Workshops and courses

ELIXIR node event Microscopy data analysis: machine learning and the BioImage Archive

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Date: 15 - 19 May 2022

This course will introduce programmatic approaches used in the analysis of bioimage data via the BioImage Archive. The content will explore a variety of data types including electron microscopy, cell and tissue microscopy, and miscellaneous or multi-modal imaging data. Participants will cover contemporary biological image analysis with an emphasis on machine learning and advanced image analysis. Further instruction will be offered using applications such as ZeroCostDL4Mic, ilastik, ImJoy, the BioImage Model Zoo, and CellProfiler.

Virtual course

Participants will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack. 

Pre-recorded material may be provided before the course starts that participants will need to watch, read or work through to gain the most out of the actual training event. In the week before the course, there will be a brief induction session. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning participants will not require access to a powerful computer or install complex software on their own machines.

Participants will need to be available between the hours of 09:00 - 17:30 BST each day of the course. Trainers will be available to assist, answer questions, and provide further explanations during these times.

 

Contact: Juanita Riveros - [email protected]

Keywords: BioImage Archive, BioStudies Database, Electron Microscopy Public Image Archive - EMPIAR, Bioimage analysis, Machine learning models, Scientific computing, Light microscopy, Electron microscopy

Organizer: European Bioinformatics Institute (EBI)

Target audience: This course is aimed at scientists working with biomage data across the life sciences. It is suitable for those involved in creating bioimages or taking their first steps in analysis. The content would also be suitable for those wanting to learn more about the BioImage Archive and gain experience with machine learning approaches for image analysis. The programme will be of particular interest to bioimage analysts with questions relating to the use of ‘big data’ and using the wealth of publically available data curated in the BioImage Archive. The course should be accessible to members of the bioimaging community and does not require prior experience with machine learning methods or use of the BioImage Archive. Applicants are encouraged to explore the resources below before starting their application. Applicants should be comfortable with basic programming tasks and have experience working with Python. Prerequisite reading: BioImage Archive: A call for public archives for biological image data ZeroCostDL4Mic: an open platform to simplify access and use of Deep-Learning in Microscopy The BioStudies database - one stop shop for all data supporting a life sciences study EMPIAR: a public archive for raw electron microscopy image data Image Data Resource: a bioimage data integration and publication platform BioImage Model Zoo  

Capacity: 40

Event types:

  • Workshops and courses

Scientific topics: Machine learning, Bioimaging, Image analysis

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