Introduction to napari

Overview

This tutorial shows how to perform and analyze image segmentations in volume Focused Ion Beam Scanning Electron Microscopy (FIBSEM) data. This workshop will take you through the basics of bioimage analysis in Python and napari. We will be performing some analysis on segmented mitochondria using a combination of napari, empanada, and napari-clusters-plotter.

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 a simple napari plugin

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. Visualize and explore IMC data

3. Segment and measure mitochondria using the cellpose plugin (part_1_segment_and_analyze_mitochondria.ipynb).

4. 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_3_spot_detection_tutorial_beginner.ipynb: this is the activity notebook for people new to image processing with python

   • part_3_spot_detection_tutorial_advanced.ipynb: this is the activity notebook for people with experience performing image processing with python

   • part_3_spot_detection_tutorial_solution.ipynb: this is the solution to the activity.

5. (optional) Turn your spot detection function into a napari plugin. Instructions here.