napari Plugins

napari Plugins#

Plugins are Python packages that allow developers to extend napari functionality. Currently, plugins can:

  • Add file format support with readers and writers

  • Add custom widgets and user interface elements for Python functions, etc.

  • Provide sample data

  • Change the look of napari with a theme

The napari hub is a repository for searching/discovering plugins. Plugins can be installed as Python packages using conda or pip as normal or from within the napari GUI using the Plugin menu.

Note

The built-in napari Plugin Manager by default will attempt to install plugins in the same fashion that napari was installed. This means that if you installed napari via conda, it will attempt to install plugins via conda and if your napari was installed via pip, it will attempt to install plugins via pip. You can control this using the Installation Info dropdown in the Plugin Manager.

Also keep in mind that plugins with complex or compiled dependencies or those that require non-Python components may not install properly. In those cases, you will need to check the documentation of the plugin for information regarding installation.

For more information on plugins, please see the official Plugin documentation.

Install Your First Plugins#

  • (Optional) Navigate to napari-hub.org—this is the platform to discover and share plugins. Actual plugin installation will be done via napari–we detail this step below.

  • napari-bio-sample-data : some additional sample data (File menu)

    • Search for sample.

    • Scroll down until you see napari-bio-sample-data.

    • Select napari-bio-sample-data.

    • Read the documentation on the plugin page.

  • napari-skimage-regionprops : widget to access scikit-image measure.regionprops

    • Search for regionprops.

    • Scroll down until you see napari-skimage-regionprops.

    • Select napari-skimage-regionprops.

    • Read the documentation on the plugin page.

  • In napari, open
    Plugins>Install/Uninstall Plugins…
    and wait for the plugin list to populate.

  • Search for sample in the top search/filter bar, and click the install button next to napari-bio-sample-data.

  • Once the install completes, search for regionprops and install that plugin as well.

    Note

    • After clicking the install button, you can monitor the installing… process by clicking Show status. This can be helpful in trouble-shooting installation issues.

    • After installing, you will typically need to close napari and reopen it, then continue.

  • Restart napari.

  • Open File>Open Sample. napari-bio-sample-data should be a menu option.

    • Select: File>Open Sample>napari-bio-sample-data>3D nuclei

    This sample data includes the same nuclei data as before, but this time a 3D labels and surface layer are present. You can explore these in the 3D view. Delete the surface layer once you’re ready to move on.

  • Open Tools>Measurement Tables>Regionprops (scikit-image, nsr)

    • Ensure that nuclei (data) is selected for the image layer and nuclei label (data) is selected in the image and labels dropdown menus for the Regionprops plugin, respectively. for the labels layer.

    • Use the checkboxes to select some properties to measure, such as perimeter or position. Refer to the scikit-image measure.regionprops documentation for more information

    • Click run, which should yield a table of measurements—depending how many you checked, this could take a moment to run.

    Tip

    Grab the titlebar of the new widget Properties of nuclei label and drag it off the napari viewer to undock. Then you can resize the table for easier browsing. You can re-dock the widget by dragging it on the existing side dock or the bottom of the viewer, by dragging the widget title bar from below the viewer onto the canvas (left of the Activity button).

    • In the labels layer controls widget, check the box show selected to only view the currently selected label. Now in the table, when you click a cell you will be shown the corresponding label.

    Tip

    You can double-click a table header to generate a heat map of that property.

A few other handy plugins#

  1. napari-skimage: a plugin that gives easy access to some scikit-image image processing functions in napari.

  2. napari-animation: a plugin that lets you make (and export) animations in napari by simply setting key frames.

  3. napari-threedee: a plugin to make interacting and annotating in 3D easier.

  4. napari-ome-zarr: a reader plugin for for zarr backed OME-NGFF images (local or remote).

  5. napari-aicsimageio: a reader plugin that uses aicsimageio as a backend. Provides access to proprietary formats (e.g. .lif, .czi) via drag-n-drop. Can also give access to bioformats if bioformats_jar is installed from conda-forge (conda install -c conda-forge bioformats_jar).

  6. napari-matplotlib: a plugin providing widgets with matplotlib based plots, such as histogram, scatter plot, line plot, etc.