Grid Atlas Qc

grid-atlas-qc

Scope

Scores grid squares and foil holes from an atlas montage, estimating ice thickness and contamination to produce a ranked acquisition queue for automated data collection.

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 image acquisition stage of the workflow.

Safety

Read-only analysis of an existing atlas montage — no instrument control. Downstream queueing must be confirmed by an operator.

Usage

{
  "tool": "score_atlas",
  "arguments": {
    "input": "/data/cryo-em/session-001",
    "output": "/data/cryo-em/session-001/score_atlas"
  }
}

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/grid-atlas-qc
pip install -r requirements.txt && python3 verify.py --fixture fixtures/sample --seed 0