Stem Drift Lock

stem-drift-lock

Scope

Estimates specimen drift between scan frames and issues stage/scan-shift corrections, keeping atomic-resolution STEM acquisitions locked over multi-hour sessions.

Expects standard STEM data products (image stacks, spectra or session directories as appropriate) with pixel size / dispersion recorded in the file metadata. Out of scope: acquisition scheduling, sample preparation, and any analysis outside the alignment & drift stage of the workflow.

Safety

Issues stage and scan-shift corrections to the microscope. Limit corrections to the configured maximum step; abort on tracking loss rather than driving the stage blind.

Usage

{
  "tool": "lock_drift",
  "arguments": {
    "input": "/data/stem/session-001",
    "output": "/data/stem/session-001/lock_drift"
  }
}

Returns a JSON object with ok, a result payload carrying the primary measurement or map, and diagnostics with per-item confidence. Units are SI unless stated otherwise in the result schema.

Reproducibility

Runtime: python 3.11. Pin dependencies in requirements.txt / package.json and run with a fixed seed. Reviewers can reproduce the reported numbers with:

cd skills/stem-drift-lock
pip install -r requirements.txt && python3 verify.py --fixture fixtures/sample --seed 0