Getting started

Note

As you are building your workshop, consider who your audience is and what their goals are. One way to do that is to come up with a few learner profiles.

Make sure this page contains basic information about your workshop, such as the main contents, instructors’ names and contact information if available, and information about the date and location for this session.

Below you can see an example of how this can be done.

This workshop will take you through the basics of bioimage analysis in Python and napari, and introduce you to the napari plugin engine. We will be performing some analysis on segmented nuclei using a combination of napari, scikit-image, scipy, and cellpose. Additionally, we will make a spot detection plugin.

Instructors

The instructors for this workshop are

• Kasia Kedziora

• Kyle Harrington

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

• use napari as an image viewer

• perform interactive analysis with napari in a jupyter notebook

• make use of the napari plugin ecosystem

• make simple plugins using the napari hookspecs

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. GUI-only instructions are here, and Python-based instructions here.

If following the Python-based instructions you will then need to:
2. Download the notebooks and launch the jupyter notebook application. Instructions here.

If you are following the GUI-only instructions, then you have already downloaded and launched the notebooks by following the instructions.

Tutorial instructions

NOTE: THE ACTIVITY INSTRUCTIONS ARE UNDER CONSTRUCTION

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

2. Segment and measure nuclei using the cellpose plugin (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.