Virtual course

Microscopy data analysis: Machine learning and the BioImage Archive

Develop programmatic skills for the analysis of bioimage data.

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, the BioImage Model Zoo, and CellProfiler.

The organisers welcome applications from scientists who have specific research questions that look to use publicly available data held in the BioImage Archive and can demonstrate use cases for the resource.

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

Who is this course for?

This course is aimed at scientists working with bioimage 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 bio-image analysts with questions relating to the use of ‘big data’ and using the wealth of publically available data curated in the BioImageArchive.

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 is necessary, but 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:

What will I learn?

Learning outcomes

After this 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:

 

Course funding

This course is funded in part by the Wellcome grant "The Image Data Resource: Making Biological Imaging Data FAIR", award number 212962/Z/18/Z.

Trainers

Alvis Brazma
EMBL-EBI
Virginie Uhlmann
EMBL-EBI
Craig Russell
EMBL-EBI
Ricardo Henriques
UCL
Romain Laine
UCL
Soham Mandal
EMBL-EBI
Ugis Sarkans
EMBL-EBI
Awais Athar
EMBL-EBI
Matthew Hartley
EMBL-EBI
Ardan Patwardhan
EMBL-EBI
Osman Salih
EMBL-EBI
Andrii Iudin
EMBL-EBI
Simone Weyand
EMBL-EBI
Jason Swedlow
University of Dundee
Jean Marie Burel
University of Dundee
Anna Kreshuk
EMBL
Beth Cimini
Broad Institute
Wei Ouyang
SciLifeLAb
Esi Gomez de Mariscal
UC3M
Dominik Kutra
EMBL
Petr Walczysko
University of Dundee
Frances Wong
University of Dundee
Nasim Jamali
Broad Institute
David Stirling
Broad Institue
Barbara Diaz-Rohrer
Broad Institute
Martin Weigert
EPFL
Guillaume Jacquemet
University of Turku
Gerard Kleywegt
EMBL-EBI

Programme

All times are given in British Summer Time (BST).

Day 1 - Monday 12 July

09:30-09:45 Arrival and networking hangouts  
09:45-10:00 Welcome and overview of virtual training Pati Carvajal Lopez & Alex Holinski
10:00-10:30 Introduction to image analysis Alvis Brazma & Virginie Uhlmann
10:30-10:45 Break  
10:45-11:30 ZeroCostDL4Mic - lecture and questions Ricardo Henriques, Romain Laine, Guillaume Jacquemet
11:30-12:30 Segmentation with StarDist and SplineDist - lecture and questions Soham Mandal, Virginie Uhlmann, Martin Weigert
12:30-13:00 Flash talks & discussion  
13:00-13:25 Break  
13:25-15:00 Practical session Romain Laine, Craig Russell, Virginie Uhlmann, Soham Mandal
15:00-15:15 Break  
15:15-16:30 Practical session Romain Laine, Craig Russell, Virginie Uhlmann, Soham Mandal
16:30-17:00 Discussion and networking  
17:00 End of day  

Day 2 - Tuesday 13 July

09:30-10:00 Arrival and networking hangouts  
10:00-11:00 BioStudies - lecture and questions Ugis Sarkans & Awais Athar
11:00-11:15 Break  
11:15-12:30 Variety - lecture and questions Matthew Hartley & Craig Russell
12:30-13:00 Flash talks & discussion  
13:00-13:30 Break  
13:30-15:30 Practical session Craig Russell, Romain Laine & Guillaume Jacquemet
15:30-15:45 Break  
15:45-16:30 Practical session Craig Russell, Romain Laine & Guillaume Jacquemet
16:30-17:00 Discussion and networking  
17:00 End of day  

Day 3 - Wednesday 14 July

09:30-10:00 Arrival and networking hangouts  
10:00-11:00 EMPIAR: past, present and future - lecture and questions Gerard Kleywegt
11:00-11:15 Break  
11:15-12:30 Depositing and accessing data at EMPIAR - lecture and questions Osman Salih
12:30-13:00 Flash talks & discussion  
13:00-13:30 Break  
13:30-15:00 Depositing and accessing data at EMPIAR - practical Andrii Iudin, Osman Salih & Simone Weyand
15:00-15:15 Break  
15:15-16:30 Depositing and accessing data at EMPIAR - practical Andrii Iudin, Osman Salih & Simone Weyand
16:30-17:00 Discussion and networking All
17:00 End of day  

Day 4 - Thursday 15 July

09:30-10:00 Arrival and networking hangouts  
10:00-11:00 Image data resource - lecture + Q&A Jason Swedlow
11:00-11:15 Break  
11:15-12:30 Image data resource - lecture and questions Frances Wong
12:30-13:00 Flash talks & discussion  
13:00-13:30 Break  
13:30-15:30 Image data resource - practical Jean Marie Burel, Petr Walczysko, Frances Wong
15:30-15:45 Break  
15:45-16:30 Discussion and networking All
17:00 End of day  

Day 5 - Friday 16 July

09:30-10:00 Arrival and networking hangouts  
10:00-11:00 BioImage Model Zoo - lecture and questions Anna Kreshuk
11:00-11:15 Break  
11:15-13:15 BioImage Model Zoo - practical ilastik team, Wei Ouyang, Esti Gomez de Mariscal, Dominik Kutra
13:15-13:45 Break  
13:45-14:45 CellProfiler - lecture and questions Beth Cimini
14:45-15:00 Break  
15:00-16:30 CellProfiler - practical Nasim Jamali, David Stirling, Barbara Diaz-Rohrer
16:30-17:00 Discussion and course wrap-up All
17:00 End of day  

Please read our application advice before starting your application. In order to be considered for a place on this course, you must do the following:

  • Complete the online application form
  • Provide a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words.
  • Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course.

Please complete the online application form by 23:59 (BST) Friday 14 May.

Incomplete applications will not be considered.

All applicants will be informed of the status of their application (successful, waiting list, rejected) no later than Tuesday 1 May.

Participant Flash Talks

All participants will be asked to give a short presentation about their research work as part of the course. These provide an opportunity to share their research with the other participants and provide a forum for discussion. Further details will be provided following registration.

This course has ended

12 - 16 July 2021
£100
Contact
Marina Pujol

Organisers
  • Pati Carvajal Lopez
    EMBL-EBI
  • Alex Holinski
    EMBL-EBI
  • Craig Russell
    EMBL-EBI
  • Virginie Uhlmann
    EMBL-EBI
  • Alvis Brazma
    EMBL-EBI
  • Jason Swedlow
    University of Dundee

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