Module Map

This page tracks the currently implemented module surface and runtime role.

Core Orchestration

Area

Primary modules

Current role

Entrypoint

clearex.main

GUI/headless launch, ingestion + analysis orchestration, OME output publication, and provenance persistence.

Shared runtime schema

clearex.workflow

Typed workflow config, operation parameter normalization, execution sequence resolution, and logical input-source mapping.

GUI

clearex.gui.app, clearex.gui.spacing

Setup dialog, backend / OME-Zarr settings dialogs, analysis selection, parameter collection, and workflow progress UI.

CLI and logging

clearex.io.cli, clearex.io.log

Command-line parser, migration entrypoints, and runtime logger setup.

Data and Metadata

Area

Primary modules

Current role

Experiment ingestion

clearex.io.experiment

Navigate experiment parsing, source discovery, canonical OME-Zarr materialization, runtime-cache generation, and completion checks.

OME store helpers

clearex.io.ome_store

OME-Zarr path helpers, namespaced metadata helpers, public HCS publication, and legacy-store migration.

Provenance

clearex.io.provenance

Append-only run records, latest-output references, history summaries, and hash-chain verification.

Data reading

clearex.io.read

Reader abstraction used for metadata loading and non-Navigate inputs, with OME-aware array selection.

Analysis Modules

The following operations are wired into clearex.main:

Operation

Primary module

Runtime status

Flatfield correction

clearex.flatfield.pipeline

Integrated and executable; writes runtime-cache image outputs and publishes public OME results.

Deconvolution

clearex.deconvolution.pipeline

Integrated and executable with OME-Zarr runtime inputs and public OME output publication.

Shear transform

clearex.shear.pipeline

Integrated and executable with runtime-cache output publication.

Registration

clearex.registration.pipeline

Integrated and executable; writes affine transform/layout metadata and optional deformable lattice metadata under clearex/results/registration/latest for downstream fusion.

Fusion

clearex.registration.pipeline

Integrated and executable; consumes the latest registration result, applies affine-only or affine-plus-deformable sampling as available, writes stitched runtime-cache outputs, and publishes public OME fusion results.

uSegment3D

clearex.usegment3d.pipeline

Integrated and executable with runtime-cache image outputs and public OME publication.

Particle detection

clearex.detect.pipeline

Integrated and executable; writes metadata/table outputs under clearex/results.

Display pyramid / visualization / movie rendering

clearex.visualization.pipeline, clearex.visualization.export

Integrated and executable; prepares internal display pyramids, launches napari, captures keyframes, renders offline movie frame sets, and compiles MP4 / ProRes deliverables.

MIP export

clearex.mip_export.pipeline

Integrated and executable; exports OME-TIFF or standalone OME-Zarr files outside the store and records metadata in clearex/results.

Supporting Algorithm Packages

ClearEx also includes reusable lower-level modules used by analysis routines:

  • clearex.filter

  • clearex.fit

  • clearex.preprocess

  • clearex.segmentation

  • clearex.stats

  • clearex.file_operations

  • clearex.context

  • clearex.plot

These modules are available for internal reuse and future analysis expansion, even when they are not direct top-level workflow steps.