Microscopy Data Analysis: Machine Learning and the Bioimage Archive 2025

Microscopy Data Analysis: Machine Learning and the Bioimage Archive 2025 is organized by  European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL - EBI) and will be held from Mar 31 - Apr 04, 2025.

Description:
This virtual course will show how public bioimaging data resources, centred around the BioImage Archive, enable and enhance machine learning based image analysis. The content will explore a variety of data types including electron and light microscopy and miscellaneous or multi-modal imaging data at the cell and tissue scale. Participants will cover contemporary biological image analysis with an emphasis on machine learning methods, as well as how to access and use images from databases. Further instruction will be offered using applications such as ZeroCostDL4Mic, ilastik, the BioImage Model Zoo, and CellProfiler.

What will I learn?
Learning outcomes:
After the course you should be able to:

• Interact programmatically with the BioImage Archive and other data resources
• Apply pre-built machine learning models to image data
• Train and retrain machine learning models on image data
• Utilise machine learning approaches for object detection, image segmentation, and de-noising
• Generate quantitative conclusions from images

Course content:
During this course you will learn about:
Data repositories

• BioImage Archive
• Image Data Resource
• EMPIAR
• BioStudies

Analysis tools

• ilastik
• Colaboratory
• BioImage Model Zoo
• ZeroCostDL4Mic
• CellProfiler
• Cellpose