Anwai Archit
University of Göttingen
Germany
Overview
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.
Participants are invited to bring their own data sets that can be used in the practical sessions.
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.
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
What past participants say about the course
“I enjoyed every single day of this course: not only have I learned so much on how to approach an image analysis problem using Deep Learning, but also I had a great great great time coding and discussing with the other participants and the instructors!” – Lucrezia Ferme, Instituto Gulbenkian de Ciência, Portugal
What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture? Find out more and meet organiser Anna Kreshuk in our 2019 ‘Meet the trainer’ series interview!
Please see EMBL’s COVID-19 safety policy for testing and other requirements to attend this on-site course.
Speakers
Speakers, trainers, and staff
Valentin Gilet
University of Angers
France
Jean-Karim Hériché
EMBL Heidelberg
Germany
Anna Kreshuk
EMBL Heidelberg
Germany
Constantin Pape
University of Göttingen
Germany
Pejman Rasti
University of Angers and ESAIP
France
David Rousseau
University of Angers
France
Uwe Schmidt
Independent researcher
Germany
Yi Sun
EMBL Heidelberg
Germany
Martin Weigert
EPFL
Switzerland
Valentyna Zinchenko
EMBL Heidelberg
Germany
Scientific organisers
Anna Kreshuk
EMBL Heidelberg
Germany
Constantin Pape
University of Göttingen
Germany
Pejman Rasti
University of Angers and ESAIP
France
Course organisers
Catherine Casas
Course and Conference Officer
EMBL Heidelberg
Germany
Irena Provaznikova
Training Laboratory Officer
EMBL Heidelberg
Germany
Programme
Got something to say? Tweet it! #EMBLDeepLearning
- Pre-course work will be needed ahead of the three mandatory webinars that will take place before the course. Further details will be shared in advance of the course and materials will be available on the EMBL eCampus platform.
- Some speakers may need to join virtually to give their lecture or Q&A
- Programme is preliminary and subject to change
- The course programme includes three mandatory virtual pre-course webinars. The purpose of the webinars is to get everyone to the level from which we can start trying things on real data.
Pre-course webinar 1
Monday 8 May 2023, 11:00 – 12:00 (CET)
Pre-course webinar 2
Monday 15 May 2023, 11:00 – 12:00 (CET)
Pre-course webinar 3
Monday 22 May 2023, 11:00 – 12:00 (CET)
Day 1 – Monday 5 June 2023
| Time (Europe/Berlin) | Session | Location |
|---|---|---|
| 11:45 – 12:00 | Bus from hotel to EMBL ATC entrance | ISG Hotel |
| 12:00 – 12:30 | Arrival and registration | Courtyard Room A & B |
| 12:30 – 13:30 | Lunch | EMBL Canteen |
| 13:30 – 14:00 | Welcome and house notes and course overview | Courtyard Room A & B |
| 14:00 – 15:00 | Participants present their data and problem at hand (2 min each) | Courtyard Room A & B |
| 15:00 – 15:30 | Coffee Break | Courtyard Room A & B |
| 15:30 – 16:30 | Lecture: Semantic segmentation Anna Kreshuk – EMBL Heidelberg, Germany | Courtyard Room A & B |
| 16:30 – 17:00 | Meet the instructors and introduction to the practicals | Courtyard Room A & B |
| 17:00 – 19:00 | Practical session: Focus on own data | Courtyard Room A & B, FlexLabs A & B and Computer Training Lab |
| 19:00 – 19:15 | Departure to Hotel | EMBL Bus Stop |
| 19:15 – 20:15 | Dinner | ISG Hotel |
Day 2 – Tuesday 6 June 2023
| Time (Europe/Berlin) | Session | Location |
|---|---|---|
| 08:40 – 09:00 | Bus from hotel to EMBL ATC Entrance | ISG Hotel |
| 09:00 – 09:05 | Overview of the day | Courtyard Room A & B |
| 09:05 – 10:05 | Lecture: Instance segmentation Constantin Pape – University of Göttingen, Germany | Courtyard Room A & B |
| 10:05 – 10:15 | Coffee break | Courtyard Room A & B |
| 10:15 – 11:15 | Lecture: Data augmentation strategies David Rousseau – University of Angers, France | Courtyard Room A & B |
| 11:15 – 11:35 | Coffee break | Courtyard Room A & B |
| 11:35 – 12:35 | Practical session: Focus on own data | Courtyard Room A & B, FlexLabs A & B and Computer Training Lab |
| 12:35 – 13:35 | Lunch break | EMBL Canteen |
| 13:35 – 15:35 | Practical session: Focus on own data | Courtyard Room A & B, FlexLabs A & B and Computer Training Lab |
| 15:35 – 16:00 | Coffee break | Courtyard Room A & B |
| 16:00 – 18:00 | Practical session: Focus on own data | Courtyard Room A & B, FlexLabs A & B and Computer Training Lab |
| 18:00 – 19:00 | Dinner | EMBL Canteen |
| 19:00 – 19:15 | Bus to ISG Hotel | EMBL Bus Stop |
Day 3 – Wednesday 7 June 2023
| Time (Europe/Berlin) | Session | Location |
|---|---|---|
| 08:40 – 09:00 | Bus from hotel to EMBL ATC Entrance | ISG Hotel |
| 09:00 – 09:05 | Overview of the day | Courtyard Room A & B |
| 09:05 – 10:05 | Lecture: Image Denoising Martin Weigert – EPFL, Switzerland | Courtyard Room A & B |
| 10:05 – 10:15 | Coffee break | Courtyard Room A & B |
| 10:15 – 11:15 | Lecture: How to approach a deep learning project: speaking from experience David Rousseau – University of Angers, France | Courtyard Room A & B |
| 11:15 – 11:35 | Coffee break | Courtyard Room A & B |
| 11:35 – 12:35 | Practical: Focus on own data | Courtyard Room A & B, FlexLabs A & B and Computer Training Lab |
| 12:35 – 13:35 | Lunch | EMBL Canteen |
| 13:35 – 13:50 | Group photo | |
| 13:50 – 17:45 | Practical: Focus on own data | Courtyard Room A & B, FlexLabs A & B and Computer Training Lab |
| 17:45 – 18:10 | Bus to Downtown | EMBL Bus Stop |
| 18:10 – 20:00 | Free time | |
| 20:00 – 23:00 | Dinner Downtown | Kulturbrauerei Heidelberg |
Day 4 – Thursday 8 June 2023
| Time (Europe/Berlin) | Session | Location |
|---|---|---|
| 08:40 – 09:00 | Bus from hotel to EMBL ATC Entrance | ISG Hotel |
| 09:00 – 09:05 | Overview of the day | Courtyard Room A & B |
| 09:05 – 10:05 | Lecture: Overview of GUI-based deep learning tools and how you can make use of them Pejman Rasti – University of Angers, France | Courtyard Room A & B |
| 10:05 – 10:15 | Coffee break | Courtyard Room A & B |
| 10:15 – 11:15 | Practical: Focus on own data | Courtyard Room A & B, FlexLabs A & B and Computer Training Lab |
| 11:15 – 11:35 | Coffee break | Courtyard Room A & B |
| 11:35 – 12:35 | Practical: Focus on own data | Courtyard Room A & B, FlexLabs A & B and Computer Training Lab |
| 12:35 – 13:35 | Lunch break | EMBL Canteen |
| 13:35 – 16:05 | Practical: Focus on own data | Courtyard Room A & B, FlexLabs A & B and Computer Training Lab |
| 16:05 – 16:35 | Coffee break | Courtyard Room A & B |
| 16:35 – 19:05 | Practical: Focus on own data | Courtyard Room A & B, FlexLabs A & B and Computer Training Lab |
| 19:05 – 21:05 | Pizza dinner and roundtable discussion | EMBL ATC-Rooftop Lounge |
| 21:05 – 21:15 | Bus to ISG Hotel | EMBL Bus Stop |
Day 5 – Friday 9 June 2023
| Time (Europe/Berlin) | Session | Location |
|---|---|---|
| 08:40 – 09:00 | Bus from hotel to EMBL ATC Entrance | ISG Hotel |
| 09:00 – 09:05 | Overview of the day | Courtyard Room A & B |
| 09:05 – 11:45 | Group activity: Finish practicals, preparation of presentations | Courtyard Room A & B |
| 11:45 – 12:45 | Lunch break | EMBL Canteen |
| 12:45 – 14:10 | Group activity: Presentations by the participants: what worked, what didn’t, what could be done next (I) | Courtyard Room A & B |
| 14:10 – 14:20 | Coffee break | Courtyard Room A & B |
| 14:20 – 15:45 | Group activity: Presentations by the participants: what worked, what didn’t, what could be done next (II) | Courtyard Room A & B |
| 15:45 – 16:00 | Wrap-up and Departures | Courtyard Room A & B |
| 16:00 – 16:30 | Bus to Heidelberg Train Station | EMBL Bus Stop |
Practical information
Registration fees and motivation letter
The course is limited to 20 participants. For selection purposes, please note that your application will not be considered without a letter of motivation.
Registration
Registration fees include admission, course materials, COVID-19 safety measures, meals and coffee breaks. Participants are expected to book and pay their own accommodation and travel expenses.
| Academia | €690 |
| PhD Student | €690 |
| Industry | €1200 |
A letter to support your visa application will be issued, on request, once payment of the registration fee is confirmed. We recommend that you book your visa appointment as soon as possible, to avoid any delay with your visa application.
Confirmation and payment
The registration fee should be paid only after acceptance to the course. The results will be announced approximately 2-3 weeks after the application deadline.
Motivation letter submission
After you have logged in and successfully registered, you will receive an email asking you to submit your motivation letter. Click on the link provided and enter your motivation letter in the text box provided. Alternatively you can submit your motivation letter by clicking on the link on the confirmation page directly after registering.
Instructions
- Include your relevant skills, experience and qualifications showing why you would be suitable for the course.
- Explain why you would like to attend, including what you can contribute and how you think you will benefit from the course.
Please note:
- The limit of 2000 characters refers to manually typed text and excludes spaces. If an error occurs try using a different web browser (preferably Google Chrome or Mozilla Firefox).
- If you copy-paste the text into the form, hidden formatting might still be included which may cause the text to exceed the 2,000 character limit resulting in an error message. We recommend you clear all formatting before pasting in the text.
- If you have special symbols in your text, make sure you are using Unicode characters, otherwise these will not be recognised.
For detailed instructions, please watch our video on how to submit a course motivation letter.
Further details
For further information about registration and motivation letter submission please refer to the FAQ page.
Financial assistance
Financial assistance
Limited financial assistance is provided by the EMBL Advanced Training Centre Corporate Partnership Programme and EMBO in the form of both registration fee waivers and travel grants. Availability is limited to participants attending on-site EMBL Courses and virtual or on-site EMBO Practical Courses in Heidelberg, and will be indicated during the motivation letter submission process.
Your place in the course is only confirmed by paying the registration fee, which is mandatory even when receiving a fee waiver.
Registration fee waiver
The fee waiver will cover the registration sum that you have paid to attend the course.
Travel grant
The travel grant will cover the cost of travel (airfare, train, bus, taxi, accommodation, visa, and/or registration fees*) and is provided up to specified caps which are normally as follows:
– up to €400 for participants travelling to an EMBL Course within Europe.
– up to €1000 for participants travelling to an EMBL Course from outside Europe.
– up to €500 for any participant travelling to an EMBO Practical Course.
– up to €1000 for any participant working in Chile, India, Singapore or Taiwan travelling to an EMBO Practical Course.
– up to €700 for any participant working in Croatia, Czech Republic, Estonia, Greece, Hungary, Italy, Lithuania, Luxembourg, Poland, Slovenia, and Turkey travelling to an EMBO Practical Course.
*Registration fees are only covered for EMBO Practical Courses
The organisers may reduce the grant cap to accommodate more participants. Recipients will be notified of their travel cap amount when they are informed of the outcome of their application. Original receipts must be provided with your signature for all costs incurred within two months of completion of travel. Scanned copies cannot be accepted.
Childcare grant (EMBO Practical Courses only)
For EMBO Practical Course participants with children, there is the possibility to apply for a childcare grant to offset child care costs incurred by participants or speakers when participating at a course. Eligible costs include fees for a babysitter or child-care facility, travel costs for a caregiver, or travel costs for taking the child to the meeting etc. Please note that priority will be given to early-stage researchers. A maximum amount of €500 can be awarded per participant applying for an EMBO childcare grant.
Boehringer Ingelheim Fonds travel grant
Applies to selected courses only. Availability will be indicated during the motivation letter submission process.
This grant covers costs related to your attendance at 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
You may apply for financial assistance when submitting your motivation letter for courses. In your application, you will be asked to answer questions regarding 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 the Boehringer Ingelheim Fonds Travel Grant, there is a pre-application question during the motivation letter submission process, and if selected you will be requested to complete a standard form and documentation consisting of your travel expense estimation.
Selection
The scientific organisers will select the recipients of all financial assistance during the motivation letter selection process. Results will be announced approximately 6-8 weeks before the event start date, however for some events this may be delayed. Selection results do not impact your admission to the course. Selection is based on scientific merit, your current work or study location, the reasons for needing financial support, and the impact this event will have on your career.
Reimbursement
Costs will be reimbursed after the meeting only once a reimbursement form and original receipts (from travel costs) have been received.
Further details
See our list of external funding opportunities and for further information about financial assistance please refer to the FAQ page.
Accommodation and shuttles
Hotel
Single rooms have been reserved for 5 nights (4-9 June 2023) at the ISG Hotel. After the selection process, selected participants should contact the hotel directly to make a booking (booking code MAC23-01). We recommend that all course participants stay at the ISG Hotel which is the dedicated hotel for the course.
Local transport
Shuttle buses will go from the ISG Hotel to EMBL and back, mornings and evenings. A bus schedule and location of the bus stops will be made available prior to the meeting.
Further details
Address: EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany
For further information on getting to EMBL Heidelberg visit our Travel Information page.
For enquiries about accommodation and local transportation please refer to the FAQ page.
Technical requirements and event software
Technical requirements
Below you will find the software and technical requirements for this course.
- Participants need to bring their own laptops, which will be used to remotely access EMBL virtual machines with pre-installed software.
- You will need admin rights to install the software required to access the virtual machines. If you do not have admin rights, please contact your technical support team in advance to make sure the software can be installed.
- Participants are invited to bring their own data sets that can be used in the practical sessions.
Event software
The EMBL eCampus learning platform will be used to collaborate, communicate and network with all of the course participants. All participants will receive information on how to join shortly before the course. We recommend using Chrome, Safari or Mozilla Firefox browsers for eCampus.
Additional information
Please find additional information including FAQs, terms and conditions, COVID-19 safety policy and travelling to EMBL on our Information for Participants page.
COVID-19 related questions
COVID-19 information for on-site events at EMBL Heidelberg can be found in our COVID-19 FAQs.
Sponsors
- Event Supporters
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 events, 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.
Warning
EMBL wishes to warn sponsors of EMBL conferences and courses of fraudulent schemes purporting to offer sponsorship opportunities on behalf of EMBL or affiliated with EMBL officials. One current scam campaign of which we are aware is conducted using the name ‘Judy Eastman’ (judy@gopcontact.a2hosted.com) and entails approaches to sponsors offering sponsorship opportunities on EMBL’s behalf. Please be kindly advised that all relevant communication regarding sponsorship of EMBL conferences, symposia and courses is handled by EMBL directly and is sent from an official EMBL account. EMBL does not work with any external providers on sponsorship acquisition.
Please also note that:
- EMBL never provides attendee lists for purchase. Any offers of such are fraudulent.
- EMBL will never call or email you to ask for your credit card details or to request a payment.
- All payments are on invoice.
Suspicious communications purportedly from, for or on behalf of EMBL should be reported to EMBL at the following email address sponsorship@embl.de.
Media kit
Want to let others know you’re attending this event? Take a look at our shareable media and feel free to use them in your social media channels or presentations.
Date: 5 - 9 Jun 2023
Location: EMBL Heidelberg
Venue: EMBL Advanced Training Centre
Deadline(s):
Application: Closed
Organisers:
-
Anna Kreshuk
EMBL Heidelberg, Germany -
Constantin Pape
University of Göttingen, Germany -
Pejman Rasti
University of Angers, France -
David Rousseau
University of Angers, France -
Martin Weigert
Swiss Federal Institute of Technology Lausanne, Switzerland
Contact: Catherine Casas