emskills-mcp tomo-align
Scope
Aligns tilt series without fiducials using patch tracking, then reconstructs a 3D volume with per-voxel confidence maps for downstream segmentation.
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 tilt series / tomography 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": "align_tilt_series",
"arguments": {
"input": "/data/tem/session-001",
"output": "/data/tem/session-001/align_tilt_series"
}
}
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 3.10. Pin dependencies in requirements.txt / package.json
and run with a fixed seed. Reviewers can reproduce the reported numbers with:
cd skills/tomo-align
pip install -r requirements.txt && python3 verify.py --fixture fixtures/sample --seed 0