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Course content
Introduction to bioimage analysis
Bioimaging data resources at EMBL-EBI
- BioImaging data resources at EMBL-EBI – an overview of the BioImage Archive, BioStudies and EMPIAR
- BioImaging data resources at EMBL-EBI – practical
Open access machine learning resources for bioimage analysis
Image Data Resource – Discovery using community repositories
Advanced computational topics in the context of bioimage analysis
Technical help sheet
Trainer biographies
Further learning
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BioImage Model Zoo – lecture

Overview: This lecture covers the BioImage Model Zoo – a community website for sharing neural networks pre-trained on bioimage analysis tasks. The speakers give the motivation behind the development of the zoo and demonstrate how it can be used together with ilastik and DeepImageJ softwares. The speakers also look into several tasks, including image classification and segmentation, and show how one can create a shareable model and submit it to the website. (Lecture authors: Anna Kreshuk, Wei Ouyang, Esti Gomez De Mariscal)

Learning outcomes:

After this section you should be able to:

Identify how to bring pre-trained models to end-user software (for bioimage analysis) and run them without code through the BioImage Model Zoo platform

Materials:

Presentation

Microscopy data analysis: machine learning and the BioImage Archive

BioImage Model Zoo – lecture