napari-micromanager

Scripting napari-micromanager¶

napari-micromanager creates and owns its own CMMCorePlus. (It deliberately does not use the global CMMCorePlus.instance(), so a core you configured with CMMCorePlus.instance() is not the one the plugin drives.) Once you have a reference to the plugin's core, anything you can do with pymmcore-plus can be combined with the GUI. There are a few ways to get it:

• main_window.core, where main_window is the plugin's MainWindow (see the script below);
• napari_micromanager.get_core(), which finds the plugin in the current napari viewer;
• in napari's console, the variable mmcore (see below).

Launching napari from a script¶

For complex scripting you will likely want to launch napari from a script or a Jupyter notebook:

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import napari

v = napari.Viewer()
dw, main_window = v.window.add_plugin_dock_widget("napari-micromanager")

# the CMMCorePlus instance that napari-micromanager is driving
mmc = main_window.core

# do any complicated scripting you want here
...

# start napari
napari.run()

Using a core you created¶

To have the plugin drive a core that you created and configured yourself, pass it as mmcore when you create the MainWindow, and add that to the viewer:

import napari
from napari_micromanager import MainWindow
from pymmcore_plus import CMMCorePlus

core = CMMCorePlus()
core.loadSystemConfiguration()  # or your own configuration file

viewer = napari.Viewer()
main_window = MainWindow(viewer, mmcore=core)
viewer.window.add_dock_widget(main_window, name="MicroManager", area="top")

napari.run()

The plugin then leaves the core's lifecycle to you. When the window closes, it doesn't cancel a running acquisition or unload the devices, as it does for a core it created itself.

Using the integrated napari console¶

After launching napari and starting the napari-micromanager plugin, open the napari console (the >_ button at the bottom left of the window). It already defines mmcore, the core the plugin is driving, along with MDASequence and MDAEvent from useq, so you can run an acquisition from there:

mmcore.run_mda(MDASequence(time_plan={"interval": 1, "loops": 5}))