Deep Learning for Image Analysis – Course and Conference Office

EMBL Course

Deep Learning for Image Analysis


EMBL is committed to sharing research advances and sustaining scientific interaction throughout the coronavirus pandemic. We are delighted to announce that the course is going virtual and invite you to join us online.

Registration is not yet open for this event. If you are interested in receiving more information please register your interest.

Course Overview

This is a blended learning course on Deep Learning for Image Analysis.


This course is aimed at both core facility staff and research scientists.

Prerequisites for this workshop are programming skills in Python and ideally Tensorflow, Keras or Pytorch as well as basic knowledge of machine learning theory.

Participants should provide an outline of one image analysis task they would like to work on during the on-site part of the course. Neural networks have been successfully applied to various medical and biological imaging modalities including PALM/STORM, light sheet fluorescence microscopy, high-throughput microscopy, electron microscopy, X-ray tomography. However, they require observation-outcome-pairs for training. Ideally, you will be provide annotated images for network training during the course.

Learning Outcomes

After this course you should be able to:

  • Understand the fundamentals of machine learning methods suitable for image analysis
  • Advise users/colleagues in strategies to obtain ground truth
  • Train and use a CNN for a bioimage analysis task studied in the course
  • Perform simple quality control on the results

Speakers and Trainers

Scientific Organisers

Course Organisers

Irena Provaznikova

Training Lab Technician

EMBL Heidelberg Germany

Diah Yulianti

Course and Conference Officer

EMBL Heidelberg Germany

Preliminary Programme

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All times in the programme below are shown as the time in Europe/Berlin.

To find out the equivalent time zone in your location, enter Berlin, the programme time and date along with your city into the Time Zone Converter.

Day 1 – Monday 17 January 2022
12:45 – 13:00Check-in of the day 
13:00 – 13:15Welcome and course overview
13:15 – 14:30Icebreaker
14:30 – 14:45Break
14:45 – 15:30Live talk followed by Q&A session
15:30 – 16:00Introduction to practicals with instructors
16:00 – 18:00Practicals in small groups
18:00 – 18:30Meet the instructors
18:30 – 19:00Speednetworking
Day 2 – Tuesday 18 January 2022
12:45 – 13:00Check-in of the day
13:00 – 13:45Live talk followed by Q&A session
13:45 – 14:15Meet the instructors
14:15 – 16:15Practicals in small groups
16:15 – 16:45Meet the instructors
16:45 – 17:00Break
17:00 – 18:00Social activity
Day 3 – Wednesday 19 January 2022
12:45 – 13:00Check-in  of the day
13:00 – 13:45Live talk followed by Q&A session
13:45 – 14:15Meet the instructors
14:15 – 16:15Practicals in small groups
16:15 – 16:45Meet the instructors
16:45 – 17:00Break
17:00 – 18:00The AI: Let’s talk about it!
Day 4 – Thursday 20 January 2022
12:45-13:0012:45 – 13:00Check-in of the day
13:00-13:2013:00 – 13:20Live talk followed by Q&A session
13:20-13:4013:20 – 13:40Real use case presentation: Segmentation
13:40-14:0013:40 – 14:00Real use case presentation: Classification
14:00-14:3014:00 – 14:30Quiz break
14:30-15:0014:30 – 15:00Meet the instructors
15:00-17:0015:00 – 17:00Practicals in small groups
17:00-17:3017:00 – 17:30Meet the instructors
Day 5 – Friday 21 January 2022
12:45 – 13:00Check-in of the day
13:00 – 15:00Group activity: Finish practicals, preparation of presentations
15:00 – 15:15Break
15:15 – 16:30Group presentations
16:30 – 16:45Break
16:45 – 18:00Group presentations
18:00 – 18:30Discussion and wrap-up
18:30 – 18:45End of course


Sponsorship Opportunities

We offer a variety of event sponsoring possibilities, with the flexibility to select a set sponsorship package or combine individual sponsorship options to suit your event budget. Discounts are available for companies sponsoring multiple events at EMBL Heidelberg. View other conferences, or contact sponsorship@embl.de for further information.

If you are interested in becoming a media partner of this event, please visit our media partnerships webpage.

Date: 17 - 21 Jan 2022

Location: Virtual


  • Anna Kreshuk
    EMBL Heidelberg, Germany
    • Constanin Pape
      EMBL Heidelberg, Germany

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