IPPN : Napari as a tool for phenotyping

This document is part of the Hands on session of the IPPN 2023. The aim of this document is to show the value of napari in plant phenotyping.

It is not intended to be a training session. That would require a lot of time to fully explore napari. The Hands on session for napari is a three-part discovery activity:

• Introducing the napari visualisation tools
• Getting started a napari plugin
• Getting started the design and development of a plugin

Prerequisites tools for this session Hands On

• Anaconda distribution
• Napari as bundle app and python library
• VS Code
• Git (Standalone Installer)

Useful links

• Finding and installing a napari plugin : Install napari

• Your First Plugin : Design your plugin

• Napari hub : Napari hub is a service of the Chan Zuckerberg Initiative in collaboration with Napari. Here, you can discover, install, and share napari plugins

• Image.sc : Help or support requests send to napari community partner

• Github issues : Bug reports

• FAQ : Reccurent questions about napari, napari-hub and the way for building and sharing plugins

Video tutorial (in french) :

• Installer NAPARI et faire son premier plugin

• NAPARI Plugin for deep segmentation and manual correction

Authors

Herearii Metuarea, Research Engineer at INRAe

Other contributors

Imhorphen team at INRAe:

• David Rousseau, Full Professor, University of Angers
• Pejman Rasti, Assistant professor, University of Angers
• Félix Mercier, Research Engineer, INRAe