Creating a napari plugin

Creating a napari plugin#

Overview#

In this tutorial, we will make a napari analysis plugin from the detect_spots() function we wrote in the first part of this practical session. The primary steps in making a napari plugin are as follows:

Choose which manifest contribution(s) your plugin requires
Create your repository using the napari cookiecutter template
Implement your contributions
Share your plugin with the community

In the following sections, we will work through steps (1) - (3). For step (4), you can refer to the in depth plugin tutorial, or the instructions on napari.org. You can also use the lecture slides as reference material if you’d like.

plugin example

Choosing a contribution#

A contribution is a construct in napari.yaml (the manifest file), that napari uses for each specific type of plugin. Each contribution conforms to a function signature, i.e. the function linked to the contribution defines what napari provides to the plugin (e.g., data and parameters) and what the plugin returns to napari. napari is then able to use the functions pointed to in napari.yaml to carry out the plugin tasks. Please see the contribution reference and contribution guide for more details. Many plugins will declare multiple contributions to provide all of the desired functionality.

The current categories of contributions are described below:

reader: allows loading of specified data formats into napari layers;
writer: this allows layer data to be written to disk in specified formats;
sample data: allows developers to provide users with sample data with their plugin;
widget: allows custom Qt widgets (GUIs) to be added to napari, either from a magic_factory widget, a plain function, or a subclass of QWidget;
theme: allows customization of the entire napari viewer appearance e.g. light theme or dark theme.

In this tutorial, we will create a spot detection plugin by implementing a widget contribution with the spot detection function (detect_spots()) we created in the first part of this practical session.

Using the cookiecutter template to create your plugin repository#

To make creating the creating plugins easier, we provide a template that automatically builds most of the infrastructure for your plugin, so you can focus on implementing the details unique to your plugin. The template is implemented using a command line utility called cookiecutter. In the following steps, you will build your plugin directory using the cookiecutter template.

First, open your terminal and navigate to the folder where you want the plugin folder to be created. As before, we recommend using your Documents folder:

cd ~/Documents

Next, activate the conda environment you created in the first part of the tutorial. This environment includes all of the packages required to make your plugin (including cookiecutter).

conda activate napari-tutorial

In this next step, we will use cookiecutter to create a directory for our plugin from the template. cookiecutter will ask a series of questions that will customize the directory for your plugin. Once completed, a new directory will be created in your current directory. It will come pre-initialized with a git repository.

cookiecutter https://github.com/napari/cookiecutter-napari-plugin

You will be asked for some information to customize the setup of your plugin. Each prompt gives the default value in square brackets ([]). The questions are explained below. Enter your answer after the prompt and press enter to continue.

full_name [Napari Developer]: enter your name here. Names entered here will be listed as the authors of the plugin in the package metadata.
email [yourname@example.com]: this email will be listed as the contact information in the package metadata
github_username_or_organization [githubuser]: if you have a github username, you can enter it here. It will be used to generate a GitHub URL for you after you enter a plugin name.
plugin_name [napari-foobar]: enter the name you would like your plugin to be called. spaces are not allowed and are often replaced with - (e.g., napari-spot-detector). This will be your PyPI package name (if you choose to deploy your plugin).
Select github_repository_url: this is used for plugin metadata and is not required now. If you don’t plan to upload it to your github, select 2.
module_name [napari_foobar]: this is the name of the module containing your plugin code. typically, this is the plugin name with the - replaced with _ (e.g., napari_spot_detector).
display_name [napari FooBar]: this name will show up in the napari viewer and on the napari hub if you release your plugin. You should pick something human readable and ideally indicative of what your plugin does. There are no restrictions on the symbols in this name.
short_description [A simple plugin to use with napari]: give a one sentence description of your plugin. This will go into the readme.
include_reader_plugin [y]: answer y (for yes) if you would like a reader contribution. We do not need a reader contribution for this tutorial, so answer n for no.
include_writer_plugin [y]answer y (for yes) if you would like a writer contribution. We do not need a reader contribution for this tutorial, so answer n for no.
include_sample_data_plugin [y]: answer y (for yes) if you would like a sample data contribution. We do not need a sample data contribution for this tutorial, so answer n for no.
include_dock_widget_plugin [y]: answer y (for yes) if you would like a widget contribution. We are implementing a widget contribution for this tutorial, so answer y for yes.
use_git_tags_for_versioning [n]: we will not be covering setting plugin versions in this tutorial, so enter n for no.
install_precommit [n]: we will not be covering precommit in this tutorial, so enter n for no.
Select license: select the license you would like to use for your plugin. The license sets the rules for how others can build upon and re-use your plugin code. For more information on typical open source licenses, choosealicense.com is a good primer. The default choice is BSD-3.

After completing all of the questions, a directory will be created containing your new napari plugin. You will be given instructions on how to upload the initialized git repository to GitHub. By default, we will not be covering this aspect in the tutorial, but please feel free to ask the teaching team if you would like to give it a try. Your new plugin directory (assuming you called the plugin napari-spot-detector and the module napari_spot_detector) will be organized as follows (with some irrelevant files/folders omitted)

napari-spot-detector
├── .github
│   └── workflows
│       └── test_and_deploy.yml
├── LICENSE
├── MANIFEST.in
├── .napari
│   └── DESCRIPTION.md
├── pyproject.toml
├── README.md
├── setup.cfg
├── src
│   └── napari_spot_detector
│       ├── __init__.py
│       ├── napari.yaml
│       ├── _tests
│       │   ├── __init__.py
│       │   └── test_widget.py
│       └── _widget.py
└── tox.ini

See below for explanations about some of the most notable files, but do not hesitate to reach out to the teaching team if you have questions about any of the other files.

.github/workflows/test_and_deploy.yml: This is a github actions workflow that will automatically run the tests and upload your plugin to pypi (thus making it available through the built-in napari plugin browser. Please ask the teaching team if you would like to learn how to set up your github repository to support this workflow.
pyproject.toml and setup.cfg: These files allow your plugin to be built as a package and installed by pip. The cookiecutter template has set everything up in these files, so you are good to go!
The src/ folder contains all the Python code for your plugin.
src/napari_spot_detector/_widget.py: This file contains example implementations for different widget contributions. This is where you will add your detect_spot() function.
The src/napari_spot_detector/napari.yaml file declares commands and contributions for each example widget in the _widget.py file. Look at these carefully and match up which command & contribution belong to what Python code in the _widget.py file.

You have now set up the directory for your new plugin! You can explore the directory and files with the file browser. In the next step, you will complete your plugin by adding your detect_spots() function to the _widget.py file.

Implementing a function GUI#

In this step, we will implement our detect_spots() function as a plugin contribution. First, we will add our spot detection function to the plugin package. Then, we will add the type annotations to the function to so that napari can infer the correct GUI elements to add to our plugin.

To edit your plugin source code, open an integrated development environment (VSCode is a good, free option) or text editor.
In VSCode, open the directory you created with cookiecutter in the section above.
- From the “File” menu, select “Open…”
- Navigate to and select the directory you created with cookiecutter (~/Documents/napari-spot-detector if you called your plugin napari-spot-detector).
You should now see your plugin directory in the “Explorer” pane in the left hand side of the window. You can double click on folders to expand them and files to open them in the editor.
Open the <module_name>/_widget.py file using VSCode by double clicking on it in the “Explorer” pane.
You will see that it has already been populated with a few code blocks by cookiecutter.
- At the top, you see the imports. You can leave unchanged for now.
```
from typing import TYPE_CHECKING

from magicgui import magic_factory
from qtpy.QtWidgets import QHBoxLayout, QPushButton, QWidget

if TYPE_CHECKING:
    import napari
```
- Next, you see three different ways to add widgets to napari.
  1. The first subclasses QWidget directly. This option provides maximum flexibility, but means you have to take care of adding all the different GUI elements, laying them out, and hooking them up to the viewer.
    class ExampleQWidget(QWidget): # your QWidget.__init__ can optionally request the napari viewer instance # in one of two ways: # 1. use a parameter called `napari_viewer`, as done here # 2. use a type annotation of 'napari.viewer.Viewer' for any parameter def __init__(self, napari_viewer): super().__init__() self.viewer = napari_viewer btn = QPushButton("Click me!") btn.clicked.connect(self._on_click) self.setLayout(QHBoxLayout()) self.layout().addWidget(btn) def _on_click(self): print("napari has", len(self.viewer.layers), "layers")
  2. The second option is to write a magic_factory decorated function. You might recognize this from our intensify widget in the lecture. With minimal extra work you can configure options for your GUI elements, such as min and max values for integers, or choices for dropdown boxes. See the magicgui configuration docs for details on what you can configure in the decorator.
    @magic_factory def example_magic_widget(img_layer: "napari.layers.Image"): print(f"you have selected {img_layer}")
  3. Finally, you see the what looks like just a plain function. We don’t need complex GUI interactions for our plugin, and we don’t want to have to lay out the GUI ourselves, so we will modify this to incorporate our detect_spots function.
    # Uses the `autogenerate: true` flag in the plugin manifest # to indicate it should be wrapped as a magicgui to autogenerate # a widget. def example_function_widget(img_layer: "napari.layers.Image"): print(f"you have selected {img_layer}")
- Find the Command ID in napari.yaml that points to example_function_widget, and then find that Command ID in the Widgets contribution section. Note that unlike the other widget contributions, this one includes autogenerate: true.
```
- command: napari-spot-detector.make_func_widget
  autogenerate: true
  display_name: Example Function Widget
```
- This means our function doesn’t need to know anything about magicgui. If we provide type annotations to the parameters, the GUI widgets will be generated for us without even a decorator!
- Let’s edit example_function_widget to do our spot detection.
You can delete everything above example_function_widget in _widget.py if you want. If you do, make sure to delete the associated Commands and Widget contributions, and the imports in napari_spot_detector/__init__.py!
Copy the gaussian_high_pass() and detect_spots() functions from your notebook from the first part of the tutorial and paste it where the example functions were (the ones you deleted in the previous step).
Next, we need to modify detect_spots() to return the necessary layer data so that napari can create a new Points layer with our detected spots. If detect_spots() returns a LayerDataTuple, napari will add a new layer to the viewer using the data in the LayerDataTuple. For more information on the LayerDataTuple type, please see the docs.
- The layer data tuple should be: (layer_data, layer_metadata, layer_type)
- layer_data: the data to be displayed in the new layer (i.e., the points coordinates)
- layer_metadata: the display options for the layer stored as a dictionary. Some options to consider: symbol, size
- layer_type: the name of the layer type as a string (i.e., 'Points')
Add type annotations to the function parameters (inputs). napari (via magicgui) will infer the required GUI elements from the type annotations. We have to add annotations to both the parameters (i.e., inputs to the function) and the return type.
Annotate the Return type as "napari.types.LayerDataTuple".
Add the required imports for the scipy.ndimage module and scikit-image blob_log() function to the top of the file.
- from scipy import ndimage as ndi
- from skimage.feature import blob_log

_function.py solution#

See below for an example implementation of the _widget.py file, and the associated changes to napari.yaml

# _widget.py
from typing import TYPE_CHECKING
import numpy as np
from scipy import ndimage as ndi
from skimage.feature import blob_log

if TYPE_CHECKING:
    import napari


def gaussian_high_pass(image: np.ndarray, sigma: float = 2):
    """Apply a gaussian high pass filter to an image.

    Parameters
    ----------
    image : np.ndarray
        The image to be filtered.
    sigma : float
        The sigma (width) of the gaussian filter to be applied.
        The default value is 2.

    Returns
    -------
    high_passed_im : np.ndarray
        The image with the high pass filter applied
    """
    low_pass = ndi.gaussian_filter(image, sigma)
    high_passed_im = image - low_pass

    return high_passed_im


def detect_spots(
    image: "napari.types.ImageData",
    high_pass_sigma: float = 2,
    spot_threshold: float = 0.01,
    blob_sigma: float = 2
) -> "napari.types.LayerDataTuple":
    """Apply a gaussian high pass filter to an image.

    Parameters
    ----------
    image : napari.types.ImageData
        The image in which to detect the spots.
    high_pass_sigma : float
        The sigma (width) of the gaussian filter to be applied.
        The default value is 2.
    spot_threshold : float
        The threshold to be passed to the blob detector.
        The default value is 0.01.
    blob_sigma: float
        The expected sigma (width) of the spots. This parameter
        is passed to the "max_sigma" parameter of the blob
        detector.

    Returns
    -------
    layer_data : napari.types.LayerDataTuple
        The layer data tuple to create a points layer
        with the spot coordinates.

    """

    # filter the image
    filtered_spots = gaussian_high_pass(image, high_pass_sigma)

    # detect the spots
    blobs_log = blob_log(
        filtered_spots,
        max_sigma=blob_sigma,
        num_sigma=1,
        threshold=spot_threshold
    )
    points_coords = blobs_log[:, 0:2]
    sizes = 3 * blobs_log[:, 2]

    layer_data = (
        points_coords,
        {
            "face_color": "magenta",
            "size": sizes
        },
        "Points"
    )
    return layer_data

# napari_spot_detector/__init__.py
__version__ = "0.0.1"

#napari.yaml
name: napari-spot-detector
display_name: Spot Detection
contributions:
  commands:
    - id: napari-spot-detector.make_func_widget
      python_name: napari_spot_detector._widget:detect_spots
      title: Make spot detection widget
  widgets:
    - command: napari-spot-detector.make_func_widget
      autogenerate: true
      display_name: Spot Detection

Explore the other files generated by cookiecutter#

In order for napari to automatically find and make your plugin available to the user once it has been installed (i.e., “discoverable”), we must add a napari.manifest entry point to the setup.cfg file. An entry point is a way that a Python package can advertise that it has a component available (our plugin in this case). napari searches the python environment for packages that have a napari.manifest and then uses the path in the entry_point to find napari.yaml, where all your plugin functionality is declared.

If we open the setup.cfg file created by cookiecutter, we see that the entry point was already added by the cookiecutter template! If you called your plugin napari-spot-detector and your module napari_spot_detector, you will see the following:

[options.entry_points]
napari.manifest =
    napari-spot-detector = napari_spot_detector:napari.yaml

Note that src doesn’t occur in the path to napari.yaml, but napari.yaml is definitely within the src folder! Python knows to look inside the src folder for your code because setup.cfg declares an options.packages.find key.

[options.packages.find]
where = src

Testing/Installing your plugin#

To test and use our plugin, we need to install it in our Python environment. First, return to your terminal and verify you have the napari-tutorial environment activated. Then, navigate to the directory that you created with the cookiecutter. For example, if you named your plugin napari-spot-detector, you would enter the following into your terminal.

cd ~/Documents/napari-spot-detector

Then, we install the plugin with pip. pip is the package installer for Python (see the documentation for more information). We will use the -e option to install in “editable” mode. This means that when we make a change to our source code, it will update the installed package the next time it is imported, without us having to reinstall it.

pip install -e .

To confirm if your installation completed successfully, you can launch napari from the command line.

napari

Once napari is open, you can open your plugin from the “Plugin” menu. You can test your plugin by locating the spots image from the tutorial notebooks folder we downloaded at the beginning of this tutorial in the File browser (<path to notebook folder>/data/stardist_masks.tif), dragging the image into the napari viewer, and try running the plugin.

Congratulations! You have made your first napari plugin!

Bonus exercises#

In case you have finished all of the exercises with some time to spare, we have provided some ideas for ways that you can extend the plugin. Please feel free to give them a go and ask the teaching team if you have any questions.

Add sample data to your plugin. To do so, you would need to implement the sample data contribution
Add an option to your detect_spots() function plugin to return the filtered image in addition to the points layer.
Add some tests to the _tests/test_widget.py file.
Upload your plugin to github
Start your own plugin
Consult with the teaching team about integrating napari into your workflow