Introduction to napari plugins#

Overview#

This workshop will take you through the basics of bioimage analysis in Python and napari and developing napari plugins. In the first part, we will be performing some analysis of fluorescently-labeled nuclei with napari, stardist, and napari-clusters-plotter. In the second part, we will make your first napari plugin.

Goals#

The aim of this workshop is to provide an introduction to bioimage analysis in Python and napari. By the end of the workshop you should be able to

Pre-tutorial setup#

So that we can best utilize our time together, please do the following before arriving at the tutorial:

  1. Install napari and dependencies. Instructions here.

  2. Download the notebooks. Instructions here.

Tutorial instructions#

  1. Do the introduction to viewing images in napari (part_0_viewer_intro.ipynb).

  2. Segment and measure nuclei using the stardist and napari-clusters-plotter plugins (part_1_segmenting_and_measuring_nuclei.ipynb).

  3. Perform spot detection using your own spot detection function. There are 3 versions of this tutorial (see description below). They all cover the same content, they just require more or less coding depending on experience level.

    • part_2_spot_detection_tutorial_beginner.ipynb: this is the activity notebook for people new to image processing with python

    • part_2_spot_detection_tutorial_advanced.ipynb: this is the activity notebook for people with experience performing image processing with python

    • part_2_spot_detection_tutorial_solution.ipynb: this is the solution to the activity.

  4. Turn your spot detection function into a napari plugin. Instructions here.

  5. Extend the plugin you must made (some ideas below) or make your own napari plugin.

    • Add a sample data plugin to provide images of the nuclei and spots

    • Add a plugin that takes a nuclei segmentation and the detected spots and assigns each spot to the nearest nucleus. Hint: you can color points by a feature value (e.g., the assigned nucleus).