Anna Kreshuk
EMBL Heidelberg
Germany
EMBL Course
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.
The advent of deep learning has brought a revolution in the field of computer vision, including most tasks and research questions concerned with microscopy image analysis. Neural networks have been successfully used for image restoration, classification and segmentation, for the detection of objects and characterisation of their morphology, for high-throughput imaging and large-scale processing in 3D. Despite these advances, training and deployment of such neural networks remains difficult for practitioners of image analysis. The aim of our course is to close this gap and teach the participants – in the most hands-on way possible – to apply deep learning-based methods to their own data and image analysis problems.
This is a blended learning course. We will begin with 3 pre-course sessions (on Friday 18 Dec 2020, Friday 15 January 2021 and Friday 29 January 2021) which will bring everyone to a good starting position for a week-long intensive virtual course in February 2021. The 3 pre-course sessions will have associated homework. The week-long course in February 2021 will include a few talks, but will mostly be devoted to hands-on work on real data, in small groups of 3-4 participants.
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 course. Ideally, you will provide annotated images for network training during the course.
After this course you should be able to:
EMBL Heidelberg
Germany
University of Angers and ESAIP, École Supérieure Angevine en Informatique
France
University of Angers
France
Independent researcher
Germany
École Polytechnique Fédérale de Lausanne (EPFL)
Switzerland
EMBL Heidelberg
Germany
ETH Zürich
Switzerland
INSA Lyon
France
University of Angers
France
University of Angers
France
ETH Zürich
Switzerland
and Tooploox
Poland
ETH Zürich
Switzerland
University of Wroclaw and Tooploox
Poland
EMBL Heidelberg
Germany
ETH Zürich
Switzerland
and Tooploox
Poland
Course and Conference Manager
EMBL Heidelberg
Germany
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Time | Speaker |
---|---|
12:50 – 13:30 (CET) 06:50 – 07:30 (EDT) | Welcome and introductions (organisers & instructors)Anna Kreshuk – EMBL Heidelberg, Germany Valentyna Zinchenko – EMBL Heidelberg, Germany Elisabeth Zielonka – EMBL Heidelberg, Germany Tim Nürnberger – EMBL Heidelberg, Germany Maryann Heck – EMBL Heidelberg, Germany Irena Provaznikova – EMBL Heidelberg, Germany |
13:30 – 14:15 (CET) 07:30 – 08:15 (EDT) | Interactive session: Flash talks from participants (2 slides / 2 min about yourself & your work) |
14:15 – 14:30 (CET) 08:15 – 08:30 (EDT) | Break |
14:30 – 15:15 (CET) 08:30 – 09:15 (EDT) | Live talk followed by Q&A session (35 min talk plus 10 min Q&A): Segmentation Anna Kreshuk – EMBL Heidelberg, Germany |
15:15 – 15:30 (CET) 09:15 – 09:30 (EDT) | Break |
15:30 – 16:00 (CET) 09:30 – 10:00 (EDT) | Introduction to practicals by instructors in Zoom breakout rooms |
16:00 – 18:00 (CET) 10:00 – 12:00 (EDT) | Practicals in small groups |
18:00 – 18:30 (CET) 12:00 – 12:30 (EDT) | Meet the instructors in Zoom breakout rooms |
18:30 (CET) 12:30 (EDT) | End of Day 1 – Continued access to networking and discussion platform, pre-recorded lectures and course materials on eCampus |
Time | Speaker |
---|---|
12:50 – 13:00 (CET) 06:50 – 07:00 (EDT) | Overview of the day |
13:00 – 13:45 (CET) 07:00 – 07:45 (EDT) | Live talk followed by Q&A session (35 min talk plus 10 min Q&A)Image Restoration and Nuclei Detection Martin Weigert – École Polytechnique Fédérale de Lausanne (EPFL), SwitzerlandUwe Schmidt – Independent researcher, Germany |
13:45 – 14:15 (CET) 07:45 – 08:15 (EDT) | Virtual Social Programme: Online Pictionary |
14:15 – 14:30 (CET) 08:15 – 08:30 (EDT) | Break |
14:30 – 14:40 (CET) 08:30 – 08:40 (EDT) | Group briefings with instructors in Zoom breakout rooms |
14:40 – 16:00 (CET) 08:40 – 10:00 (EDT) | Practicals in small groups |
16:00 – 16:30 (CET) 10:00 – 10:30 (EDT) | Meet the instructors in Zoom breakout rooms |
16:30 – 18:00 (CET) 10:30 – 12:00 (EDT) | Practicals in small groups (continued) |
18:00 – 18:30 (CET) 12:00 – 12:30 (EDT) | Meet the instructors in Zoom break out rooms |
18:30 (CET) 12:30 (EDT) | End of Day 2 – Continued access to networking and discussion platform, pre-recorded lectures and course materials on eCampus |
Time | Speaker |
---|---|
12:50 – 13:00 (CET) 06:50 – 07:00 (EDT) | Overview of the day |
13:00 – 13:45 (CET) 07:00 – 07:45 (EDT) | Live talk followed by Q&A session (35 min talk plus 10 min Q&A) Data augmentation strategies David Rousseau – University of Angers, France |
13:45 – 14:15 (CET) 07:45 – 08:15 (EDT) | Virtual Social Programme: Pub Quiz |
14:15 – 14:30 (CET) 08:15 – 08:30 (EDT) | Break |
14:30 – 14:40 (CET) 08:30 – 08:40 (EDT) | Group briefings with instructors in Zoom breakout rooms |
14:40 – 16:00 (CET) 08:40 – 10:00 (EDT) | Practicals in small groups |
16:00 – 16:30 (CET) 10:00 – 10:30 (EDT) | Meet the instructors in Zoom breakout rooms |
16:30 – 18:00 (CET) 10:30 – 12:00 (EDT) | Practicals in small groups (continued) |
18:00 – 18:30 (CET) 12:00 – 12:30 (EDT) | Meet the instructors in Zoom breakout rooms |
18:30 (CET) 12:30 (EDT) | End of Day 3 – Continued access to networking and discussion platform, pre-recorded lectures and course materials on eCampus |
Time | Speaker |
---|---|
12:50 – 13:00 (CET) 06:50 – 07:00 (EDT) | Overview of the day and group photo |
13:00 – 13:20 (CET) 07:00 – 07:20 (EDT) | Live talk followed by Q&A session (15 min talk plus 5 min Q&A): Image classification Valentyna Zinchenko – EMBL Heidelberg, Germany |
13:20 – 13:25 (CET) 07:20 – 07:25 (EDT) | Break (to switch to next live talk) |
13:25 – 13:45 (CET) 07:25 – 07:45 (EDT) | Real use case presentation: Classification (15 min talk plus 5 min Q&A) David Rousseau – University of Angers, France |
13:45 – 13:50 (CET) 07:45 – 07:50 (EDT) | Break (to switch to next live talk) |
13:50 – 14:10 (CET) 07:50 – 08:10 (EDT) | Real use case presentation: Segmentation (15 min talk plus 5 min Q&A) David Rousseau – University of Angers, France |
14:10 – 14:30 (CET) 08:10 – 08:30 (EDT) | Break |
14:30 – 14:40 (CET) 08:30 – 08:40 (EDT) | Group briefings with instructors in Zoom breakout rooms |
14:40 – 16:00 (CET) 08:40 – 10:00 (EDT) | Practicals in small groups |
16:00 – 16:30 (CET) 10:00 – 10:30 (EDT) | Meet the instructors in Zoom breakout rooms |
16:30 – 18:00 (CET) 10:30 – 12:00 (EDT) | Practicals in small groups (continued) |
18:00 – 18:30 (CET) 12:00 – 12:30 (EDT) | Meet the instructors in Zoom breakout rooms |
18:30 (CET) 12:30 (EDT) | End of Day 4 – Continued access to networking and discussion platform, pre-recorded lectures and course materials on eCampus |
Time | Speaker |
---|---|
12:50 – 13:00 (CET) 06:50 – 07:00 (EDT) | Overview of the day |
13:00 – 15:00 (CET) 07:00 – 09:00 (EDT) | Group activity: Finish practicals, preparation of presentations |
15:00 – 15:10 (CET) 09:00 – 09:10 (EDT) | Break |
15:10 – 16:20 (CET) 09:10 – 10:20 (EDT) | Group activity: Group presentations (Groups 1-3: What worked, what didn’t, what could be done next? (20 min per group) |
16:20 – 16:30 (CET) 10:20 – 10:30 (EDT) | Break |
16:30 – 17:40 (CET) 10:30 – 11:40 (EDT) | Group activity: Group presentations (Groups 4-6: What worked, what didn’t, what could be done next? (20 min per group) |
17:40 – 17:50 (CET) 11:40 – 11:50 (EDT) | Break |
17:50 – 18:30 (CET) 11:50 – 12:30 (EDT) | Interactive: Discussion & Wrap-up |
18:30 (CET) 12:30 (EDT) | End of the course – Continued access to networking and discussion platform, pre-recorded lectures and course materials on eCampus for two weeks |
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Time | Session |
---|---|
10:45-11:00 | Opening remarks |
11:00-11:15 | Session |
11:15-11:45 | Invited speaker |
11:45-12:15 | Invited speaker |
12:15-12:30 | Selected short talk |
12:30-12:45 | Selected short talk |
12:30-14:00 | Lunch |
14:00-14:15 | Selected short talk |
14:15-14:30 | Selected short talk |
14:30-14:45 | Selected short talk |
14:45-15:00 | Selected short talk (Virtual) |
15:00-15:15 | Coffee Break |
00:00-00:00 | Session |
15:15-15:45 | Invited speaker |
15:45-16:15 | Invited speaker |
16:15-16:30 | Selected short talk |
16:30-16:45 | Selected short talk |
Time | Session |
---|---|
10:45-11:00 | Opening remarks |
11:00-11:15 | Session |
11:15-11:45 | Invited speaker |
11:45-12:15 | Invited speaker |
12:15-12:30 | Selected short talk |
12:30-12:45 | Selected short talk |
12:30-14:00 | Lunch |
14:00-14:15 | Selected short talk |
14:15-14:30 | Selected short talk |
14:30-14:45 | Selected short talk |
14:45-15:00 | Selected short talk (Virtual) |
15:00-15:15 | Coffee Break |
00:00-00:00 | Session |
15:15-15:45 | Invited speaker |
15:45-16:15 | Invited speaker |
16:15-16:30 | Selected short talk |
16:30-16:45 | Selected short talk |
Application is no longer possible. The course was limited to 18 participants.
The results will be announced approximately 2 weeks after the application deadline.
Registration Fees (included admission, course materials and access to computational resources):
Academia | 295 Euro |
PhD Student | 295 Euro |
Industry | 520 Euro |
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Below you will find the software and technical requirements for this course.
Participants are asked to use a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) and to install a few specific software packages. You will need admin rights to be able to install the software on your computer and we recommend you try this before the course. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.
A classroom application like Zoom will be used for the live talks and Q&A sessions. More information will be provided closer to the start of the course.
While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection.
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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.
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