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Deep Learning for Image Analysis – Course and Conference Office

EMBL Course

Deep Learning for Image Analysis

Overview

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.

Course Overview

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.

Audience

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.

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

Pejman Rasti

University of Angers and ESAIP, École Supérieure Angevine en Informatique, France

Martin Weigert

École Polytechnique Fédérale de Lausanne (EPFL), Switzerland

Trainers

Scientific Organisers

Course Organiser

Maryann Heck

EMBL Heidelberg, Germany

Tim Nürnberger

EMBL Heidelberg, Germany

Programme

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Day 1 – Monday 8 February 2021
TimeSpeaker
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
Day 2 – Tuesday 9 February 2021
TimeSpeaker
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
Day 3 – Wednesday 10 February 2021
TimeSpeaker
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

Day 4 – Thursday 11 February 2021
TimeSpeaker
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

Day 5 – Friday 12 February 2021
TimeSpeaker
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

Practical information

Registration Fees and Motivation Letter

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):

Academia295 Euro
PhD Student295 Euro
Industry520 Euro

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Financial Assistance

Registration Fee Waivers

All academic and student registrants are invited to apply for a registration fee waiver, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO. The registration fee waiver covers the registration sum that you have paid to attend the meeting. Conference participants are not required to pre-pay the registration fee to be selected for a fee waiver for a virtual meeting. If you have already paid the registration fee and are awarded a fee waiver, it will be reimbursed after the meeting. Course participants are required to pay the course fee in advance, which will then be reimbursed after the recipient has attended the course.

Childcare Grants 

For participants and speakers with childcare responsibilities there is the possibility to apply for a grant, provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO, to offset childcare costs incurred when participating at a virtual event. Eligible costs include fees for a babysitter or childcare facility or travel costs for a care giver. Please note that priority will be given to early stage researchers. Costs will be reimbursed after the meeting only once a reimbursement form and original receipts have been received. In order to apply for this grant, you must be registered by the abstract submission deadline.

Boehringer Ingelheim Fonds Travel Grant

Applies to selected courses only. Availability will be indicated during the abstract or motivation letter submission process.

This grant covers costs related to your attendance to the course (registration, travel and accommodation costs). The grant is restricted to PhD students and postdocs who conduct basic biomedical research.
Whether you are eligible to apply for a travel grant, depends on when you received your university entrance qualification (e.g. Abitur, A-Levels, High School Diploma, Final State Examination):

– for PhD and MD students, as well as graduates, the university entrance qualification must not have been obtained more than 11 years ago at the time of the envisaged course
– for postdocs, the university entrance qualification must not have been obtained more than 13 years ago at the time of the envisaged course

Application

Applications for financial assistance can be submitted via the submission portal* (for the submission of abstracts for conferences or the submission of motivation letters for courses) by completing the Financial Assistance Application Section (underneath the section for entering abstract/motivation letter information). The link to the portal can be found in the registration confirmation email that you will receive after registering for the conference or course.

For conferences, if you are not submitting an abstract, you can still apply for financial assistance in the submission portal by following the instructions here. Note that priority will be given to those submitting an abstract to present at the conference. In your application you will be asked to answer questions regarding your motivation for applying, and, for registration fee waivers, the reasons why your lab cannot fund your attendance and how your attendance will make a difference to your career. Application for financial support will not affect the outcome of your registration application.

*For some events, applications for Childcare Grants will still be done by email. Information about the grant will be sent out shortly after the abstract/motivation letter deadline. Please contact the event Conference Officer if you have any questions.

Selection

The scientific organisers will select the recipients of registration fee waivers during the abstract selection process for conferences and the participant selection process for courses. Results will be announced approximately 3 – 4 weeks before the event start date. Selection results do not impact your admission to the meeting. Registration fee waiver selection is based on your current work or study location, your motivation for applying, the reasons for needing financial support and the impact this event will have on your career. Childcare grants are allocated based on career stage, with priority given to early stage researchers.

Further details

A list of external funding opportunities can be found here, and information on attending a conference as an event reporter here.

For further information about financial assistance please refer to the FAQ page.

Technical Requirements

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.

Additional Software

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.

Other Information

While using the software during the course, please make sure you have nothing else using your bandwidth. We recommend using a wired connection.

Sponsors

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: 8 - 12 Feb 2021

Location: Virtual


Deadline(s):

Application: Closed


Contact: Tim Nürnberger


EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

Corporate partners

Associate partners

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