Bioimage Analysis with Napari

Description: In this course, we will learn how to use the free open-source software (FOSS) Napari for bioimage analysis. Napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images. Being highly extensible, Napari can be used to perform state-of-the-art image analysis in a user-friendly environment. The course focuses on the practical application of Napari and requires no preliminary knowledge of Python.

Next course time: Neuronal Circuit Dysfunction of C­NS diseases (WPM31), July 09, 2024, 9:30 am to 3 pm
Venue: DZNE Bonn, B.1.008

duration: 12.5 h for lectures including hands-on sessions
course held in: 2024, 2023
published: June 25, 2023
latest update: October 28, 2024 (09:02 pm)

Jump to Syllabus

Current announcements

Troubleshooting session: On Monday, June 8, 2024, 1 pm, there will be a 1 h troubleshooting session for those who have problems installing Napari. Please bring your laptop with you. We will meet in room B.1.008.

Functional 2p image analysis course on July 10, 2024: Please also bring your laptop for this course.

Course requirements

• Please, bring a laptop.
• Please, install conda and Napari before the course starts. Follow the steps described in this installation guide.
• Please, download the course material, the links are provided in the installation guide.
• You can also bring your own images you have taken in the lab.

Syllabus

Tutorial 1: Napari installation guide

Tutorial 2: Basic handling of Napari

Tutorial 3: Reslicing stacks in Napari

Tutorial 4: Cropping images in Napari

Tutorial 5: Scale bars and adjusting image scaling

Tutorial 6: The Napari Assistant

Tutorial 7: Image denoising and background subtraction in Napari

Tutorial 8: Bleach correction in Napari

Tutorial 9: Spectral unmixing in Napari

Tutorial 10: Image registration in Napari

Tutorial 11: Image segmentation and feature extraction

Tutorial 12: Advanced cell segmentation with Cellpose

Tutorial 13: Advanced cell segmentation with StarDist

Tutorial 14: Changing labels in Napari

Tutorial 15: Colocalizing cells

Tutorial 16: Tracking cell migration

Tutorial 17: Filament tracing

Tutorial 18: Data exploration, dimensionality reduction and clustering with Napari

Acknowledgements

Image credits

Exercises

Unless otherwise stated, please perform the examples shown in each tutorial. Use the image file(s) shown in the example or any other file provided in GitHub data folder. You can also use your own images taken in the lab or an appropriate sample image from the Cell Image Libraryꜛ. Also try to combine the techniques you have already learned in the previous tutorials (if appropriate). Each tutorial including reading time and exercise takes around 15-30 minutes.

Past courses

• N­euronal Circuit Dysfunction of C­NS diseases (WPM31), June 24, 2024
• N­euronal Circuit Dysfunction of C­NS diseases (WPM31), June 30 and July 5 and 6, 2023

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This course material is under Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License (CC BY-NC-SA 4.0).