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ipa-mcp

by unige-biochem
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ipa-mcp: the department's imaging site for AI assistants (draft)

Lets an AI assistant answer questions about the UNIGE Biochemistry imaging site, biochem-ipa: the microscopes, hoods and lab VMs, their protocols, and the measurements made on them.

Is there a water objective on the Nikon scope? Has the laser power of the 3i spinning disk dropped since last year? Get me the PSF of the 60x. Is napari installed on the VMs? Open the booking page for the spinning disc.

When the answer is on the site, the assistant gives it with the page to check. When it is not, it says so and gives the way forward: the protocol, and that the facility can measure it with you.

It is an MCP server, so it is not tied to one assistant: any application that can start a local MCP server, with any model it offers. It reads your own synced copy of the site's library, read-only, with no credentials: what the assistant sees is what your account can already read. What you then send to a model is your decision, as with any file you open.

Install

  1. Sync the library once. Open the site's library and click Sync. OneDrive creates a folder named biochem-ipa - Documents. Large raw files stay placeholders until something reads them.

  2. Install uv and git (uv uses it to fetch the server).

  3. Register the server as a local (stdio) MCP server in your application. It runs straight from the repository, with uvx --from git+https://github.com/unige-biochem/ipa-mcp ipa-mcp:

    • VS Code: Install in VS Code

    • Claude Code: claude mcp add ipa -- uvx --from git+https://github.com/unige-biochem/ipa-mcp ipa-mcp

    • Claude Desktop: the .mcpb bundle attached to a release, or Settings, Developer, Edit config with the same command.

    • Anything else: command uvx, arguments --from git+https://github.com/unige-biochem/ipa-mcp ipa-mcp.

The server finds the synced folder by itself (OneDrive's registry on Windows, the usual places on macOS). If it does not, set IPA_LIBRARY to the folder, or tell the assistant where it is. The first time it matters, the assistant asks who you are and which lab you are in, and remembers it in ~/.ipa-mcp/config.json.

It is not on PyPI, and will not be: it only makes sense for the department's site, so it is installed from git. uvx ipa-mcp alone does not work. To stay on one version, add it to the URL (git+https://github.com/unige-biochem/ipa-mcp@v0.1.0). uvx keeps what it built: to pick up a newer version, run the same command once with --refresh after uvx.

Testing from a checkout (Windows)

Clone the repository, then double-click one script in install/. Each one registers the checkout as the server named ipa, pointing at uv run --directory <checkout> ipa-mcp:

Script

Registers in

Undo

install\claude-desktop.bat

Claude Desktop (%APPDATA%\Claude\claude_desktop_config.json); restart it

claude-desktop.bat --remove

install\claude-code.bat

Claude Code, user scope

claude mcp remove ipa

install\vscode.bat

VS Code, user profile

MCP: List Servers in VS Code

install\check.bat

nothing: prints whether the library was found

Or, for Claude Desktop without a checkout: pack the bundle (see DEVELOPMENT.md) and open the .mcpb file with Claude Desktop, which asks for the library folder; uv must be installed.

Related MCP server: knowledgehub

What it knows

From

Every page of the site: hardware, software, start-up, quirks, protocols, VMs

site/*.md

The equipment registry: objectives, light paths, laser lines, rooms

site/registry.json

Laser power at the sample over time

data/laser-power/laser-power.csv

PSFs per objective and light path, with the PSF images

data/psf/psf.csv, data/psf/<session>/

Courses, presentations, viewers

builds/*/*/build.yaml

The copy is as fresh as OneDrive's last sync. The site is the reference, and the assistant cites its pages. The library's private/ folder is never read.

Development

See DEVELOPMENT.md.

Created by: Nicolas Chiaruttini. GitHub (code, issues, releases): https://github.com/unige-biochem/ipa-mcp. The facility's project record stays on GitLab: https://gitlab.unige.ch/unige-biochem/common/ipa-mcp

Data folder (Windows): I:\common\ipa-mcp. macOS (Finder, Go, Connect to Server): smb://isis.unige.ch/nasac/s/biochem/biochem-ipa/ipa_biochemistry/common/ipa-mcp.

Confidentiality level for this project: open: code, scientific question and sample images may be shown to AI tools.

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