
          • 🚨 Critical bug fixed
          • 🐞 Minor bug fixed
          • Technical details
      • 🚀 MotilA v1.0.6 Release notes
        • 🐞 Bugfix: skip processing for invalid projection ranges
          • Bug fixed
          • Technical details
      • 🚀 MotilA v1.0.5 Release notes
        • 🐞 Bugfix: projection range and layer count consistency
          • Bug fixed
          • Technical details
      • 🚀 MotilA v1.0.4 Release notes
        • 🐞 Bugfix & 🚀 New feature: registration improvements
          • 🐞 Bug fixes
          • 🚀 New features
        • Parameter updates
      • 🚀 MotilA v1.0.3 Release notes
        • 🐞 Bugfix: Zarr v3+ compatibility
          • Highlights
      • 🚀 MotilA v1.0.2 Release notes
        • 🐞 Bugfix & improvement: projection range calculation
          • Highlights
          • Bug fixed
          • Other
      • 🚀 MotilA v1.0.1 - Dummy release
      • 🚀 MotilA v1.0.0 – Initial public release
        • ✨ Features
        • 📦 Dataset and tutorials
  • Contributing and community guidelines
    • How to contribute
    • Contribution guidelines
    • Code of Conduct
    • Where to start
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