Bioimage Model Zoo

BioImage Model Zoo – Lecture

Trainer: Anna Kreshuk

Lecture authors: Anna Kreshuk, Wei Ouyang, Esti Gomez De Mariscal

Overview: This lecture will cover the BioImage Model Zoo – a community website for sharing neural networks pre-trained on bioimage analysis tasks. We will give the motivation behind the development of the zoo and demonstrate how it can be used together with ilastik, DeepImageJ and ImJoy softwares. We will look into several tasks, including image classification and segmentation, and show how one can create a shareable model and submit it to the website.

Learning outcomes

By the end of this session you will be able to:

• Identify the main utilities of the BioImage Model Zoo portal
• Perform basic interactions of the portal with ilastik, DeepImageJ and ImJoy softwares

Materials:

• Presentation slides Anna
• Presentation slides Wei
• Presentation slides Estibalis

BioImage Model Zoo – Practical

Trainers: Anna Kreshuk, Dominik Kutrra, Wei Ouyang, Esti Gomez De Mariscal, Fynn Beuttenmüller

Overview: Follow the GitHub page for advanced bioimage analysis workflows, tools and datasets – Practical task