Skip to content

LSM strip processing workflow

This guide describes the end-to-end workflow for processing LSM strips using the process_strip_flow and related tasks in opticstream.flows.lsm.strip_process_flow.

At a high level, the flow:

  1. Parses slice / strip / camera IDs from the strip folder name.
  2. Resolves output, archive, and resource settings from an LSMScanConfig block.
  3. Optionally compresses the strip to Zarr, generates MIP images, and backs up the raw strip to an archive location.
  4. Performs basic validation checks before optionally renaming or deleting the original strip.

See the configuration and deployment guides for how to wire this into your Prefect environment.

Watching for new strip folders

Use the LSM watcher on a machine that can see the acquisition directory where the instrument writes new strip folders (immediate children whose names start with Run, case-insensitive).

  1. Ensure an LSMScanConfig block exists for the project (same naming convention as elsewhere in OpticStream).
  2. Run:

bash opticstream lsm watch PROJECT_NAME --watch-dir /path/to/parent

Common options: --stability-seconds (how long a folder must be unchanged before processing), --poll-interval (polling fallback if filesystem events are missed), --force-resend (emit even if strip state already exists).

The watcher waits until each new folder is stable, then emits STRIP_READY for Prefect and ensures strip state exists.

For design intent (pipeline stages, state gate, LSM vs OCT patterns), see Acquisition watchers (design layer). For implementation detail (modules, logging, scripts), see LSM and OCT acquisition watchers (design).