OpenReadout — Claude Code MCP server: reads lab instrument files
Reads raw files from microscopes, mass specs, flow cytometers, NMR and 120+ formats without vendor software.
claude mcp add openreadout -- npx -y openreadoutWhat OpenReadout does
The server extracts metadata, renders previews, checks integrity and exports to open formats. Runs offline — no proprietary drivers or subscriptions required.
Inside an agent you can ask about a file (cells.czi, sample.fcs), request experiment parameters or plot the data. It recognizes formats from Leica, Zeiss, BD, Bruker, Agilent, Waters, Thermo and dozens of other vendors.
Without npx in PATH the command will not start. Supported platforms: Claude Code, Codex, Cursor, GitHub Copilot, Gemini CLI, Cline, Zed and Windsurf.
What it helps with
- read .czi, .lif, .fcs, .d files without installing vendor software
- extract experiment metadata from instrument files
- verify file integrity before analysis
- export data to an open format
- plot or preview a raw file
Example prompts for the agent
- What's inside
experiment.czi? - Extract parameters from
sample.fcsand show them in a table - Plot
nmr_data.dxand save as PNG
How to install OpenReadout
Platform CLI
claude mcp add openreadout -- npx -y openreadoutPlatform CLI
codex mcp add openreadout -- npx -y openreadoutConfig file
{
"mcpServers": {
"openreadout": {
"command": "npx",
"args": [
"-y",
"openreadout"
]
}
}
}Config file
{
"servers": {
"openreadout": {
"type": "stdio",
"command": "npx",
"args": [
"-y",
"openreadout"
]
}
}
}Platform CLI
gemini mcp add openreadout npx -y openreadoutStep by step, with commands for each platform: How to add an MCP server to Claude Code, Codex, Cursor, VS Code, Gemini CLI and more
Questions about OpenReadout
How to install OpenReadout in Claude Code?
Run claude mcp add openreadout -- npx -y openreadout in the terminal. After that you can ask the agent about instrument files.
What does OpenReadout do?
It reads raw files from lab instruments — microscopes, mass spectrometers, flow cytometers, NMR — and extracts metadata, renders previews, checks integrity, exports to open formats. Runs offline, supports 120+ formats.
Which formats does OpenReadout support?
More than 120 formats: Leica LIF, Zeiss CZI, BD FCS, Bruker TopSpin, Agilent .d, Waters RAW, Thermo RAW, Gatan DM3/DM4, Imaris, OIR, MRC, mzML, ABI .ab1/.fsa, SoftMax .pda and many others. Full list in the project documentation.
