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Installing the Neurosift Tools MCP Server for Cline

The Neurosift Tools MCP server provides access to DANDI archive functionality and other neuroscience data tools through Cline in VSCode. This guide explains how to set it up.

Prerequisites

  • VSCode with the Cline extension installed
  • Node.js installed on your system
  • Git for cloning the repository

Installation Steps

  1. Clone the neurosift-v2 repository:

    git clone https://github.com/flatironinstitute/neurosift.git
cd neurosift

  2. Build the neurosift-tools MCP server:

    cd mcps/neurosift-tools
npm install
npm run build

  3. Create or open the Cline MCP settings file:

    ~/.config/Code/User/globalStorage/saoudrizwan.claude-dev/settings/cline_mcp_settings.json

    (This file can also be accessed from the Cline settings in VSCode)

  4. Add the neurosift-tools configuration to your settings:

    {
  "mcpServers": {
    "neurosift-tools": {
      "command": "node",
      "args": ["PATH_TO_REPO/mcps/neurosift-tools/build/index.js"],
      "disabled": false,
      "autoApprove": []
    }
  }
}

    Note: Replace PATH_TO_REPO with the actual path where you cloned the neurosift repository.

Available Tools

Once installed, the MCP server provides tools for:

  • dandi_search: Search for datasets in the DANDI archive
  • dandi_semantic_search: Semantic search for DANDI datasets using natural language
  • dandiset_info: Get detailed information about a specific DANDI dataset including neurodata objects and metadata
  • dandiset_assets: List assets/files in a DANDI dataset
  • nwb_file_info: Get information about an NWB file including neurodata objects
  • openneuro_search: Search for datasets on OpenNeuro
  • dandi_list_neurodata_types: List all unique neurodata types in DANDI archive
  • dandi_search_by_neurodata_type: Search for datasets containing specific neurodata types

Verification

After adding the configuration:

  1. Restart VSCode to apply the changes
  2. Open a new conversation in Cline
  3. The tools should be available in Cline's capabilities

Troubleshooting

If tools are not appearing:

  • Verify the path in args points to your local neurosift repository
  • Check that the repository is built correctly
  • Ensure the settings file is properly formatted JSON
  • Restart VSCode after making changes

Local Development

For local development of the neurosift-chat-agent-tools API, you can configure the MCP server to use your local development server by adding the NEUROSIFT_TOOLS_API_URL environment variable to your settings:

{
  "mcpServers": {
    "neurosift-tools": {
      "command": "node",
      "args": ["PATH_TO_REPO/mcps/neurosift-tools/build/index.js"],
      "env": {
        "NEUROSIFT_TOOLS_API_URL": "http://localhost:3001/api"
      },
      "disabled": false,
      "autoApprove": []
    }
  }
}

This allows you to test changes to the API locally before deploying to production.