napari-micromanager

napari-micromanager

Micro-Manager GUI interface in napari.

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    GUI interface between napari and micromanager powered by pymmcore-plus and pymmcore-widgets

    🚧 Experimental! Work in progress! Here be 🐲 🚧


    mm

    Installation

    You can install napari-micromanager via pip:

    pip install napari-micromanager

    You will also need a Qt backend such as PySide2/6, or PyQt5/6. If you've previously installed napari into this environment with pip install napari[all], then you will likely already have it. If not, you will also need to install a Qt backend of your choice:

    pip install pyqt5  # or any of {pyqt5, pyqt6, pyside2, pyside6}

    Getting micromanager adapters:

    The easiest way to get the micromanager adapters is to use:

    mmcore install

    this will install micromanager to the pymmcore_plus folder in your site-package; use this to see where:

    python -c "from pymmcore_plus import find_micromanager; print(find_micromanager())"

    alternatively, you can direct pymmcore_plus to your own micromanager installation with the MICROMANAGER_PATH environment variable:

    export MICROMANAGER_PATH='/path/to/Micro-Manager-...'

    Contributing

    Contributions are very welcome.

    Launching napari with plugin

    You can launch napari and automatically load this plugin using the launch-dev.py script:

    python launch-dev.py

    Alternatively you can run:

    napari -w napari-micromanager

    License

    Distributed under the terms of the BSD-3 license, "napari-micromanager" is free and open source software

    Issues

    If you encounter any problems, please file an issue along with a detailed description.

    Version:

    • 0.1.0

    Last updated:

    • 06 March 2024

    First released:

    • 15 August 2021

    License:

    Supported data:

    • Information not submitted

    Plugin type:

    GitHub activity:

    • Stars: 57
    • Forks: 20
    • Issues + PRs: 16

    Python versions supported:

    Operating system:

    Requirements:

    • fonticon-materialdesignicons6
    • napari>=0.4.13
    • pymmcore-plus>=0.9.3
    • pymmcore-widgets>=0.7.0rc1
    • superqt>=0.5.1
    • tifffile
    • useq-schema>=0.4.1
    • zarr

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