CellTypist Remote Tool (MCP Server)

Serves CellTypist (Domínguez Conde et al., Science 2022; Xu et al., Cell 2023) — automated single-cell type annotation — as a ToolUniverse remote tool: run_celltypist_annotate (per-cell predicted labels + cell-type counts).

Served remotely (not bundled) because celltypist pulls in scikit-learn + scanpy and downloads pre-trained model files on first use.

Deploy

pip install -r requirements.txt          # celltypist + scanpy
python celltypist_tool.py                  # starts the MCP server on 127.0.0.1:8014

Inputs are referenced by adata_path (a server-accessible .h5ad), since single-cell matrices are large. The matrix is log1p-normalised to 10,000 counts per cell before annotation (CellTypist’s expected input). Expose remotely only behind TOOLUNIVERSE_API_TOKEN (SMCP bind guard).

Models

model selects a CellTypist pre-trained model (default Immune_All_Low.pkl). The full list of built-in models is at https://www.celltypist.org/models; required model files are downloaded automatically.

Register in ToolUniverse

Tool definitions: src/tooluniverse/data/remote_tools/celltypist_tools.json (type: RemoteTool). Connect via the standard MCPAutoLoaderTool/server_url mechanism.