API Reference

This section contains automatically generated documentation for the photon-mosaic-pipeline package.

Modules

photon_mosaic_pipeline.cli	Command line interface for photon-mosaic-pipeline.
photon_mosaic_pipeline.logging_config	Logging configuration for photon-mosaic-pipeline with formatting and colors.
photon_mosaic_pipeline.paths_selection
photon_mosaic_pipeline.preprocessing.contrast	Contrast enhancement preprocessing step.
photon_mosaic_pipeline.preprocessing.derotation	Derotation preprocessing step for photon-mosaic-pipeline.
photon_mosaic_pipeline.preprocessing.noop	No-operation preprocessing step using symlinks.
photon_mosaic_pipeline.preprocessing.stiminterpolation	Photonstimulation artefact removal step for photon-mosaic-pipeline.
photon_mosaic_pipeline.rules.preprocessing	Snakemake rule for preprocessing image data.
photon_mosaic_pipeline.rules.suite2p_run	Snakemake rule for running Suite2P.
photon_mosaic_pipeline.snakemake_utils	Snakemake utility functions for photon-mosaic-pipeline.