emskills-mcp ctf-fitter
Scope
Per-tilt contrast transfer function estimation and refinement for TEM diffraction patterns. Handles amorphous-carbon reference subtraction, astigmatism fitting, and defocus drift across a tilt series.
Expects standard TEM 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": "fit_ctf",
"arguments": {
"input": "/data/tem/session-001",
"output": "/data/tem/session-001/fit_ctf"
}
}
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/ctf-fitter
pip install -r requirements.txt && python3 verify.py --fixture fixtures/sample --seed 0