Fib Mill Seg

fib-mill-seg

Scope

Segments the mill volume from live FIB imagery and plans a lift-out path for serial-sectioning workflows, including lamella thickness targets and redeposition avoidance.

Expects standard FIB 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 segmentation stage of the workflow.

Safety

Plans ion-beam milling paths. Milling and stage moves are destructive; this skill only emits a plan — a human must confirm before any FIB current is applied.

Usage

{
  "tool": "plan_liftout",
  "arguments": {
    "input": "/data/fib/session-001",
    "output": "/data/fib/session-001/plan_liftout"
  }
}

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/fib-mill-seg
pip install -r requirements.txt && python3 verify.py --fixture fixtures/sample --seed 0