OpenReadout

OpenReadout

OpenReadout lets AI agents read and analyze raw files from lab instruments like microscopes, mass specs, flow cytometers, plate readers and NMR. It reads 120+ formats without vendor software, and runs as an MCP server, a CLI, or a Python or R package.

🧪 Try it: browser demo | 📖 Docs: openreadout.github.io/openreadout

Gallery

Light Microscopy

Leica LIF · fly egg chamber DeltaVision · HeLa cells Imaris · plant root section

Imaris · a single neuron Yokogawa CellVoyager · Cell Painting Evident OIR · testes, confocal

Electron Microscopy

EMDB MRC · virus capsid Gatan DM3 · atoms by ptychography Gatan DM4 · ZnO nanorods

Gatan DM4 · electron diffraction Velox EMD · STEM HAADF FEI SER · silica particles

Figures

ABI .ab1 · Sanger read WITec · Raman of graphene MicroCal ITC · titration

BD FCS + FlowJo · gated T cells SoftMax .pda · 96 growth curves Bruker TopSpin · NMR from the FID

Bruker EPR · power series ABI .fsa · fragment sizing mzML · TIC and spectrum

Axon ABF · firing against current Gamry · cyclic voltammogram Applied Biosystems .eds · qPCR

All read from the raw files. More in the gallery , and image credits in CREDITS.md .

Get Started

Install it, then connect it to your agent:

brew install openreadout/tap/openreadout    # other ways under Installation below

openreadout mcp --install claude-desktop # or claude, codex, cursor, vscode, gemini

Then ask your agent about a file, like "What's in cells.czi?" In Claude Code you can install it as a plugin instead (see AI Integration).

Or try the browser demo with no install. Your files never leave your computer.

With an Agent

Claude finds the cerebellum in a 3.7 GB slide scan and labels its layers.

https://github.com/user-attachments/assets/7ee0f9fe-e6e0-4378-a46d-5cdc04d57151

Data: Zenodo 10577621 (CC BY 4.0).

Claude checks a gene knockout with files from five instruments.

https://github.com/user-attachments/assets/658d300b-dc9d-4164-af84-bb48261fd33f

Data: Edyanto et al., figshare (CC BY 4.0).

What It Does

• Inspect images, channels, traces, spectra, tables, and metadata, in plain text or structured JSON
• Check files for truncation, missing planes, and damaged structure, with exit code 4 when a file is corrupt
• Export to OME-TIFF, OME-Zarr, mzML, NWB, CSV, Parquet, Arrow, JCAMP-DX, Allotrope ASM, and RDML, reading every export back to verify it
• Preview image planes, traces, spectra, and plate heat maps as PNG
• Analyze chromatographic peaks, plate assays (IC50, standard curves), qPCR (Cq, ΔΔCq), NMR peaks, patch-clamp features, spikes, and flow-cytometry gates, with documented methods
• Batch over whole directories, index lab shares, and watch running acquisitions

On the Command Line

# Install (macOS / Linux; other ways under Installation)

curl -fsSL https://raw.githubusercontent.com/openreadout/openreadout/main/scripts/install.sh | sh

What is in the file?

openreadout info cells.lif

→ format: Leica LIF (lif) v2 size: 16.0 MiB images: 1 planes: 2

→ [0] PEI_laminin_35k 2048x2048 z=1 c=2 t=1 uint16 px=0.3250 µm

→ objective: HC PL FLUOTAR L 20x/0.40 DRY

Is it complete?

openreadout check partial-copy.lif

→ error truncated block chain runs past end of file

→ error missing_planes geometry needs 16777216 bytes but only 8969789 are stored

Integrate the peaks of a chromatogram

openreadout analyze peaks gc-run.ch --min-height 1

→ 4 peaks, area in pA·min

→ 1 4.852 min area 0.2779 25.08 %

→ ...

Structured JSON for scripts and agents

openreadout info cells.lif --json

{

"ok": true, "schema_version": "2", "data": { "format": { "id": "lif", "name": "Leica LIF", "vendor": "Leica Microsystems" }, "images": [ { "size_x": 2048, "size_y": 2048, "size_c": 2, "pixel_type": "uint16", "physical_size": { "x": 0.325, "y": 0.325, "unit": "µm" } } ] } }

Formats

The format list lists every format OpenReadout reads, with its known gaps.

Installati