ClearEx Documentation

ClearEx is a Python package for scalable analytics of cleared and expanded tissue imaging data.

Documentation

• Getting Started
  • Installation
  • Running ClearEx
  • Documentation Build
• Runtime Architecture
  • Architecture Overview
  • Module Map
  • CLI and Execution Modes
  • Dask Backends
  • Ingestion and Canonical Store
  • Provenance and Reproducibility
• Workflows
  • OME-Zarr Materialization and Migration Workflow
  • Analysis Workflow: Particle Detection (OME-Zarr + Dask)
  • Analysis Workflow: Volume Export
• API Reference
  • Core Runtime
  • I/O, Experiment, and Provenance
  • Analysis Modules
  • Visualization and GUI
  • Utilities
• Development Notes
  • Documentation Workflow
  • API Docs Generation
  • Useful Commands