Usage ===== This section documents the practical, script-based usage model of ``spectral-unmixing``. The package is designed to be driven from project-specific Python scripts that can be executed cell by cell in the VS Code interactive window or a similar notebook-like environment. The reusable package functions live in ``spectral_unmixing/``, while the repository's ``user_scripts/`` folder shows how these functions are combined for real workflows. .. toctree:: :maxdepth: 2 usage_example_datasets usage_functionality_overview usage_unmix_example usage_unmix_full_tzcyx_synthetic_example usage_unmix_bidirectional_example usage_unmix_picasso_2color_example usage_unmix_picasso_3color_example usage_unmix_picasso_5color_example usage_filter_and_register_stack How to read the tutorials ------------------------- Each tutorial page is based on one interactive script from the repository's ``user_scripts/`` folder. The documentation follows the script cell by cell and explains: - what each cell does, - which parameters matter most, - what a user can modify for a new dataset, - and how those changes affect the unmixing result. Recommended starting point -------------------------- If you are new to the package, start in this order: 1. :doc:`usage_unmix_example` 2. :doc:`usage_unmix_full_tzcyx_synthetic_example` 3. :doc:`usage_filter_and_register_stack` 4. :doc:`usage_unmix_bidirectional_example` 5. the PICASSO-family blind-unmixing tutorials The standard two-channel tutorial introduces the core package logic with the least complexity. The ``TZCYX`` tutorial then shows the same logic on full time-lapse z-stacks. The helper tutorial then shows how filtering, registration, histogram matching, and projection can be chained after unmixing. The bidirectional tutorial adds a more advanced alpha-estimation strategy for cases where the cross-talk is not strictly unidirectional. The PICASSO tutorials build on the same ideas but add blind coefficient estimation and multi-channel (more than two) configuration.