OpenReadout

https://openreadout.github.io/openreadout/
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OpenReadout is an open-source reader for lab-instrument files that extracts metadata, images,...
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### openreadout self completions example commands

Source: https://openreadout.github.io/openreadout/reference/commands/self.html

Example commands for installing completions for bash, zsh, fish, and powershell.

```bash
openreadout self completions bash > ~/.local/share/bash-completion/completions/openreadout
openreadout self completions zsh  > "${fpath[1]}/_openreadout"
openreadout self completions fish > ~/.config/fish/completions/openreadout.fish
openreadout self completions powershell >> $PROFILE
```

--------------------------------

### Install and configure MCP clients

Source: https://openreadout.github.io/openreadout/reference/commands/mcp.html

Examples of installing the MCP server for Claude Code at user level, installing for Cursor at project level, and printing the configuration snippet for VS Code.

```bash
openreadout mcp --install claude                 # Claude Code, user level
openreadout mcp --install cursor --project       # .cursor/mcp.json in this directory
openreadout mcp --config vscode                  # print the snippet only
```

--------------------------------

### Install via Homebrew

Source: https://openreadout.github.io/openreadout/getting-started/install.html

Installs the `openreadout` binary from the Homebrew tap. Alternatively, you can install the attached formula file directly with `brew install --formula ./openreadout.rb`.

```bash
brew install openreadout/tap/openreadout
```

--------------------------------

### Install script for macOS and Linux

Source: https://openreadout.github.io/openreadout/getting-started/install.html

Downloads and runs the install script, placing the binary in `~/.local/bin`. The script verifies the download against the release's `SHA256SUMS`. If `~/.local/bin` is not on your `PATH`, the script prints the line to add to your shell's startup file; until then, run the program as `~/.local/bin/openreadout`.

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

--------------------------------

### Get image info via command line without package

Source: https://openreadout.github.io/openreadout/guides/python.html

Call the openreadout command line tool and parse its JSON output to get image information when the package cannot be installed. Raises RuntimeError if the command reports an error.

```python
import json, subprocess

def info(path):
    p = subprocess.run(["openreadout", "info", path, "--json"], capture_output=True, text=True)
    env = json.loads(p.stdout)
    if not env["ok"]:
        raise RuntimeError(f"{env['error']['code']}: {env['error']['message']} ({env['error'].get('hint')})")
    return env["data"]
```

--------------------------------

### Install via npm (npx and global)

Source: https://openreadout.github.io/openreadout/getting-started/install.html

Runs `openreadout` directly with `npx` or installs it globally with `npm install -g`. The binary comes in a platform package (e.g., `@openreadout/cli-linux-x64`) installed as an optional dependency. Nothing is downloaded from GitHub and no install script runs, so it works behind proxies and from registry mirrors. If optional dependencies are turned off (`--omit=optional`), `openreadout` names the package to add. `OPENREADOUT_BINARY` points it at a binary you already have.

```bash
npx openreadout info run42.czi
```

```bash
npm install -g openreadout
```

--------------------------------

### Install and run OpenReadout MCP over HTTP with token

Source: https://openreadout.github.io/openreadout/reference/mcp.html

Commands to install OpenReadout with the mcp-http feature and start the MCP server over HTTP on 127.0.0.1:8765. The second command sets an authentication token via OPENREADOUT_MCP_TOKEN. The server only serves /mcp and requires the token for all requests when set.

```bash
cargo install openreadout --features mcp-http
openreadout mcp --http 127.0.0.1:8765                     # endpoint http://127.0.0.1:8765/mcp
OPENREADOUT_MCP_TOKEN=$(openssl rand -hex 16) openreadout mcp --http 127.0.0.1:8765
```

--------------------------------

### MCP server entry using npx

Source: https://openreadout.github.io/openreadout/guides/agents.html

JSON entry to start the OpenReadout MCP server via npx without installing the program globally.

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

--------------------------------

### openreadout info basic example with output

Source: https://openreadout.github.io/openreadout/reference/commands/info.html

Runs info on mini.czi and shows the resulting text output, including format, size, image count, and per-image details.

```bash
$ openreadout info mini.czi
mini.czi
  format: Zeiss CZI (czi) v1.0  size: 2.0 KiB  images: 1  planes: 1
  assurance: validated - …
  [0] -  8x8 z=1 c=1 t=1  uint8 XYCZT  px=0.1000 µm
      ch0 c0
```

--------------------------------

### Plate layout example

Source: https://openreadout.github.io/openreadout/guides/batch.html

A plate layout grid with a header row numbering columns from 1 and rows starting with a plate-row letter. The top-left cell names the annotation.

```csv
condition,1,2,3
A,DMSO,DMSO,drug
B,DMSO,drug,drug
```

--------------------------------

### Install via Nix (run and profile)

Source: https://openreadout.github.io/openreadout/getting-started/install.html

Runs `openreadout` directly with `nix run` or installs it into your profile with `nix profile install`.

```bash
nix run github:openreadout/openreadout -- info run42.czi
```

```bash
nix profile install github:openreadout/openreadout
```
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