OpenReadout

Name: OpenReadout
Author: openreadout

by openreadoutversion 0.4.0i★ –iRuns on your computer

Registry nameio.github.openreadout/openreadout

Install

Overview

Description from the maker (original English)

Read raw lab-instrument files offline: metadata, previews, integrity checks, open-format export.

PopNx MCP’s three pillars

These three are never merged into one score: opinions, measurements and popularity are different things.

User voiceiNo reviews yetReviews open together with accounts in a later step
Our basic checksi1 of 1 passedChecked from public information; code not scanned yet
UsageiNot measured yet★ –

What you can do with it

We have not written a plain-language summary for this one yet. Below are the facts we read from the registry.

Connection: Runs on your computer
Transport: stdio
Category: Other

Install

Pick the AI app you use, then copy the settings.

Before you install

Basic checks: 1 of 1 passed
Runs on your computer with your user’s permissions (files, network, apps).
The registry lists no key to fill in.

You need

npmNode.js installed (for the npx command)

Which app do you use?

ClaudeClaude CodeCursorVS CodeChatGPT

Pick your app above. We remember it, so next time the button says “Install in …”.

Download the maker’s .mcpb file

The link goes to the maker’s own file; we do not host or repackage it. Open the file and Claude Desktop installs it.

Run this in your terminal

claude mcp add openreadout -- npx -y openreadout mcp

Open in Cursor

Or copy the settings yourself

Paste into .cursor/mcp.json in your project, or ~/.cursor/mcp.json

{
  "mcpServers": {
    "openreadout": {
      "command": "npx",
      "args": [
        "-y",
        "openreadout",
        "mcp"
      ]
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

Open in VS Code

Or copy the settings yourself

Paste into .vscode/mcp.json in your project

{
  "servers": {
    "openreadout": {
      "type": "stdio",
      "command": "npx",
      "args": [
        "-y",
        "openreadout",
        "mcp"
      ]
    }
  }
}

Your browser asks to open the app, then the app shows the settings and asks you to confirm. Key values are left empty for you to fill in.

This one runs on your computer, and ChatGPT can only connect to servers on the internet. Pick another app.

Your choice stays on this device in a cookie; no account needed.

These settings are generated from the maker’s registry entry. If the README says otherwise, follow the README.

What it can do

Runs on your computer; the tool list appears in your AI app after you install it.

Basic checksi

We check information anyone can see; we have not read the code. Checks that do not apply are left out of the count. · Checked Nov 6, 2026

✓ Pass
Maker matches the repo
The registry name was verified with the GitHub account openreadout, which owns the repo
… Not checked yet
Still maintained
We have not read this repo from GitHub yet
… Not checked yet
Has a licence
We have not read this repo from GitHub yet
– Not applicable
Endpoint responds
This one runs on your computer; there is no internet endpoint
– Not applicable
Sign-in with OAuth
Runs on your computer and uses local settings instead
… Not checked yet
No hidden instructions in tool descriptions
Runs on your computer; we can only read tool lists from internet endpoints

Compared with others in Otheri

More stars than 0% of the other 32424 servers in this category
Published to the registry more recently than 66% of the other 32424 servers in this category
Basic checks equal to or better than 100% of the other 32424 servers in this category

Compared with every active server in this category in the registry. Stars count only when the publisher owns the repo.

Common questions

Is OpenReadout safe?

It passed 1 of 1 applicable basic checks. We have not read the code. Before adding a key or token, see what access the server asks for and use a key with only the permissions you need.

What keys or codes does it need?

The registry does not list a required key, though some servers ask you to sign in on first use.

Does it run on my computer or in the cloud?

It runs on your computer. Your AI app starts it when needed, and data does not pass through the maker’s servers (unless it calls an online service itself).

Is it still maintained?

The GitHub repo last changed –, and the latest version (0.4.0) reached the registry 19 days ago.

Which apps can use it?

Apps that support MCP, such as Claude Desktop, Claude Code, Cursor and VS Code. You also need Node.js, Rust, MCPB on your computer.

What can I use instead?

In the same category: Spec Driven Development, Remote Desktop Commander, BankBridge

Alternatives

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Reading a card:★ GitHub starsiThree pillars: reviews · checks · usageiUpdated = latest version published to the registryi

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README from the maker

Open the README

Copied from the maker’s repo as written. PopNx MCP has not reviewed or endorsed it. HTML, images and scripts are removed. Links lead off this site.

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

Area	Formats	Export to
Light microscopy	Zeiss CZI, Nikon ND2, Leica LIF, Olympus OIR/VSI/OIB, Imaris, OME-TIFF and other TIFF variants, OME-Zarr, whole-slide images (including Philips iSyntax, Hamamatsu VMS and MIRAX)	OME-TIFF, OME-Zarr
High-content screening	Harmony (Opera Phenix, Operetta), ImageXpress, CellVoyager	OME-Zarr plate, OME-TIFF
Electron microscopy	MRC, Gatan DM3/DM4, FEI SER/EMI, Velox EMD, EER movies, SerialEM mdoc	OME-TIFF, OME-Zarr, MRC
Structural biology	CBF/miniCBF, SMV, EIGER NeXus (NXmx) diffraction images	MRC, OME-TIFF
Medical imaging	DICOM (files, series, studies, DICOMDIR), NIfTI, Analyze, Bruker ParaVision	NIfTI, OME-TIFF
Mass spectrometry	Thermo RAW, Bruker timsTOF and BAF, Agilent MassHunter, Waters MassLynx, Sciex WIFF, mzML	mzML, Parquet, Arrow
Chromatography	Agilent ChemStation and OpenLab, Shimadzu, Chromeleon, AIA/ANDI	CSV, JCAMP-DX, Parquet
Electrophysiology	Axon ABF, Intan, SpikeGLX, Open Ephys, Neuralynx, Blackrock, Plexon, HEKA, Spike2, TDT, Axona, NWB	NWB, CSV, Parquet
NMR and spectroscopy	Bruker TopSpin and OPUS, Varian, JEOL, Thermo OMNIC, Renishaw, JCAMP-DX, SPC	JCAMP-DX, CSV
Flow cytometry	FCS, FlowJo workspaces, Gating-ML	CSV, Parquet, Arrow
Plate readers and qPCR	Plate-reader exports, RDML, Applied Biosystems, LightCycler, Rotor-Gene	Allotrope ASM, RDML, CSV
DNA sequencing and electrophoresis	Illumina run folders, Oxford Nanopore POD5 and FAST5, FASTQ, BAM, ABIF Sanger and fragment-analysis files, Agilent Bioanalyzer and TapeStation	FASTQ, CSV, Parquet
Other	NanoDrop, Qubit, Incucyte, gel and blot imagers, ÄKTA, ITC, Biacore, Seahorse, Octet, Zetasizer, XRD, EPR, electrochemistry, thermal analysis	CSV, Parquet

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

Installati

Only the beginning is shown; read the rest in the repo

OpenReadout

Overview

PopNx MCP’s three pillars

What you can do with it

Install

Before you install

What it can do

Basic checksi

Maker matches the repo

Still maintained

Has a licence

Endpoint responds

Sign-in with OAuth

No hidden instructions in tool descriptions

Compared with others in Otheri

Common questions

Alternatives

Spec Driven Development

Remote Desktop Commander

BankBridge

README from the maker

OpenReadout

Gallery

Get Started

With an Agent

What It Does

On the Command Line

What is in the file?

→ 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?

→ 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

→ 4 peaks, area in pA·min

→ 1 4.852 min area 0.2779 25.08 %

→ ...

Structured JSON for scripts and agents

Formats

Installati