Skip to content
napari-micromanager PyPI version

Installing and Launching napari-micromanager

Installation

Installing napari-micromanager

pip install "napari-micromanager[PyQt6]"
# or, for the PySide6 Qt backend: pip install "napari-micromanager[PySide6]"

(The quotes keep zsh, the default shell on macOS, from complaining about the square brackets.) If you've already installed napari with a Qt backend in this environment (e.g. pip install "napari[all]"), plain pip install napari-micromanager is enough.

You will then also need to grab the Micro-Manager device adapters:

mmcore install

See Installing Micro-Manager device adapters for details on the mmcore helper command.

Usage

napari-micromanager

This will open a new napari window with the micromanager plugin enabled. To load a configuration file right away, pass it with -c:

napari-micromanager -c path/to/config.cfg
napari-micromanager -c MMConfig_demo.cfg  # Micro-Manager's demo devices

Otherwise, select a MM Config file at the top left of the window, then click load. (You can also add the plugin to a napari window that's already open, from the Plugins menu, or start napari with it: napari -w napari-micromanager.)

The plugin adds a row of toolbars along the top of the napari window: the configuration file, the channel group and channel, the objective, the shutters, Snap and Live, and the exposure time. The buttons at the end of the row open more panels, docked in the napari window: the device property browser, configuration groups and presets, illumination, stage control, camera ROI, pixel size, and MDA for multi-dimensional acquisitions. Snapped and live images go to a napari layer called "preview", and each acquisition gets layers of its own, so you can use any napari tool or plugin on them. A MinMax panel shows the minimum and maximum pixel values of the layers. Then ... much of the rest is hopefully self explanatory 😄.

Underlying napari-micromanager is the pymmcore-plus package, which is a python wrapper around pymmcore and the C++ CMMCore library (not pycro-manager and not the Java-based MMStudio). See the User Guide for more on pymmcore-plus; the widgets in the GUI are all powered by pymmcore-widgets.