emskills-mcp particle-picker
Scope
Template-free particle picking with a denoising front-end for low signal-to-noise micrographs. Emits coordinate star files and per-pick confidence.
Expects standard cryo-EM 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
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": "pick_particles",
"arguments": {
"input": "/data/cryo-em/session-001",
"output": "/data/cryo-em/session-001/pick_particles"
}
}
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/particle-picker
pip install -r requirements.txt && python3 verify.py --fixture fixtures/sample --seed 0