Sem Topography

sem-topography

Scope

Reconstructs 3D surface relief from four-quadrant backscattered electron stacks, returning a height field with per-pixel confidence and roughness statistics.

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 reconstruction 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": "reconstruct_relief",
  "arguments": {
    "input": "/data/sem/session-001",
    "output": "/data/sem/session-001/reconstruct_relief"
  }
}

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/sem-topography
pip install -r requirements.txt && python3 verify.py --fixture fixtures/sample --seed 0