API Reference

The API reference is generated from docstrings in src/clearex.

Core Runtime

`clearex.main`
`clearex.workflow`

`clearex.io.cli`
`clearex.io.dask`
`clearex.io.experiment`	Navigate experiment ingestion and 6D Zarr analysis-store utilities.
`clearex.io.log`
`clearex.io.provenance`	Utilities for FAIR-aligned provenance and latest-only outputs in Zarr stores.
`clearex.io.read`

`clearex.deconvolution.petakit`	Typed helpers for running PyPetaKit5D deconvolution wrappers.
`clearex.detect.particles`
`clearex.detect.pipeline`	Chunk-parallel particle-detection workflow on canonical 6D Zarr stores.
`clearex.filter.filters`
`clearex.filter.kernels`
`clearex.fit.points`
`clearex.preprocess.pad`
`clearex.preprocess.scale`
`clearex.registration`	Image registration module.
`clearex.registration.common`
`clearex.registration.linear`
`clearex.registration.nonlinear`
`clearex.registration.tre`
`clearex.segmentation.otsu`
`clearex.segmentation.pointsource`
`clearex.segmentation.regions`
`clearex.segmentation.tubes`
`clearex.stats.intensity`

`clearex.gui.app`
`clearex.visualization.napari`
`clearex.visualization.pipeline`	Napari visualization workflow for canonical ClearEx analysis stores.

`clearex.context.environment`
`clearex.file_operations.dask`
`clearex.file_operations.tools`
`clearex.plot.data`
`clearex.plot.images`