emskills-mcp scalebar-calibrate
Scope
Calibrates magnification and pixel size against certified cross-grating standards, producing a drift-corrected calibration record suitable for audit trails.
Expects standard SEM 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 calibration stage of the workflow.
Safety
Read-only — no instrument control. The skill reads data from disk and returns results; it never moves the stage, changes dose, or alters column settings.
Usage
{
"tool": "calibrate_scale",
"arguments": {
"input": "/data/sem/session-001",
"output": "/data/sem/session-001/calibrate_scale"
}
}
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: node 20. Pin dependencies in requirements.txt / package.json
and run with a fixed seed. Reviewers can reproduce the reported numbers with:
cd skills/scalebar-calibrate
npm install && node verify.js --fixture fixtures/sample --seed 0