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PhenoMePhenoMe

MCP for PhenoMe

The MCP server is optional. It helps a scientist use PhenoMe: build an analysis tool on the public API, or run an analysis and either save it or summarize it. It does not modify PhenoMe, does not change defaults, and does not run embedding extraction.

The server is a helper layer, not a second API. For a symbol, use phenome-api.json, the function location guide, or llms-full.txt. llms-small.txt is the short usage guide. Do not invent methods from a partial search hit.

Install

Section titled “Install”
Terminal window
pip install "phenome[mcp]"

From a clone (editable):

Terminal window
pip install -e ".[mcp]"

Then run:

Terminal window
phenome-mcp

Cursor example

Section titled “Cursor example”

In MCP settings, point stdio at the phenome-mcp executable from the same environment where PhenoMe is installed:

{
  "mcpServers": {
    "phenome": {
      "command": "phenome-mcp"
    }
  }
}

Tools

Section titled “Tools”
  • search_docs — keyword search. A checkout is searched first, then bundled recipes, then the published llms-small.txt. Each hit names its source.
  • get_recipe — one snippet: first-analysis, export-settings, summarize, path-metadata, property-presets, batch-correction, or checkpoint. get_recipe("list") lists them. An unknown name is an error. export-settings saves the HDF5 file and only the extra files the user asked to keep. summarize keeps the plot and the run text in memory.
  • list_public_api — top-level imports and PhenoMe methods.
  • inspect_dataset — find_files and inspect_data on a folder. No model and no embeddings.
  • format_run_settings — pretty-print a top-level JSON object, usually the file from export_experiment_config. A missing file, unreadable file, or non-object JSON is an error.
  • get_api_symbol — one exact name. A PhenoMe method returns its purpose, signature, and a documentation link. Another public import returns its name, import path, and a link to the API overview.
  • troubleshoot — match an error or question against a small set of known causes (masks, metadata keys, processing order, checkpoint order).
  • validate_analysis_code — static check only. It flags call names that start with find_, process_, compute_, plot_, save_, or load_ when they are not public PhenoMe methods or top-level imports. It flags process_images or load_results before find_files. A {name} path template is a warning. It does not check keyword arguments or presets.
  • get_version_info — package version, the llms-small.txt / llms-full.txt URLs, and the two assistant roles: build the analysis tool, or run the analysis and save or summarize it.

The same method list is published at phenome-api.json.

Pass a seed into PhenoMe so the run is reproducible. Pass other extra parameters (include_run_settings, log level, plot kwargs) only when the user asked. See Using with LLMs.