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pymmcore-plus PyPI version

CLI Reference

This page provides documentation for the mmcore command line tool, which is installed along with pymmcore-plus.

The CLI can be used to interact with the pymmcore_plus package from the command line, including the installation, removal, and selection of Micro-Manager device adapters, showing log files, and running a test acquisition (mmcore run, which doesn't save anything). (The default --dest folder for install and build-dev depends on your platform; see Micro-Manager device adapters.)

mmcore

mmcore: pymmcore-plus command line.

For additional help on a specific command: type mmcore COMMAND --help

Usage:

$ mmcore [OPTIONS] COMMAND [ARGS]...

Options:

  • --version: Show version and exit.
  • --install-completion: Install completion for the current shell.
  • --show-completion: Show completion for the current shell, to copy it or customize the installation.
  • --help: Show this message and exit.

mmcore clean

Remove all Micro-Manager installs downloaded by pymmcore-plus.

Usage:

$ mmcore clean [OPTIONS] [glob]

Arguments:

  • glob: glob pattern to clean [default: *]

Options:

  • --help: Show this message and exit.

mmcore list

Show all discovered Micro-Manager installations.

Usage:

$ mmcore list [OPTIONS]

Options:

  • --help: Show this message and exit.

mmcore mmstudio

Run the Java Micro-Manager GUI.

This command will attempt to locate and execute an ImageJ application found in the active Micro-Manager directory.

Usage:

$ mmcore mmstudio [OPTIONS]

Options:

  • --help: Show this message and exit.

mmcore install

Install Micro-Manager device adapters from https://download.micro-manager.org.

On Windows and Intel macOS, this downloads a nightly build of Micro-Manager. Micro-Manager doesn't publish nightly builds for Linux or Apple Silicon, so on those platforms only the test adapters (DemoCamera, Utilities, etc...) are installed, from https://github.com/micro-manager/mm-test-adapters.

Usage:

$ mmcore install [OPTIONS]

Options:

  • -d, --dest <directory>: Installation directory. [default: <user data dir>/pymmcore-plus/mm]
  • -r, --release <str>: Release date. e.g. 20210201 [default: latest-compatible]
  • --plain-output: Do not use rich output. Useful for scripting.
  • --test-adapters: Install only test adapters (e.g. DemoCamera and others for testing).
  • --help: Show this message and exit.

mmcore run

Run a Micro-Manager acquisition from a useq-schema MDASequence file.

Nothing is saved to disk (this is mostly useful for testing and profiling).

Usage:

$ mmcore run [OPTIONS] [useq]

Arguments:

  • useq: Path to useq-schema file.

Options:

  • -c, --config <file>: Path to Micro-Manager system configuration file.
  • --z-go-up / --no-z-go-up: Acquire from bottom to top.
  • --z-top <float>: Top of z-stack.
  • --z-bottom <float>: Bottom of z-stack.
  • --z-range <float>: Symmetric range of z-stack around position.
  • --z-above <float>: Asymmetric range of z-stack above position.
  • --z-below <float>: Asymmetric range of z-stack below position.
  • --z-step <float>: Step size of z-stack.
  • -zr <float>: Relative z-positions to acquire (may use multiple times).
  • -za <float>: Absolute z-positions to acquire (may use multiple times).
  • --t-interval <float>: Interval between timepoints.
  • --t-duration <float>: Duration of time lapse.
  • --t-loops <float>: Number of time points to acquire.
  • --dry-run / --no-dry-run: Do not run the acquisition. [default: no-dry-run]
  • --axis-order <str>: Order of axes to acquire (e.g. 'TPCZ').
  • --channel <str>: Channel to acquire. Argument is a string of the following form:
    • name: "DAPI"
    • name;exposure: "DAPI;0.5"
    • useq-schema JSON: '{"config": "DAPI", "exposure": 0.5, "z_offset": 0.5}'
  • --channel-group <str>: Name of Micro-Manager configuration group for channels. [default: Channel]
  • --help: Show this message and exit.

mmcore build-dev

Build Micro-Manager device adapters from the git repo.

Currently only supports macos and linux.

Usage:

$ mmcore build-dev [OPTIONS] [devices]...

Arguments:

  • devices...: Device adapters to build. Defaults to ['DemoCamera', 'Utilities', 'SequenceTester']

Options:

  • -d, --dest <directory>: Installation directory. [default: <user data dir>/pymmcore-plus/mm]
  • -y: Overwrite existing if git sha is already built. If not specified, will prompt.
  • --help: Show this message and exit.

mmcore logs

Display recent output from pymmcore-plus log.

Usage:

$ mmcore logs [OPTIONS]

Options:

  • -n, --num <int>: Number of lines to display.
  • -t, --tail: Continually stream logs.
  • -c, --clear: Delete all log files.
  • --reveal: Reveal log file in Explorer/Finder.
  • --help: Show this message and exit.

mmcore info

Display information about the Micro-Manager and pymmcore install.

Usage:

$ mmcore info [OPTIONS]

Options:

  • --help: Show this message and exit.

mmcore use

Change the currently used Micro-Manager version/path.

Usage:

$ mmcore use [OPTIONS] {pattern}

Arguments:

  • pattern: Path to an existing directory, or pattern to match against installations found by mmcore list [required]

Options:

  • --help: Show this message and exit.

mmcore bench

Run a benchmark of Core and Devices loaded with config (or Demo).

Usage:

$ mmcore bench [OPTIONS]

Options:

  • -c, --config <file>: Path to Micro-Manager system configuration file.
  • -n, --number <int>: Number of iterations for each test. [default: 10]
  • --help: Show this message and exit.