Ocean Insight Spectrometer — MCP Server

Let an AI agent acquire spectra, set or auto-tune the integration time, store dark and reference spectra, and measure absorbance and transmittance with peak positions and FWHM on Ocean Insight (Ocean Optics) spectrometers. It works through the open-source python-seabreeze library.

Try it without hardware

uvx labmcp-ocean-spectrometer --simulate --check
uvx labmcp-ocean-spectrometer --simulate --option sim_source=hg-ar --check      # Hg-Ar calibration lamp
uvx labmcp-ocean-spectrometer --simulate --option sim_model=QE-PRO --check      # TE-cooled, 1044 pixels

The simulator models a USB2000+ (or QE Pro) looking at a tungsten-halogen lamp, a white LED or a Hg-Ar lamp. It includes shot and read noise, dark offset and dark current, electric-dark pixels, detector nonlinearity, saturation, and the stale first spectrum after an integration-time change. In simulation a "virtual user" blocks the beam before store_dark_reference, inserts a blank before store_reference, and inserts a dye sample (absorbance band at 520 nm, 0.8 AU) before measure_absorbance/measure_transmittance. With real hardware your scientist does these steps.

Connect your spectrometer

1. Drivers / permissions (once per computer), as documented by python-seabreeze:

   uvx --from seabreeze seabreeze_os_setup      # or, inside the environment: seabreeze_os_setup
   

   • Linux: this installs the udev rules (/etc/udev/rules.d/10-oceanoptics.rules, needs sudo). Re-plug the spectrometer afterwards.
   • Windows: this installs the USB driver files. The pyseabreeze backend also needs libusb-1.0.dll (see the seabreeze README).
   • macOS: works out of the box.
2. Close OceanView (or any other program using the spectrometer). Only one program can open it.
3. Test the connection:

   uvx labmcp-ocean-spectrometer --check                        # the only connected spectrometer
   uvx labmcp-ocean-spectrometer --address USB2+H01234 --check  # choose by serial number
   uvx labmcp-ocean-spectrometer --option backend=pyseabreeze --check
   

   --address is the spectrometer's serial number and is only needed when several are connected (list_spectrometers shows them). The default backend is cseabreeze (compiled libseabreeze); if it can't load, seabreeze falls back to the pure-Python pyseabreeze (pyusb).

On connect the server sets the integration time to 10 ms (--option integration_ms=…), clamped to the device range. It has to set it, because seabreeze cannot read the integration time back.

Add to your MCP client

Claude Code

claude mcp add spectrometer -- uvx labmcp-ocean-spectrometer

Claude Desktop / Cursor / Windsurf (claude_desktop_config.json, .cursor/mcp.json, …)

{
  "mcpServers": {
    "spectrometer": {
      "command": "uvx",
      "args": ["labmcp-ocean-spectrometer", "--address", "USB2+H01234"]
    }
  }
}

Add --read-only to allow acquisitions and absorbance measurements with the present settings while blocking integration-time changes, reference storage and TEC control. For other clients, generate the snippet with uvx labmcp config ocean-spectrometer --client vscode (also cursor, codex, claude-code).

Tools

get_connection_info, get_command_log and reconnect are built into every LabMCP server.

Safety limits

Override at launch: --limit max_integration_time_ms=60000. Whatever the limits say, one acquisition (scans × integration time, plus the spectrum discarded after an integration-time change) must fit in 540 s, the time one tool call may take; auto_integration_time stops early for the same reason and says so.

Example prompts

• "Auto-adjust the integration time on the lamp, then take a 20-scan averaged spectrum and tell me where the peak is and how wide it is."
• "I'm going to measure a Beer–Lambert series. Walk me through dark, blank and each of my five standards, and report the absorbance at 520 nm for each."
• "Here's the Hg-Ar lamp. Find the lines between 400 and 600 nm and tell me how far they are from 404.66, 435.83 and 546.07 nm."
• "Measure the transmittance of this filter from 400 to 700 nm and save it to ~/data/filter_T.csv."
• "Cool the QE Pro to −10 °C and tell me when the detector temperature has settled."

Notes

• Raw counts. Intensities are detector counts, not irradiance. Radiometric calibration is out of scope.
• Saturation is judged on the raw ADC counts of every averaged scan: a pixel is saturated at ≥ 98 % of max_intensity. Saturated pixels are flagged, and they're excluded from absorbance/transmittance (with boxcar smoothing, so are the pixels within the boxcar half width of them). seabreeze notes that some detectors saturate below max_intensity, so keep peaks at 70–85 %.
• Corrections. correct_dark_counts subtracts the mean of the optically masked electric-dark pixels; correct_nonlinearity applies the EEPROM polynomial. The driver reads raw spectra and applies both corrections with the same formula as seabreeze.spectrometers.Spectrometer.intensities, so saturation can still be detected on raw data. A stored dark (store_dark_reference) is still required for absorbance, because electric-dark correction doesn't remove fixed-pattern dark signal.
• Absorbance is A = −log10((S − D)/(R − D)). Pixels where the reference has less than 0.5 % of its peak signal above dark, or where the reference or sample is saturated, are returned as null. The dark, reference and sample must share integration time, boxcar and corrections; the server enforces this and asks you to re-take references when they differ.
• First spectrum after an integration-time change is discarded. It may have been integrated partly with the old setting; the QE Pro manual notes that it returns the most recently completed spectrum.
• Boxcar follows OceanView's convention: boxcar_half_width = pixels averaged on each side. Peaks are found on the full-resolution spectrum. The returned curve is bin-averaged down to max_points.
• TEC tools use seabreeze's thermo_electric feature (enable_tec, set_temperature_setpoint_degrees_celsius, read_temperature_degrees_celsius) and only work when the backend exposes it for your model. In pyseabreeze 2.11 that is only the NIRQuest512. For the QE Pro it depends on libseabreeze (cseabreeze); this is unverified on hardware. The QE Pro manual says the TEC cools only ~15–40 °C below ambient.
• Not exposed: shutter and lamp (light_source/strobe_lamp) control, trigger modes, and irradiance calibration. seabreeze documents these features, but device support isn't specified and several aren't implemented in pyseabreeze, so they could not be verified.
• Peaks next to invalid pixels. Invalid (null) pixels are treated as unknown: a pixel next to one is not reported as a peak, and prominence and FWHM do not extend across them. When invalid pixels lie inside the requested range (for example the centre of a band too strong to measure), absorbance/transmittance results carry a warning.
• Dark and reference spectra live in the server's memory and are lost on reconnect or restart. Save data with save_path: it must end in .csv, missing folders are created, and an existing file is never overwritten (choose a new name). The path is checked before the spectrum is acquired.

Hardware verification