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Project overview

OpticStream provides Prefect-based workflows and utilities for processing large microscopy and imaging datasets, including LSM strips and PS-OCT tiles.

At a high level, OpticStream is organized into:

  • configuration models and Prefect Blocks under opticstream.config
  • Prefect flows for LSM and PS-OCT processing under opticstream.flows
  • command-line interface for deploying and operating flows under opticstream.cli
  • PostgreSQL-backed project state services under opticstream.state
  • event constants and trigger helpers under opticstream.events
  • shared upload/archive tasks under opticstream.tasks
  • flow artifact publishing hooks under opticstream.artifacts
  • lower-level stitching and grid utilities under opticstream.data_processing
  • shared helper utilities under opticstream.utils
  • standalone utility scripts under opticstream.scripts

For a package-level view of the code structure, see the developer architecture page. For a deep dive into the OCT processing design and trade-offs, see the detailed design document.