NUANCE-MCP

NUANCE-MCP lets an LLM (Claude Desktop, a local Ollama model ...) drive a microscope through the Model Context Protocol. NUScope plugs into it, so

• every acquisition is saved as a sealed, signed NUScope file, with calibrated axes, the column state as metadata and the tool call as provenance;
• the model gets data tools that work in physical units and check integrity.

pip install nuance-mcp nuscope          # NUScope-TOMO adds its own tools when installed
emdb identity create "Your Name" --orcid 0000-0000-0000-0000
nuance-mcp serve --adapter simulator     # or gatan, jeol, hitachi

The server finds NUScope through the nuance_mcp.plugins entry point; list_plugins shows what loaded.

Note

Plugin support is new in NUANCE-MCP (the nuance_mcp.plugins entry point and acquisition hooks). Use a NUANCE-MCP version that includes it.

Acquisitions

After acquire_tem_image, acquire_stem, acquire_4d_stem, acquire_diffraction or acquire_eels, the response gains

"plugins": {"nuscope": {
  "file": "~/NUScope/acquisitions/2026-10-13/211932_528_acquire_stem_SimSTEM.h5",
  "seal": "31ce1e35…", "integrity": "signed",
  "signed_by": ["Your Name [1a2b:3c4d:5e6f:7a8b]"]}}

The file records:

• the image or spectrum with calibrated axes (nm for images and scans; eV for spectra);
• the column state (high tension, magnification, mode, focus, stage position, detectors) as metadata;
• the tool and its validated parameters as the first step of the history;
• you, from your identity, as the operator.

Files go to $NUSCOPE_ACQUISITION_DIR (default ~/NUScope/acquisitions), one folder per day. NUSCOPE_SAMPLE sets the sample name.

Tools

Tool	What it does
nuscope_describe(path)	calibration, key metadata and integrity of any supported file
nuscope_verify(path)	the seal check and signers
nuscope_history(path)	every step with its parameters, and the source files with SHA-256
nuscope_analyze(path, op, params)	stats, denoise, fft, radial_profile, line_profile, particles, ... Image results are saved as new sealed files next to the input
nuscope_list(folder)	files saved from acquisitions, newest first
nuscope_identity()	who signs, and where files are saved

NUScope-TOMO adds tomo_project, tomo_table, tomo_volume, tomo_ops, tomo_run and tomo_job.

Turn plugins off with nuance-mcp serve --no-plugins, or choose them with NUANCE_MCP_PLUGINS=nuscope.