SwissBIAS napari intro and plugins 11/21

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 session are Guillaume Witz (@guiwitz), Kevin Yamauchi (@ky396), Lorenzo Gaifas (@brisvag).

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

Tutorial instructions

1. Install napari and dependencies. Instructions here.

2. Download the notebooks and launch jupyter notebook. Instructions here.

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

4. Segment and measure nuclei using the cellpose plugin (part_1_segmenting_and_measuring_nuclei.ipynb).

5. 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.

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